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Results for “Principal Component Analysis”

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PubMed2006

Influence of molecular parameters on the sink effect in test chambers.

UNLABELLED: The determination of the specific emission rates of individual products and materials under indoor-related conditions requires the use of climate-controlled emission test chambers. However, most chambers demonstrate an inherent sink effect, i.e. the released components undergo adsorption/desorption processes with construction materials. Furthermore, this sink effect is enhanced by introducing an adsorbing sample surface into the test chamber. The degree of adsorption, as well as the extent of the recovery, can vary significantly for different chambers and samples and also depends on the physical properties of the relevant substance. Whereas the sink effect caused by the chamber itself can be reduced by using appropriate construction materials, it is not possible to avoid the sink effect attributable to the actual sample. For this reason it is of importance to evaluate chambers and samples for possible sink effects, taking into consideration the physical properties of substances. This can be achieved by kinetic modeling of emission data and determination of rate constants. The kinetic parameters obtained from curve fitting were combined with molecular parameters and applied to multivariate statistics. The properties of three different chambers with and without sink could be compared by cluster analysis. Principal component analysis revealed that the sink effect essentially depends on the boiling point of the substances examined. PRACTICAL IMPLICATIONS: Emission test chambers are operated by research institutions and testing laboratories for different purposes. The determined emission rate value of a building product is a function of the chamber construction, the material to be tested and the molecular properties of the target compound. In this work it is demonstrated, which parameters have the main influence on the test result. Furthermore it is shown how multivariate statistical analysis can be applied to experimental data to characterize the sink effect under dynamic conditions. This new technique provides a suitable tool for the evaluation and comparison of test chambers.

Air Pollution, Indoor↗

PubMed2002

Factorial validation of the Severe Impairment Battery for patients with Alzheimer's disease. A pilot study.

The Severe Impairment Battery (SIB) estimates the cognitive aptitudes and other skills of severely impaired dementia patients. The main objective of this pilot study was to clearly identify the number of factors present in the SIB and to analyze the relationships between the different cognitive domains explored by the SIB and loss of autonomy. We administered the SIB, the Mini Mental State Examination (MMSE) and two scales of dependency to 48 patients with Alzheimer's disease in its late stages. A factorial analysis (Principal Components Analysis) showed a 4-factor solution for the SIB: a cognitive factor, a praxis and visuospatial functions factor, the reactivity to external stimuli factor and the social aptitudes factor. A factorial analysis involving the dependency scales showed a cognitive factor, a dependency and constructional praxis factor, the reactivity to external stimuli factor and the social aptitudes factor. Reactivity to external stimuli and social aptitudes were not significantly correlated to cognitive aspects nor to dependency. The finding of dependency as a factor different from cognitive deterioration suggests that, in setting a treatment strategy for demented patients, attempts should be made to treat dependency in its own right. In addition, since reactivity to external stimuli and social aptitudes are not related to cognitive aspects nor to dependency, these functions should also be encouraged and stimulated.

Alzheimer Disease↗

PubMed2004

Metabolic profiles to define the genome: can we hear the phenotypes?

There is an increased reliance on genetically modified organisms as a functional genomic tool to elucidate the role of genes and their protein products. Despite this, many models do not express the expected phenotype thought to be associated with the gene or protein. There is thus an increased need to further define the phenotype resultant from a genetic modification to understand how the transcriptional or proteomic network may conspire to alter the expected phenotype. This is best typified by the description of the silent phenotype in genetic manipulations of yeast. High-resolution proton nuclear magnetic resonance ((1)H NMR) spectroscopy provides an ideal mechanism for the profiling of metabolites within biofluids, tissue extracts or, with recent advances, intact tissues. These metabolic datasets can be readily mined using a range of pattern recognition techniques, including hierarchical cluster analysis, principal components analysis, partial least squares and neural networks, with the combined approach being termed metabolomics. This review describes the application of NMR-based metabolomics or metabonomics to genetic and chemical interventions in a number of different species, demonstrating the versatility of such an approach, as well as suggesting how it may be integrated with other "omic" technologies.

Animals↗

PubMed2005

Comparison of metabolic profiles from serum from hepatotoxin-treated rats by nuclear-magnetic-resonance-spectroscopy-based metabonomic analysis.

Hepatotoxicities were induced in rats using alpha-naphthylisothiocyanate (ANIT), carbon tetrachloride (CCl(4)), and hydrazine (HYD). Male Wistar rats were treated with three typical hepatotoxins, and serum samples were collected after 48 h. Biochemical effects of these toxins on plasma composition were evaluated by high-resolution (1)H nuclear magnetic resonance (NMR) spectroscopy of serum. The biochemical effects of CCl(4) were characterized by an elevated level of 3-d-hydroxybutyrate (HB), acetoacetate (Aca), and creatinine (Cn) in serum, and ANIT led to increases in the amounts of low-density lipoprotein (LDL), alanine, acetate, glycoprotein, succinate, Cn, acetone, 3-d-hydroxybutyrate, and Aca. For the HYD-treated group, LDL, HB, acetate, and Cn were obviously increased in serum. The region delta 0.0-10.0 of each spectrum was segmented into 0.04 ppm. The area under the spectrum was calculated for each segmented region and expressed as an integral value. After removal of the water signal (delta 4.6-5.0) the remaining 235 intensity-related descriptors were used for the pattern recognition analysis. Principal component analysis was used to visualize the similarities and differentiations in biochemical profiles of serum from the rats treated with various hepatotoxins. This work showed the power of the combination of NMR and pattern recognition for the study of biochemical effects of xenobiotics.

1-Naphthylisothiocyanate↗

PubMed2005

Delay correlation subspace decomposition algorithm and its application in fMRI.

This paper reports a new delay subspace decomposition (DSD) algorithm. Instead of using the canonical zero-delay correlation matrix, the new DSD algorithm introduces a delay into the correlation matrix of the subspace decomposition to suppress noises in the data. The algorithm is applied to functional magnetic resonance imaging (fMRI) to detect the regions of focal activities in the brain. The efficiency is evaluated by comparing with independent component analysis and principal component analysis method of fMRI.

Algorithms↗

PubMed2002

Redescription of Proteocephalus bagri and p. Rhamdiae (Cestoda: Proteocephalidae), parasites of Rhamdia quelen (Siluriformes: Pimelodidae) from South America, with comments on morphological variation.

The pimelodid fish Rhamdia quelen (Quoy et Gaimard, 1824) in South America harbours two species of proteocephalid cestodes, Proteocephalus bagri Holcman-Spector et Mañé-Garzón, 1988 and P. rhamdiae Holcman-Spector et Mañé-Garzón, 1988. These species are redescribed based on a detailed morphological study, supported by multivariate analysis (principal component analysis). Features distinguishing these species are: (1) the shape of proglottides, (2) the mean number of testes, (3) the topography of vitelline follicles, (4) the thickness of internal longitudinal musculature, (5) the mean number of uterine branches, (6) the ratio of cirrus pouch length to proglottis width, (7) the shape of ovary in mature and gravid proglottides and (8) the genital pore position in mature proglottides. The specific status of P. bagri and P. rhamdiae is confirmed and neotypes of both species are designated.

Animals↗

PubMed2006

Study of amine composition of botrytized grape berries.

Aliphatic primary and biogenic amines of grape varieties from two vintages were studied. We established that appearance and/or increase of both primary aliphatic and biogenic amines is due to microbiota living in/on grape berries. Aszú, gray rotten grapes infected mainly with Botrytis cinerea, grape berries infected mainly with Penicillium species, and intact grape berries were compared on the basis of amine composition using t-test, analysis of variance, and multivariate statistical analysis (principal component analysis and linear discriminant analysis). The amine composition and amine content of Aszú grapes were significantly different (p < 0.05) from those of intact grapes despite the effect of the vineyards and the vintages. Grape samples coming from the same growing location, intact, Aszú grapes, and grape berries infected mainly with Penicillium species could be separated from each other with multivariate statistical analysis. We distinguished intact, Aszú (noble rotten), and gray rotten berries from each other as well. Evaluating amine values of grape samples independently of the place of origin, the Aszú and green rotten berries could not be differentiated. The varieties and vineyards have affected the amine composition of Aszú grapes, while these effects on intact grapes appeared only slightly.

Biogenic Amines↗

PubMedDate not supplied

Relation of environmental characteristics to fish assemblages in the upper French Broad River basin, North Carolina.

Fish assemblages at 16 sites in the upper French Broad River basin, North Carolina were related to environmental characteristics using detrended correspondence analysis, principal components analysis, and linear regression. The primary gradient affecting sites in this basin was related to agricultural influence, characterized by high levels of agricultural land cover, nitrate plus nitrite, sulfate, specific conductance, and sediment. Agricultural influence on the fish assemblage was represented as a trophic shift from specialized insectivores to generalized insectivores and an herbivore. A secondary influence on variation among sites was related to urban land cover, population density, increased concentrations of metals, and soil erodibility. This primarily urban gradient was characterized by an increase in the number of native and introduced fish species, particularly sunfish and omnivores species, and a decline in the percent of piscivores. These results support the identification of indicators for different environmental influences, which can improve the ability of resource managers to diagnose impairment in this basin and in similar basins.

Agriculture↗

PubMed2003

Relationship of dehydroepiandrosterone and its 7-hydroxylated metabolites to thyroid parameters and sex hormone-binding globulin (SHBG) in healthy subjects.

The concentrations of four immunomodulatory steroids, namely dehydroepiandrosterone (DHEA), its sulfate and its 7-hydroxylated metabolites, and sex hormone-binding globulin (SHBG) and major laboratory parameters of thyroid function were determined in sera from 104 healthy females and 48 males, screened for iodine deficiency in one region of the Czech Republic. The mutual relationships of the laboratory parameters were investigated by using four statistical approaches: correlation analysis, principal component analysis, canonical correlation and linear model relationship. In addition to expected correlations among thyroid parameters and substrate-product relationships among the steroids, several new relationships were revealed: The only thyroid parameter tightly correlating with SHBG was free triiodothyronine. The latter hormone was also associated with one of the 7-OH-DHEA epimers, namely with 7beta-OH-DHEA. Thyroid hormones are known to possess thermogenic properties, as does another 7-oxygenated DHEA metabolite, 7-oxo-DHEA, the major metabolite of which is 7beta-OH-DHEA. It may indicate a link between the two thermogenic factors. The results should serve for further investigation of changes in the thyroid hormone concentrations, together with SHBG and dehydroepiandrosterone metabolites, under various pathological situations.

Adolescent↗

PubMedDate not supplied

Observed, GIS, and self-reported environmental features and adolescent physical activity.

PURPOSE: Examine associations among observed, self-reported, and Geographical Information Systems (GIS) environmental features and physical activity among adolescent males. DESIGN: Cross-sectional study. SETTING: Boy Scout troops and neighborhoods in Houston, Texas. SUBJECTS: Two hundred and ten 10- to 14-year-old Boy Scouts. MEASURES: Accelerometry to obtain minutes of sedentary, light, and moderate to vigorous activity per day. GIS sources were used to identify the numbers of parks, gymnasiums, trails, bus stops, grocery stores, and restaurants within a 1-mile radius of participant residences as well as residential density, connectivity, and crime. Participants provided a self-report of their environment. ANALYSIS: Principal component analysis was used to reduce the number of GIS and self-reported items. Four factors were previously obtained from direct observations of the neighborhoods. Correlations were conducted among factors and physical activity. Regression models were run in which minutes of sedentary behavior, light, or moderate to vigorous physical activity were the dependent variables and environmental factors were the independent variables. Nonsignificant variables were removed in a backward deletion process. RESULTS: Three GIS factors, Parks, Crime, and Gyms, were obtained as were two self-reported factors: difficulty and access and safety. Factor scores were interrelated and associated with the four observed factors. Only observed sidewalk characteristics were correlated with physical activity and were retained in the regression models. CONCLUSION: Environmental factors were interrelated. Only sidewalk characteristics were associated with sedentary behavior and light intensity physical activity.

Adolescent↗

PubMed2002

Investigatory and analytical approaches to differential gene expression profiling in mantle cell lymphoma.

Mantle cell lymphoma (MCL) is a non-Hodgkin's lymphoma of B-cell lineage. The blastoid variant of MCL, characterized by high mitotic rate, is clinically more aggressive than common MCL. We used the cDNA array technology to examine the gene expression profiles of both blastoid variant and common MCL. The data was analysed by regression analysis, principal component analysis and the naive Bayes' classifier. Eight genes were identified as differentially deregulated between the two groups. Oncogenes CMYC, BCL2 and PIM1 were upregulated more frequently in the blastoid variant than in common MCL. This implied that the gp130-mediated signal transducer and activator of transcription 3 (STAT3) signalling pathway was involved in the blastoid variant transformation of MCL. Other differentially deregulated genes were TOP1, CD23, CD45, CD70 and NFATC. By using the eight differentially deregulated genes, we created a classifier to distinguish the blastoid variant from common MCL with high accuracy. We also identified 18 genes that were deregulated in both groups. Among them, BCL1, CALLA/CD10 and GRN were suggested to be oncogenes. The products of RGS1, RGS2, ANX2 and CD44H were suggested to promote tumour metastasis. CD66D was suggested to be a tumour suppressor gene.

Aged↗

PubMed2004

Principal geodesic analysis for the study of nonlinear statistics of shape.

A primary goal of statistical shape analysis is to describe the variability of a population of geometric objects. A standard technique for computing such descriptions is principal component analysis. However, principal component analysis is limited in that it only works for data lying in a Euclidean vector space. While this is certainly sufficient for geometric models that are parameterized by a set of landmarks or a dense collection of boundary points, it does not handle more complex representations of shape. We have been developing representations of geometry based on the medial axis description or m-rep. While the medial representation provides a rich language for variability in terms of bending, twisting, and widening, the medial parameters are not elements of a Euclidean vector space. They are in fact elements of a nonlinear Riemannian symmetric space. In this paper, we develop the method of principal geodesic analysis, a generalization of principal component analysis to the manifold setting. We demonstrate its use in describing the variability of medially-defined anatomical objects. Results of applying this framework on a population of hippocampi in a schizophrenia study are presented.

Algorithms↗

PubMed1998

[A multiple variable analysis about the risk factors of breast cancer in women].

A comprehensive investigation to the risk factors of breast cancer was carried out in 146 pairs of women subjects, with the method of 1:1 matched case-control study, and of logistic regression analysis and principal component analysis. As a result, a regression equation which includes 5 independent variables has been established by logistic regression analysis; Ten principal components were extracted from 22 risk factors of breast cancer through principal component analysis, and the cumulative contribution of variances of the 10 principal components is 64.8%. The result combining the mono-factor analysis and the multiple variables analysis indicated that the principal risk factors of breast cancer are cadre occupation, the age of primiparity and late marriage, more intake of salted meat and sausage, passive smoking, having the history of family tumor, of breast benign tumor, and of the mastadenitis; but the more number of giving births, longer period of time of lactation, more vegetable intake, and taking more vitamin may have preventive effect for breast cancer.

Adult↗

PubMed2003

Multispectral magnetic resonance image analysis using principal component and linear discriminant analysis.

PURPOSE: To explore the possibilities of combining multispectral magnetic resonance (MR) images of different patients within one data matrix. MATERIALS AND METHODS: Principal component and linear discriminant analysis was applied to multispectral MR images of 12 patients with different brain tumors. Each multispectral image consisted of T1-weighted, T2-weighted, proton-density-weighted, and gadolinium-enhanced T1-weighted MR images, and a calculated relative regional cerebral blood volume map. RESULTS: Similar multispectral image regions were clustered, while dissimilar multispectral image regions were scattered in a single plot. Both principal component and linear discriminant analysis allowed discrimination between healthy and tumor regions on the image. In addition, linear discriminant analysis allowed discrimination between oligodendrogliomas and astrocytomas. However, the discriminant analysis method was partially capable of recognizing the tumor identity in unknown multispectral images. CONCLUSION: The proposed method may help the radiologist in comparing multispectral MR images of different patients in a more easy and objective way.

Brain↗

PubMed2002

Prediction of the bitterness of single, binary- and multiple-component amino acid solutions using a taste sensor.

The purpose of this study was to develop a quick, quantitative, prediction method for the determination of the bitterness of solutions containing one or more of five amino acids (L-isoleucine, L-leucine, L-valine, L-phenylalanine, and L-tryptophan), using an artificial taste sensor. The bitterness of various solutions containing different concentrations (1, 3, 10, 30, and 100 mM) of five amino acids, singly and in combination, was estimated using a multichannel taste sensor and compared with the results of human gustatory sensation tests with nine volunteers. The relative response electric potential patterns were similar for all five amino acids. Large sensor outputs were observed in channels 1-4 (which are negatively charged) while there were no responses in channels 5-8 (positively charged). The sensor output for channel 1, which was the largest output value, was used for prediction of bitterness. The change of membrane potential caused by adsorption (CPA), which corresponds to aftertaste, could not be used as an explanatory variable since the adsorption of the amino acids to the sensor membrane was weak and CPA values were small. The bitterness intensity scores for single, binary, and multi-component amino acid solutions, could be easily predicted on the basis of the sensor output value of channel 1 using regression analysis. Principal component analysis of the sensor output data suggested that the sourness, astringency and/or smell of the solutions also played a role in the perception of bitterness.

Amino Acids↗

PubMed1993

[Grouping of countries according to indicators of standard of living].

The position of 125 countries is studied on the basis of a collection of 26 basic, health, economic and educational indicators. Multivariate statistical methods were used, including Cluster Analysis, Principal Component Analysis and Multivariate Analysis of Variance. The most discriminating variables were life expectancy the child mortality rate, the mortality rate of children of less than five years of age, the birth and fertility rates and the high-school female matriculation rate. The first principal component was interpreted as a measure of the living standard which made it possible to place the countries in order. Five clusters of countries are suggested.

Global Health↗

PubMed2005

Rapid monitoring of antibiotics using Raman and surface enhanced Raman spectroscopy.

Comparatively few studies have explored the ability of Raman spectroscopy for the quantitative analysis of microbial secondary metabolites in fermentation broths. In this study we investigated the ability of Raman spectroscopy to differentiate between different penicillins and to quantify the level of penicillin in fermentation broths. However, the Raman signal is rather weak, therefore the Raman signal was enhanced using surface enhanced Raman spectroscopy (SERS) employing silver colloids. It was difficult by eye to differentiate between the five different penicillin molecules studied using Raman and SERS spectra, therefore the spectra were analysed by multivariate cluster analysis. Principal components analysis (PCA) clearly showed that SERS rather than the Raman spectra produced reproducible enough spectra to allow for the recovery of each of the different penicillins into their respective five groups. To highlight this further the first five principal components were used to construct a dendrogram using agglomerative clustering, and this again clearly showed that SERS can be used to identify which penicillin molecule was being analysed, despite their molecular similarities. With respect to the quantification of penicillin G it was shown that Raman spectroscopy could be used to quantify the amount of penicillin present in solution when relatively high levels of penicillin were analysed (>50 mM). By contrast, the SERS spectra showed reduced fluorescence, and improved signal to noise ratios from considerably lower concentrations of the antibiotic. This could prove to be advantageous in industry for monitoring low levels of penicillin in the early stages of antibiotic production. In addition, SERS may have advantages for quantifying low levels of high value, low yield, secondary metabolites in microbial processes.

Culture Media↗

PubMed1979

A methodology for determining high risk components in urban environments.

A method of data collection and analysis is proposed for identifying environmental indicators significant to community health. The methods were applied to a study of child mortality in the city of Cali, Colombia. Pridit analysis (principal component analysis of ridits) is described. The methods have potential usefulness for monitoring and health care planning.

Colombia↗