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PubMed1989

Some aspects of the organization and evolution of the genetic code.

In this paper, I define a measure of the relative position of each amino acid in the genetic code by means of a 21-dimensional vector describing its potential for mutation, in a single step, to each of the other amino acids, or to a chain termination codon. This measure allows us to make a systematic investigation of the type and number of the physicochemical properties of the amino acids that were involved in evolution. The polar character and size of amino acids are identified in this analysis as properties that played a leading role in the evolutionary history of the genetic code. The application of cluster analysis and discriminant analysis reveals the characteristics of the structural organization of the genetic code. Finally, I suggest the existence of a relationship between the molecular weight of the amino acids and the number of synonymous codons.

Amino Acids↗

PubMed2005

Polymorphism of the solute carrier family 12 (sodium/chloride transporters) member 3, SLC12A3, gene at exon 23 (+78G/A: Arg913Gln) is associated with elevation of urinary albumin excretion in Japanese patients with type 2 diabetes: a 10-year longitudinal study.

AIMS/HYPOTHESIS: We have shown previously that the SLC12A3 +78G/A polymorphism in exon 23 (Arg913Gln) was a new candidate for conferring susceptibility to diabetic nephropathy. The aim of this study was to confirm the effect of this polymorphism on the elevation of urinary albumin excretion in type 2 diabetic patients. METHODS: We retrospectively studied 264 Japanese patients with type 2 diabetes over a ten-year period. The subjects were classified into two groups: (1) persistent normoalbuminuria or microalbuminuria, or improvement from microalbuminuria to normoalbuminuria (group N); and (2) progression from normoalbuminuria to microalbuminuria or overt proteinuria, or progression from microalbuminuria to overt proteinuria (group P). They were assessed for association with the +78G/A polymorphism. RESULTS: The frequency of the +78A allele was significantly higher in group N than in group P (10% vs 1%, p=0.021). By logistic regression analysis and discriminant analysis, the substituted allele was shown to be an independent factor correlating negatively to the elevation of albumin excretion (p=0.043 and 0.022, respectively). CONCLUSIONS/INTERPRETATION: The SLC12A3 +78A(+) genotype may have a protective effect against the development and/or progression of diabetic nephropathy in Japanese type 2 diabetic patients.

Albuminuria↗

PubMed2002

Application of headspace-mass spectrometry for differentiating sources of olive oil.

In the present work we propose the use of headspace-mass spectrometry (HS-MS) for the characterisation of monovarietal olive oils, an issue of interest when the origin of an oil has to be determined. The HS-MS procedure involves the direct introduction of the sample into a vial, headspace generation and automatic injection of the volatiles into a mass spectrometer. The results were compared with those obtained using more conventional approaches, including chromatographic, spectrophotometric and other types of analysis. Linear Discriminant Analysis (LDA) was applied to the data obtained with both analytical methodologies to achieve the differentiation of the three types of samples. The proposed method is faster and cheaper than those usually employed for edible oil analysis and no sample preparation is required. Additionally, the measuring process is simple and the results obtained from chemometric treatment are 100% correct as regards classification and prediction, making it an appropriate method for routine control.

Food Industry↗

PubMed2006

Combining visible and near-infrared spectroscopy with chemometrics to trace muscles from an autochthonous breed of pig produced in Uruguay: a feasibility study.

Visible (Vis) and near-infrared reflectance (NIR) spectroscopy combined with chemometrics was explored as a tool to trace muscles from autochthonous and crossbreed pigs from Uruguay. Muscles were sourced from two breeds, namely, the Pampa-Rocha (PR) and the Pampa-Rocha x Duroc (PRxD) crossbreed. Minced muscles were scanned in the Vis and NIR regions (400-2,500 nm) in a monochromator instrument in reflectance. Principal component analysis (PCA), discriminant partial least square regression (DPLS), linear discriminant analysis (LDA) based on PCA scores and soft independent modelling of class analogy (SIMCA) were used to identify the origin of the muscles based on Vis and NIR data. Full cross validation was used as validation method when classification models were developed. DPLS correctly classified 87% of PR and 78% of PRxD muscle samples. LDA calibration models correctly classified 87 and 67% of muscles as PR and PRxD, respectively. SIMCA correctly classified 100% of PR muscles. The results demonstrated the usefulness of Vis and NIR spectra combined with chemometrics as rapid method for authentication and identification of muscles according to the breed of pig.

Animals↗

PubMed1977

Fatty acid composition of adipose tissue in patients with coronary heart disease.

In order to study the relationship between the fatty acid composition of adipose tissue and coronary heart disease (CHD), 34 consecutive male patients with acute myocardial infarction and 33 hospitalized men free of CHD were compared. Patients with diabetes mellitus, endocrine disorders, liver and kidney diseases, recent changes in body weight and deviations from the "normal", customary diet were exlcuded. A statistically significant difference between the two groups was observed only in stearic acid, its proportion being lower in CHD patients (3.25% vs. 4.13%). Using multivariate discriminant analysis, age discriminated best between the groups, followed by stearic acid. The signs observed were positive for the former and negative for the latter. All other acids, relative body weight, and skinfold measurements did not significantly contribute to the discrimination. Age did not correlate with the proportion of stearic acid. Blood lipids from samples taken within 24 h of admission did not significantly differ between the groups. Three months later they had risen considerably in the infarct patients. The metabolic basis of the relationship between CHD and stearic acid is not clear at present. Additional studies are necessary to substantiate the importance of this acid as an indicator of CHD.

Acute Disease↗

PubMed1986

Personal preferences and ethnic variations among Anglo and Hispanic breast and bottle feeders.

The preferences of Spanish-speaking Hispanics and English-speaking Anglos for breast and bottle feeding were evaluated using marketing research techniques. Preliminary interviews with 55 mothers conducted within the first 48 hr post-partum elicited a list of verbatim responses regarding the positive and negative aspects of both feeding methods. An additional 195 women rank-ordered the most frequently mentioned statements in terms of their preference for each. Socio-demographic data on the mothers were analyzed with chi-square analysis and discriminant analysis. Multidimensional scaling was used to assess the preferred characteristics of breast and bottle feeding. Results indicated that most mothers prefer a method of infant feeding that allows the mother to be 'closer to her baby' and allows the baby to 'grow up healthier.' Bottle feeders perceived bottle feeding to be superior because it insured that baby would be 'full and satisfied' and would 'get all the vitamins and nutrients it needed,' especially when 'mother was not eating right" or was 'on medications.' Analysis of cultural preference patterns revealed that there exists a strong culture pattern or preference for breast feeding and its characteristics among Anglos. In contrast, the Hispanics show no clear preference for either breast or bottle feeding.

Adult↗

PubMed1991

Clinical and psychological diversity of non-specific low-back pain. A new approach towards the classification of clinical subgroups.

This study explored the clinical and psychological features of non-specific low-back pain (LBP) using multivariate statistical methods including correspondence analysis, cluster analysis and discriminant analysis. An unselected population of subjects (n = 330) complaining of localized LBP to hospital rheumatologists during 1988 was studied. 41% of the subjects (n = 136) were classified as having a psychiatric disorder according to the DSM-III criteria (Axis I). A number of different organic syndromes were identified and the importance of psychological influences on the clinical presentation of LBP was demonstrated. Cluster analyses provided further evidence for a four-group typology of LBP, which may be interpreted through the relationships or interactions between psychological disturbances and the clinical features of LBP. This study highlights the need, in etiological research, to take into account the clinical diversity of non-specific LBP and to investigate further the complex relationships between psychological disturbances and back pain.

Adult↗

PubMed2006

Application of NMR-based metabonomics in the investigation of myocardial ischemia-reperfusion, ischemic preconditioning and antioxidant intervention in rabbits.

NMR based metabonomics was applied in rabbit plasma samples during myocardial ischemia-reperfusion injury, with the following interventions: (1) Control (no intervention); (2) ischemic preconditioning (IpC); (3) administration of melatonin; (4) IpC+administration of melatonin; (5) treatment of the indole derivative C6458. The (1)H NMR signal intensity ratio of lactate/glucose was found to increase in Control samples during reperfusion compared to baseline, while lactate+alanine/acetate was decreased suggesting impairment of aerobic glycolysis and concomitant lipid utilization. In contrast, after IpC or treatment with C6458, the lactate/glucose ratio was similar to baseline in accordance with the previously reported decrease in infarct size. Multivariate statistical methods such as Principal Component Analysis (PCA), and Discriminant Analysis (DA) were used for the discrimination of samples. The use of ANOVA variable preselection prior to PCA was advantageous in producing adequate models. PCA could classify the Control group in three clusters according to the condition of the heart (baseline-ischemia-reperfusion) while in the IpC groups no classification was evident. PCA discrimination upon treatment with melatonin and C6458 provided further evidence of their effect on the metabolic profile. The supervised DA resulted in fine discrimination between the different subgroups. Plasma NMR spectra in combination with pattern recognition techniques proved to be an efficient and simple method to depict the metabolic changes produced upon ischemia-reperfusion of the myocardium.

Acetates↗

PubMed1999

Spatial features in body surface potential maps of patients with ventricular tachyarrhythmias with or without coronary artery disease.

Body surface potential maps (BSPM) from patients with coronary artery disease or no structural heart disease were analyzed with respect to their spatial features and QT/QTc dispersion in order to determine whether BSPM allows identification of patients with ventricular fibrillation. QRST integral maps and QT/QTc dispersion were acquired from simultaneous recordings of 62 ECG leads during sinus rhythm in patients with idiopathic ventricular fibrillation (n=13), ventricular fibrillation and coronary artery disease (n=22), coronary artery disease without ventricular fibrillation (n=21) and healthy controls (n=18). The Karhunen-Loeve transformation was applied to reduce the dimensionality of the data matrix of the QRST map to eight coefficients. Linear discriminant analysis allowed discrimination between idiopathic ventricular fibrillation patients and controls with high sensitivity (85%) and specificity (89%). However, discrimination between coronary artery disease patients with or without ventricular fibrillation was poor (68% and 67%, respectively). QTc dispersion calculated from BSPM was longer in idiopathic ventricular fibrillation patients than in controls (99+/-30 ms vs 70+/-14 ms, P=0.009) in contrast to QTc dispersion taken from 12-lead ECG (53+/-21 ms vs. 47+/-12 ms, P=n.s.). No significant difference was noted for coronary artery disease patients with or without ventricular fibrillation. In conclusion, repolarization disturbances detected by BSPM allow identification of ventricular fibrillation patients without structural heart disease. However, our results do not suggest a major impact of QT/QTc dispersion or QRST integral mapping for identification of ventricular fibrillation patients with coronary artery disease.

Body Surface Potential Mapping↗

PubMed2001

Intraspecific chemical variability of the leaf essential oil of Juniperus phoenicea subsp. turbinata from Corsica.

The composition of 50 samples of essential oil of individual plants of Juniperus phoenicea subsp. turbinata from Corsica was investigated by GC, GC-MS and 13C NMR. alpha-Pinene, beta-phellandrene, alpha-terpinyl acetate, Delta-3-carene, myrcene and alpha-phellandrene were found to be the main constituents. The results were submitted to cluster analysis and discriminant analysis which allowed two groups of essential oils to be distinguished with respect to the content of alpha-pinene, beta-phellandrene and alpha-terpinyl acetate.

Journal Article↗

PubMed2001

Multivariate analysis of U.K. salt marsh sediment contaminant data with reference to the significance of PCB contamination.

A data set acquired to establish an inventory of pollutants in salt marsh sediments has been evaluated using two numerical techniques, principal component analysis and discriminant analysis. Results indicate that sites proximate to the River Thames exhibit a greater degree of contamination, and numerical analysis supports the hypothesis that the river has been the major source of contaminants to the region. The presence of the contaminants within salt marsh sediments may be of concern due to changes in flood defense techniques. The use of managed realignment, where the line of flood defense is moved back to higher ground which requires only a low, minimal cost, sea-wall protected by newly created salt marsh from former farmland, is not free from problems of historical pollution. Mature salt marsh, laid down during previous decades, may be eroded and reworked within the new coastal geomorphology created by breaching existing seawalls and what were previously considered to be sinks of pollutants may have become sources. However, evaluation of the sediment burden of PCB within the salt marshes of the U.K. Essex coast indicates that they are not likely to be a major source of pollutants should sediments be remobilized during managed realignment programs.

Conservation of Natural Resources↗

PubMed2001

Using an ion-trap MS sensor to differentiate and identify individual components in grapefruit juice headspace volatiles.

An ion-trap mass spectrometer chemical sensor has been utilized to differentiate between grapefruit juices that differ only in the concentration of a single component, and the sensor was able to identify that component. Grapefruit juice was fortified with 40 to 2000 ppm vanillin, a low-level naturally occurring compound in citrus juices. Principal components analysis and discriminant analysis of mass spectral data (m/z 50-200) provided clear separation of the grapefruit juice samples. Vanillin was observed in the juice headspace at the 40 ppm level, with identification possible at the 100 ppm level using either MS or MS/MS.

Benzaldehydes↗

PubMed2005

Chemometric characterization of the cypriot spirit "zivania".

In 42 alcoholic beverages produced in Cyprus and other countries, 26 chemical and physical-chemical variables were determined by HPLC and GC chromatography, (1)H NMR and ICP spectroscopy, and other techniques. Data were processed using multivariate chemometric techniques, involving principal component analysis, cluster analysis, regularized discriminant analysis, and classification and regression trees. Zivania can be differentiated from beverages from other countries. Using 2- and 3-methyl-butanol, 2-methyl-propanol, furfural, methanol, and the alcoholic grade and the chemical shift of -CH(3) in (1)H NMR spectra as features, a nearly correct classification for zivania was achieved. The reasons for diversions are given.

Alcoholic Beverages↗

PubMed2006

Discrimination of storage conditions and freshness in virgin olive oil.

Virgin olive oil samples stored in the light at ambient temperature, in the dark at ambient temperature, and at low temperature in the dark for 12 months both with and without headspace were separated into recognizable patterns with stepwise linear discriminant analysis. The discrimination with variables volatile and phenolic compounds, free fatty acid (FFA), peroxide values, K232, and K270 revealed a departure of stored oil from freshness and showed significant (p < 0.01) differences between storage conditions. Virgin olive oil stored at low temperature had characteristics closest to fresh oil while oil stored in the light showed the largest departure from freshness. Parameters that exclusively and significantly (p < 0.01) discriminated storage conditions were identified as potential markers of the storage condition. In the presence of oxygen, hexanal was a marker of storage in the light, FFA was a marker for dark storage, and markers of low-temperature storage were acetic acid and pentanal. In the absence of oxygen, octane was the marker for storage in the light whereas tyrosol and hexanol were markers of virgin olive oil stored in the dark, with no marker indicative of low-temperature storage. E-2-Hexenal, K232, and K270 were identified as markers of virgin olive oil freshness.

Cold Temperature↗

PubMed1979

Multivariate analysis and quantitative structure-activity relationships. Inhibition of dihydrofolate reductase and thymidylate synthetase by quinazolines.

Quantitative structure-activity relationships (QSAR) have been established for the inhibition of dihydrofolate reductase and thymidylate synthetase by 2,4-diaminoquinazoline-glutamic acid analogues. For dihydrofolate reductase from both human acute lymphocytic leukemia cells and murine L1210R cells, QSAR's obtained with 50 quinazolines were similar. On the other hand, for the inhibition of thymidylate synthetase from murine L1210S cells and from Lactobacillus casei, QSAR's formulated on the basis of data measured with 33 compounds were different, indicating that the two enzymes are dissimilar. The use of multivariate statistics including cluster analysis, factor analysis, and discriminant analysis is shown to facilitate the formulation of a satisfactory correlation equation. The procedure is demonstrated by the development of QSAR for the inhibition of thymidylate synthetase.

Analysis of Variance↗

PubMed2002

The 3 mm skin prick test (SPT) threshold criterion is not reliable for Tyrophagus putrescentiae: the re-evaluation of SPT criterion to dust mites.

BACKGROUND: The mean wheal diameter >/= 3 mm is the usual criterion for positive skin prick test (SPT) reaction to dust mites. The study assessed the accuracy of this SPT criterion with respect to specific IgE values of above 0.35 kUA/l (+ sIgE). METHODS: Specific IgE (ImmunoCAP, Pharmacia AB Diagnostics, Uppsala, Sweden) and standard SPT to Dermatophagoides pteronyssinus (DP) and farinae (DF), Lepidoglyphus destructor (LD) and Tyrophagus putrescentiae (TP) (ALK, Hørsholm, Denmark) were performed in a random sample of 457 subjects, of whom 273 men (mean age 35.3 +/- 11.0 years) and 184 women (mean age 37.9 +/- 9.5 years). Statistical analysis was performed using the chi-square test, regression analysis and discriminant analysis. RESULTS: When the mean wheal diameter of >/= 3 mm was considered positive (+ SPT), the correlation between + SPT and + sIgE was 0.47 for DP (P < 0.001), 0.43 for DF (P = 0.004), 0.35 for LD (P = 0.03) and 0.37 for TP (P = 0.014). Regarding + sIgE, this SPT criterion has a specificity of 92.2% for DP, 82.3% for DF, 80.8% for LD and 70.1% for TP. When the value 4.5 mm was taken as the threshold for the positive SPT reaction to TP, specificity increased significantly from 70.1% to 86.4% (chi2 = 32.04, P < 0.001). CONCLUSIONS: The 3 mm SPT threshold criterion is not reliable in evaluating sensitization to TP due to an insufficient specificity of the allergen extract to this mite. It is advisable either to re-evaluate the TP allergen extract or change the threshold criterion for positive SPT reaction to TP.

Adult↗

PubMed2003

Finding the "genuine" schizotype: a model and method for resolving heterogeneity in performance on laboratory measures in experimental psychopathology research.

Heterogeneity in the performance of persons affected with schizophrenia or schizotypic psychopathology on various laboratory tasks has long been recognized, both for its consistency across tasks and studies and for the massive methodological and substantive challenges it poses for experimental psychopathology, genetic, and other investigations. Traditional multivariate techniques, such as factor analysis, discriminant function analysis, and cluster analysis, have all been deemed inadequate for resolving heterogeneity, because of one or another statistical limitation. Here, an objective statistical approach based on a formal statistical model that uses the ubiquitous and well-developed expectation-maximization (EM) algorithm (A. P. Dempster, N. M. Laird, & D. B. Rubin, 1977) is presented, which enables one effectively to partition a group of experimental subjects, in this case identified initially using the well-known Perceptual Aberration Scale (L. J. Chapman, J. P. Chapman, & M. L. Raulin, 1978), in a manner that reduces heterogeneity and allows for the separation of what are termed genuine and false-positive schizotypes. The validity of the parsing strategy was supported by reference to other laboratory indexes of relevance to schizophrenia and schizotypy that were not included in the initial EM-based analyses. The potential utility of this approach is discussed with reference to future schizophrenia and schizotypy research.

Adolescent↗

PubMed2001

Evaluation of the effect of data pre-treatment procedures on classical pattern recognition and principal components analysis: a case study for the geographical classification of tea.

A simple transformation that uses the half-range and central value has been used as a data pre-treatment procedure for principal component analysis (PCA) and pattern recognition techniques. The results obtained have been compared with the results from classical normalisation of data (mean normalisation, maximum normalisation and range normalisation), autoscaling and the minimum-maximum transformation. Three data sets were used in the study. The first was formed by determining 17 elements in 53 tea samples (901 pieces of data). The second and third data sets arose from two long-term drift studies performed to examine instrumental stability at standard and robust conditions. The instruments used were an inductively coupled plasma atomic emission spectrometer and an inductively coupled plasma mass spectrometer. Each drift diagnosis experiment consisted of replicate determinations of a test solution containing 15 analytes at 10 mg l-1 over 8 h without recalibration. Twenty-nine emission lines were determined 99 times, thus, each data set was formed by 2881 pieces of data. Data pre-treatment was applied to the three data sets prior to the use of principal component analysis, cluster analysis, linear discrimination analysis and soft independent modelling of class analogy. The study revealed that the half-range and central value transformation resulted in a better classification of the tea samples than that achieved using the classical normalisation. The loadings in the PCA for the long-term stability study, under both standard and robust conditions, were found to be similar to the drift trends only when the minimum-maximum transformation and the mean or maximum normalizations were used as data pre-treatments.

Humans↗