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Results for “Principal Component Analysis”

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PubMed2003

Chemical taxonomy of the Xibei tree peony from China by floral pigmentation.

Petal flavonoid compositions of 39 tree peony cultivars from Xibei (northwest China) were investigated in order to study the chemotaxonomic relationship among tree peony species. Six anthocyanins, the 3- O-glucosides and 3,5-di- O-glucosides of three anthocyanidins-pelargonidin (Pg), cyanidin (Cy), and peonidin (Pn)-exist in petals without a blotch at the base. The flowers are classified into three anthocyanidin phenotypes: 'Pn, Pg>Cy'; 'Pn, Cy'; and 'Pn, Cy>Pg'. Furthermore, the yellow pigments are identified as three flavones and three flavonols: apigenin, luteolin, chrysoeriol, and kaempferol, quercetin, and isorhamnetin, respectively. Ward's minimum-variance cluster analysis with principal component analysis produced a dendrogram using standardized scores of 20 pigment variables. Of 39 cultivars, 11 clustered with white flowered Paeonia rockii and 17 with pink flowered P. rockii. The other 11 cultivars matched either P. delavayi or P. potaninii. The result suggests that the Xibei tree peony originated mainly from P. rockii.

Anthocyanins↗

PubMed2006

Metabolomic differentiation of Brassica rapa following herbivory by different insect instars using two-dimensional nuclear magnetic resonance spectroscopy.

The metabolic alterations of Brassica rapa (L.) leaves attacked by larvae of the specialist Plutella xylostella L. (Lepidoptera: Yponomeutidae) and the generalist Spodoptera exigua Hubner (Lepidoptera: Noctuidae) were investigated with nuclear magnetic resonance (NMR) spectroscopy, followed by a multivariate data analysis. The principal component analysis (PCA) of (1)H NMR spectra showed that metabolic changes in B. rapa leaves induced by the 2nd and the 4th instars were different from each other. However, the congestion of the one-dimensional (1)H NMR spectrum made it difficult to identify discriminating metabolites. To overcome the spectral complexity, several two-dimensional NMR techniques were applied. Of those evaluated, J-resolved spectroscopy, which affords an additional coupling constant, provided a wide range of structure information on differentiating the metabolites. Based on the J-resolved spectra combined with PCA, the major signals contributing to the discrimination were alanine, threonine, glucose, sucrose, feruloyl malate, sinapoyl malate, and gluconapin.

Animals↗

PubMed1996

Towards a texture naming system: identifying relevant dimensions of texture.

Recently, researchers have started using texture for data visualization. The rationale behind this is to exploit the sensitivity of the human visual system to texture in order to overcome the limitations inherent in the display of multidimensional data. A fundamental issue that must be addressed is what textural features are important in texture perception, and how they are used. We designed an experiment to help identify the relevant higher order features of texture perceived by humans. We used twenty subjects, who were asked to rate 56 pictures from Brodatz's album on 12 nine-point Likert scales. Each subject was also asked to group these pictures into as many classes as desired. We applied the techniques of hierarchical cluster analysis and non-parametric multidimensional scaling (MDS) to the pooled similarity matrix generated from the subjects' groupings. We used Classification and Regression Tree Analysis (CART), discriminant analysis, and principal component analysis on the data from the scale ratings. The clusters generated from hierarchical cluster analysis remained intact in the MDS plots. We found that the MDS solutions fit the data well. The stress in the three-dimensional case is 0.12. The CART and discriminant analyses provided further justification for our interpretation. The three orthogonal dimensions we identified for texture are repetitive vs non-repetitive; high-contrast and non-directional vs low-contrast and directional; granular, coarse and low-complexity vs non-granular, fine and high-complexity.

Adult↗

PubMed1991

Polycyclic aromatic hydrocarbon (PAH) concentrations in ambient airborne particles from local traffic and distant sources; variation of the PAH profile.

The temporal and spatial dependence of the PAH profile, i.e. the relative concentrations of polycyclic aromatic hydrocarbons, was investigated for ambient airborne particles during a period with moderate photochemical air pollution. The concentrations of 14 PAH were measured; they differed in volatility, sensitivity to atmospheric chemical conversion and contributing sources. Multivariate analysis (principal-component analysis and factor analysis) revealed that temporal dependence was predominantly determined by five factors clearly linked with volatility, reactivity and sources of the PAH, the first being by far the most important. The results, therefore, indicate that volatilization, conversion and a varying contribution of local sources were the major causes of the variation of the profile with time. The contribution of local sources was investigated by comparison of samples that were taken simultaneously at three different sites, one a background site and two sites downwind of traffic. A marked site dependence was found. The comparison suggested that the differences were not only determined by sources, but also by volatilization and/or conversion during residence of the particles in the air.

Air Pollutants↗

PubMed1990

Relationship between the hydrophobic and hydrophilic molecular parameters of some synthetic nucleosides, determined by means of adsorptive and reversed-phase thin-layer chromatography.

The adsorption capacity, the specific adsorptive surface, the lipophilicity and the specific hydrophobic surface of 59 natural and synthetic nucleoside derivatives were determined by means of adsorptive chromatography and reversed-phase thin-layer chromatography for the future application of these molecular parameters in quantitative structure-activity relationship studies. Stepwise regression analysis and principal component analysis proved that each of the physico-chemical parameters has a different information content, and their application in the design of new bioactive derivatives is therefore justified.

Adsorption↗

PubMed1986

Cardiovascular mortality as it relates to the geographic distribution of employment in non-metropolitan Quebec.

This exploratory analysis examines relationships between employment-specific cardiovascular mortality and certain spatially-based potential risk factors. Standard mortality ratios (SMRs) are mapped on the basis of non-metropolitan primary and secondary employment basins of Quebec. In order to control for geographical anomalies, the data are broken down into three spatial grids: employment basins with the employment poles, employment basins without the employment poles and the employment poles (municipalities) taken alone. This cartography suggests a certain number of cardiovascular disease-prone employment areas in Quebec. Linkage analysis and principal components analysis are used to simplify and clarify the complex relationships that exist among selected independent variables (potential risk factors) and multiple regression analysis is used to identify the functional relationships between these employment, geographic and demographic variables and the study's dependent variable (ischaemic heart disease and cerebrovascular mortality) in the form of standard mortality ratios (SMRs). Cardiovascular mortality (SMRs) are found to be related negatively to an employment age-factor and, in the case of women, negatively to agricultural employment, marginally and positively to pulp and paper employment. It would appear that outside the very large cities in areas of primary and industrial employment, men are at greater risk of cardiovascular mortality during their working lives than those who are over the age of 65. Although it was not possible to establish strong positive links between most employment sectors and cardiovascular mortality, it is possible to conclude that there is a negative association for men between textile employment and cerebrovascular mortality; that in the case of women, those who work in agriculture are less at risk than women who are working in industrial employment. There is also some statistical evidence that there is an association between women in the pulp and paper industry and cardiovascular risk levels. This research provides some clues as to the need to investigate certain areas of employment that may be creating unnecessary risks to health, especially in the case of female workers.

Adult↗

PubMed1989

Multivariate statistical analysis of electron probe microanalytical data on cell nuclear constituents.

A multivariate statistical analysis (the principal component analysis) has been used to process electron probe microanalytical data from cell nuclei. Fifty-seven measurements from different areas of chromatin and nucleolus in follicular rat cells have been studied. The variables are the X-ray characteristic signals for P, S, Al, Fe, Cu and Zn. This method demonstrates three groups of individuals - the chromatin area which is associated with a stronger concentration of P and two groups of nucleolar areas, one of them being connected with a higher content in S, Al and Zn. This high degree of correlation between these three elements proves the chemical affinity of the metals with the protein, S being the signature for proteins.

Animals↗

PubMed2006

Structure-activity relationship study of flavone compounds with anti-HIV-1 integrase activity: a density functional theory study.

Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Flavone compounds have been very much studied due to their activity during the inhibition process of HIV-1 IN. In this study, we employed density functional theory (DFT) using the B3LYP hybrid functional to calculate a set of molecular properties for 32 flavonoid compounds with anti-HIV-1 IN activity. The stepwise discriminant analysis (SDA), principal component analysis (PCA) and hierarchical cluster analysis (HCA) methods were employed to reduce dimensionality and investigate possible relationship between the calculated properties and the anti-HIV-1 IN activity. These analyses showed that the molecular hydrophobicity (ClogP), charge on atom 11 and electrophilic index (omega) are responsible for the separation between anti-HIV-1 IN active and inactive compounds.

Cluster Analysis↗

PubMed2005

Pollution topography of chlorobenzenes and hexachlorobutadiene in sediments along the Kaohsiung coast, Taiwan--a comparison of two consecutive years' survey with statistical interpretation.

Forty sediments were analyzed for chlorobenzenes (CBs) and hexachlorobutadiene (HCBD) to investigate their pollution topography along the Kaohsiung coast, Taiwan. Maximum CB concentrations found, varied from 15.4ng/gdw for 1,2,3-TCB to 56.8ng/gdw for 1,2,4-TCB, while higher HCBD concentrations were detected among north-bound stations (around the exit of the Tsoying outfall pipe) and its concentration decreases from north to south. Compared to a previous survey executed a year before, there is no statistically significant difference in CB and HCBD congeners between these two surveys (p = 0.68-0.87, two-tailed paired t-test). The spatial distribution of toxic index reveals that biological effects might occur near Tsoying and Dalinpu outfall pipe outlets which dispose of petro-chemical wastewater. Evidence found in this study also shows distinct CB patterns from the two nearby sources, the Dalinpu outfall pipe outlet and the Kaoping estuary. Principal component analysis shows that four principal components conducting CBs and HCBD distribution were extracted. Both the first two components (accounted for 58.8% of the total variance), comprised all of the CBs except HCB (DCBs to PeCB), were found not capable of differentiating any distinct pollution source. On the other hand, HCBD and HCB were extracted as third and fourth components, respectively, pointing out their distinct sources in this area.

Butadienes↗

PubMed2006

A GC-based metabonomics investigation of type 2 diabetes by organic acids metabolic profile.

"Metabonomics" method requires the development of rapid, advanced analytical tools and GC will play an important role for its special advantage. In this study we show the application of GC-based metabonomics to investigate the control and type 2 diabetes (DM2) patients by urinary organic acids metabolic profile. After peak matching, multivariate statistical analysis methods: principal components analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) were used. The results showed that there was a relationship between organic acids metabolic profiles and DM2, and PLS-DA can distinguish the DM2 patients from the control. Five organic acids as potential biomarkers were identified.

Acids↗

PubMed2005

Modulation of multigene expression and proteome profiles by chemopreventive agents.

Analysis of transcriptome and proteome profiles by microarray technologies provides a formidable, new tool in cancer chemoprevention research. An ideal chemopreventive agent should not excessively alter per se the basal make-up of multigene expression and protein synthesis and should at the same time be able to attenuate alterations induced by risk factors. In order to validate this working hypothesis, we previously performed a series of studies in animal models using the thiol N-acetyl-l-cysteine (NAC) and the nonsteroidal antiinflammatory drug sulindac. We report herein the results of new studies evaluating modulation of DNA adduct levels and expression of 4858 genes in lung and liver of Sprague-Dawley rats, either unexposed or exposed to environmental cigarette smoke (ECS). The tested chemopreventive agents included NAC, oltipraz (OPZ), 5,6-benzoflavone (5,6-BF), phenethyl isothiocyanate (PEITC), and indole 3-carbinol (I3C). Combinations of OPZ with NAC and of PEITC with I3C were also assayed. Excepting OPZ, all treatments inhibited by at least 50% the formation of bulky DNA adducts in the lung of ECS-exposed rats. Hierarchical cluster analysis and principal component analysis allowed us to classify the agents according to their influence on basal gene expression and their ability to attenuate ECS-induced transcriptome alterations. PEITC and I3C were the most effective but the least safe agents. 5,6-BF displayed intermediate patterns. OPZ was poorly effective in lung and considerably altered the basal gene expression in liver. NAC had a medium efficacy and was the safest agent, as also supported by the analysis of 518 proteins in rat lung.

Acetylcysteine↗

PubMed2006

Schizophrenia with prominent catatonic features ('catatonic schizophrenia'). II. Factor analysis of the catatonic syndrome.

Previous factor analyses of catatonia have yielded conflicting results for several reasons including small and/or diagnostically heterogeneous samples and incomparability or lack of standardized assessment. This study examined the factor structure of catatonia in a large, diagnostically homogenous sample of patients with chronic schizophrenia using standardized rating instruments. A random sample of 225 Chinese inpatients diagnosed with schizophrenia according to DSM-IV criteria were selected from the long-stay wards of a psychiatric hospital. They were assessed with a battery of rating scales measuring psychopathology, extrapyramidal motor status, and level of functioning. Catatonia was rated using the Bush-Francis Catatonia Rating Scale. Factor analysis using principal component analysis and Varimax rotation with Kaiser normalization was performed. Four factors were identified with Eigenvalues of 3.27, 2.58, 2.28 and 1.88. The percentage of variance explained by each of the four factors was 15.9%, 12.0%, 11.8% and 10.2% respectively, and together they explained 49.9% of the total variance. Factor 1 loaded on "negative/withdrawn" phenomena, Factor 2 on "automatic" phenomena, Factor 3 on "repetitive/echo" phenomena and Factor 4 on "agitated/resistive" phenomena. In multivariate linear regression analysis negative symptoms and akinesia were associated with 'negative' catatonic symptoms, antipsychotic doses and atypical antipsychotics with 'automatic' symptoms, length of current admission, severity of psychopathology and younger age at onset with 'repetitive' symptoms and age, poor functioning and severity of psychopathology with 'agitated' catatonic symptom scores. The results support recent findings that four main factors underlie catatonic signs/symptoms in chronic schizophrenia.

Adolescent↗

PubMed2004

Characterization and implication of potential fugitive dust sources in the Paso del Norte region.

A series of analyses were performed to provide chemical signatures for surface soils and to evaluate potential sources of fugitive dust in the Paso del Norte (PdN) region. Eighteen sites were selected for soil sampling based on an assessment of the soil types in the region and the main upwind source areas with a potential for wind erosion. Analyses of the soil samples provided chemical 'fingerprints' of the surface soil that are presumed responsible for much of the fugitive dust loading in the region. Analysis of chemical data through multivariate statistical techniques combined with information on lithologic units, soil types, and enrichment factors identified several groups of elements associated with either natural or anthropogenic origins. Cluster analysis and principal components analysis defined four groups of elements while a redundancy analysis implied a strong association between certain elements (Ag, As, Cd, Mo, Mn, Pb, Sb) and an anthropogenic point source in the region. The conclusions from the statistical analyses are further supported by the enrichment factor (EF) analysis, using aluminum as the reference element. That is, a group of presumed anthropogenic trace elements had their highest EFs in the fine size fraction at a site close to the anthropogenic point source. Thus, the statistical analyses of surface soil data provide a useful means for quantifying the extent of anthropogenic perturbations and for highlighting some implications of contaminated fugitive dust sources.

Journal Article↗

PubMed2001

Modern pollen and stomate deposition in lake surface sediments from across the treeline on the Kola Peninsula, Russia.

We sampled and analyzed surface sediments from 31 lakes along a latitudinal transect crossing the coniferous treeline on the Kola Peninsula, Russia. The major vegetation zones along the transect were tundra, birch-forest tundra, pine-forest tundra, and forest. The results indicate that the major vegetation types in our study area have distinct pollen spectra. Sum-of-squares cluster analysis and principal components analysis (PCA) groupings of pollen sites correspond to the major vegetation zones. PCA ordination of taxa indicates that the first axis separates taxa typical of the forest zone (Pinus, Picea) from taxa typical of tundra and forest-tundra zones (Polypodiaceae, Ericaceae, and Betula). The current position of the coniferous treeline, defined in our region by Pinus sylvestris, occurs roughly where Pinus pollen values reach 35% or greater. Arboreal pollen (AP)/non-arboreal pollen (NAP) ratios were calculated for each site and plotted against geographic distance along the transect. AP/NAP ratios of 7 or greater are found within pine-forest tundra and forest vegetation zones. Pinus stomates (dispersed stomatal guard cells) are absent from sites north of the coniferous treeline and all but two samples from the forested sites contain stomates. Stomate concentrations among the samples are highly variable and range from 10 to 458 per ml and positively correlate with the changing Pinus pollen values.

Journal Article↗

PubMed1998

Long-term quantitative ecological assessment of insecticides treatments in four African rivers: a methodological approach.

In West Africa different insecticides had been applied in selected river areas for the reduction of the blackfly populations vectors of Onchocerca volvulus, a parasite causing blindness. To evaluate the possible long term effects of the larvicides on the non target fauna an aquatic monitoring programme has been up from the initial phase of the project. Addressing the attention to the invertebrates data collected in four countries during a maximum period ranging from 1977 to 1996, this paper shows and discusses the data analysis strategy for the measure and interpretation of the biological variation. In particular the application of quantitative ecological analysis methods: Principal Component Analysis, rank abundance models and the community diversity indexes, is critically discussed and comments are given to the ecological interpretation of the results.

Africa↗

PubMed1999

Interpretation of analytical data on n-alkanes and polynuclear aromatic hydrocarbons in Arbacia lixula from the coasts of Tenerife (Canary Islands, Spain) by multivariate data analysis.

The hydrocarbons contents (n-alkanes, polycyclic aromatic hydrocarbons) were determined in the sea urchin Arbacia lixula. Multivariate data analysis as principal component analysis, factor analysis and, cluster analysis were applied to elucidate sources of pollution. PCA and FA were performed to establish the relationships between variables (hydrocarbons), samples (sea urchin) and sources of pollution.

Alkanes↗

PubMed2002

Heavy metals in urban soils: a case study from the city of Palermo (Sicily), Italy.

Concentrations of V, Mn, Cd, Zn, Ni, Cr, Co, Cu, Pb, Hg and Sb were measured on 70 topsoil samples collected from green areas and parks in the city of Palermo (Sicily) in order to: (1) assess the distribution of these heavy metals in the urban environment; (2) discriminate natural and anthropic contributions; and (3) identify possible sources of pollution. Mineralogy, physico-chemical parameters, and major element contents of the topsoils were determined to highlight the influence of 'natural' features on the heavy metal concentrations and their distribution. Medians of Pb, Zn, Cu and Hg concentrations of the investigated urban soils are 202, 138, 63 and 0.68 mgkg(-1), respectively. These values are higher, in some case by different orders of size, than those of unpolluted soils in Sicily that average 44, 122, 34 and 0.07 mg kg(-1). An ensemble of basic and multivariate statistical analyses (cluster analysis and principal component analysis) was performed to reduce the multidimensional space of variables and samples, thus defining two sets of heavy metals as tracers of natural and anthropic influences. Results demonstrate that Pb, Zn, Cu, Sb and Hg can be inferred to be tracers of anthropic pollution, whereas Mn, Ni, Co, Cr, V and Cd were interpreted to be mainly inherited from parent materials. Maps of pollutant distribution were constructed for the whole urban area pointing to vehicle traffic as the main source of diffuse pollution and also showing the contribution of point sources of pollution to urban topsoils.

Environmental Monitoring↗

PubMed2003

Polycyclic aromatic hydrocarbons (PAHs) in bottom sediments of the Kara Sea shelf, Gulf of Ob and Yenisei Bay.

PAH concentration and distribution has been examined in surface sediments samples from the Kara Sea, Russia. The study includes 13 samples from the South-eastern Kara Sea shelf, one sample from the south-western part of the sea, 4 samples from the Baydaratskaya Bay, 5 samples from the Gulf of Ob and 4 samples from the Yenisei Bay, collected in August-September 1993-1994. Cluster analysis and principal component analysis (PCA) were used to identify common patterns and possible sources of PAHs. The total PAH concentration (sum of two- to six-ring aromatic hydrocarbons) in the Kara Sea sediments was generally lower than in the Barents Sea sediments and comparable to the levels in the Pechora and White seas. Two- and three-ring aromatic hydrocarbons predominated in Kara Sea sediments, which indicate a relatively stronger petrogenic origin than that in the adjacent seas. The highest total PAH concentrations within the Kara Sea were found in sediments from the Yenisei Bay and in the South-western part of the Kara Sea in the Eastern Novaya Zemlya Trough. The PAHs of the Yenisei Bay sediments were dominated by perylene and PAHs of petrogenic origin, but had also a strong indication of PAHs of pyrogenic origin. The dominating PAH group in the South-western part of the Kara Sea were four- to six-ring aromatic hydrocarbons, indicating pyrogenic origin. Perylene levels were high in all the Kara Sea samples, and highest levels were found in areas of strong terrigenous influence. The most probable source is decaying peat products being transported to the Kara Sea by both large and small rivers.

Biological Availability↗