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PubMed2001

Authentication of Galician (N.W. Spain) quality brand potatoes using metal analysis. Classical pattern recognition techniques versus a new vector quantization-based classification procedure.

The objective of this work was to develop a classification system in order to confirm the authenticity of Galician potatoes with a Certified Brand of Origin and Quality (CBOQ) and to differentiate them from other potatoes that did not have this quality brand. Elemental analysis (K, Na, Rb, Li, Zn, Fe, Mn, Cu, Mg and Ca) of potatoes was performed by atomic spectroscopy in 307 samples belonging to two categories, CBOQ and Non-CBOQ potatoes. The 307 x 10 data set was evaluated employing multivariate chemometric techniques, such as cluster analysis and principal component analysis in order to perform a preliminary study of the data structure. Different classification systems for the two categories on the basis of the chemical data were obtained applying several commonly supervised pattern recognition procedures [such as linear discriminant analysis, K-nearest neighbours (KNN), soft independent modelling of class analogy and multilayer feed-forward neural networks]. In spite of the fact that some of these classification methods produced satisfactory results, the particular data distribution in the 10-dimensional space led to the proposal of a new vector quantization-based classification procedure (VQBCP). The results achieved with this new approach (percentages of recognition and prediction abilities > 97%) were better than those attained by KNN and can be compared advantageously with those provided by LDA (linear discriminant analysis), SIMCA (soft independent modelling of class analogy) and MLF-ANN (multilayer feed-forward neural networks). The new VQBCP demonstrated good performance by carrying out adequate classifications in a data set in which the classes are subgrouped. The metal profiles of potatoes provided sufficient information to enable classification criteria to be developed for classifying samples on the basis of their origin and brand.

Journal Article↗

PubMed2002

Proton nuclear magnetic resonance characterisation of glycosaminoglycans using chemometric techniques.

Various types of glycosaminoglycans (GAGs) including heparins, chondroitin sulfates, dermatan sulfate and hyaluronic acid were studied from their proton nuclear magnetic resonance (1H NMR) spectra using chemometric techniques. Despite the complexity of the 1H NMR signals, data analysis using principal component analysis enabled the different GAG classes to be distinguished and permitted their classification according to their chemical structure. The analysis of the composition of the major disaccharide unit and other relevant chemical structures in the heparin samples was performed using partial least squares regression.

Electrophoresis, Capillary↗

PubMed1998

Numerical taxonomy of Skermania piniformis and related isolates from activated sludge.

The microscopic morphology of nocardioforms causing foaming problems in activated sludge usually consists of filaments with branches at either right angles (Nocardia amarae-Like Organisms, NALO) or acute angles (Pine Tree-Like Organisms, PTLO). Fifty-nine nocardioforms, mainly with PTLO morphology, isolated from mixed liquor and foam samples from Australian activated sludge plants, and 39 reference strains of nocardioforms, including type strains, were characterized using 109 morphological and physiological characters. Cluster analysis and Principal Component Analysis showed that the activated sludge isolates clustered in six groups. All isolates that had typical PTLO morphology clustered unambiguously with the Skermania piniformis type strain (formerly called Nocardia pinensis) showing that, unlike NALO, reliable unequivocal identification of S. piniformis, based on microscopic morphology in activated sludge, was possible. Other foam isolates whose morphology consisted of branches with both acute angles and right angles clustered as two separate groups, probably representing new species. These could not be confused microscopically with S. piniformis, despite some branches showing acute angles. The remaining three groups had typical NALO morphology. One of these groups did not cluster with any reference cultures and may be a new species or genus.

Actinomycetales↗

PubMed2003

Validation of Rome II criteria for functional gastrointestinal disorders by factor analysis of symptoms in Asian patient sample.

BACKGROUND: It has been unclear as to whether the Rome II criteria could be applied to patients in the Asia region with functional gastrointestinal (GI) diseases. The aim of the present study was to determine if symptoms of Asian patients with functional gastrointestinal disorders formed groups which corresponded to the Rome II diagnostic criteria. METHODS: A modified English version of Talley's bowel disease questionnaire was developed in collaboration with various research teams in accordance with the Rome II criteria. This instrument was translated into the local languages of the following nine Asian regions: China, Hong Kong, Indonesia, Korea, Malaysia, Singapore, Taiwan, Thailand and Vietnam. From September to December 2001, newly enrolled outpatients attending 14 GI or medical clinics in these regions were invited to complete the questionnaire. From these respondents, patients with functional gastrointestinal disorders fulfilling the '12 weeks out of 12 months' criteria were separated for further analysis. Principal component factor analysis with varimax rotation was used to identify symptom clusters or factors. These factors were compared with the existing classification of functional GI diseases derived from the Rome II criteria. RESULTS: Factor analysis of symptoms from 1012 functional GI patients supported the Rome II classification of the following groups of functional GI disorders: diarrhea-predominant irritable bowel syndrome, functional constipation, functional dyspepsia, functional abdominal pain syndrome, functional heartburn, and functional vomiting. Functional diarrhea was combined with functional anorectal disorders, and globus merged with functional dysphagia into one factor. Some of the functional dyspepsia, abdominal bloating and belching symptoms were loaded into one factor. CONCLUSIONS: Factor analysis of symptoms from a sample of Asian patients with functional GI disorders partially supported the use of the Rome II classification.

Asia↗

PubMed2001

Contrasting bacterioplankton community composition and seasonal dynamics in two neighbouring hypertrophic freshwater lakes.

We characterized the bacterioplankton community and its seasonal dynamics in two neighbouring hypertrophic lakes by denaturing gradient gel electrophoresis (DGGE) analysis of short (193 bp) 16S ribosomal DNA polymerase chain reaction (PCR) products obtained with primers specific for the domain Bacteria. Lake Blankaart is turbid and has a high phytoplankton biomass and episodic cyanobacterial blooms, whereas biomanipulated Lake Visvijver is characterized by clearwater conditions and the establishment of a dense charophyte vegetation. Both lakes were dominated by bacterial groups commonly found in freshwater habitats (e.g. ACK4 cluster of Actinomycetes; ACK stands for clones isolated from the Adirondack mountain lakes). Yet, cluster analysis and principal components analysis (PCA) revealed that taxon composition of the bacterioplankton community of the two lakes differs substantially and consistently throughout the season. During the study year (1998), the bacterioplankton community of both lakes showed a distinct seasonal pattern. Lake Blankaart showed a clear differentiation between winter, spring, summer and autumn. In Lake Visvijver, summer samples differed greatly from spring, autumn and winter samples. We hypothesize that the contrasting bacterioplankton in the two neighbouring shallow lakes is determined largely by the presence or absence of macrophytes.

Bacteria↗

PubMedDate not supplied

Hepatic temporal gene expression profiling in Helicobacter hepaticus-infected A/JCr mice.

Helicobacter hepaticus infection of A/JCr mice is a model of infectious liver cancer. We monitored hepatic global gene expression profiles in H. hepaticus infected and control male A/JCr mice at 3 months, 6 months, and 1 year of age using an Affymetrix-based oligonucleotide microarray platform on the premise that a specific genetic expression signature at isolated time points would be indicative of disease status. Model based expression index comparisons generated by dChip yielded consistent profiles of differential gene expression for H. hepaticus infected male mice with progressive liver disease versus uninfected control mice within each age group. Linear discriminant analysis and principal component analysis allowed segregation of mice based on combined age and lesion status, or age alone. Up-regulation of putative tumor markers correlated with advancing hepatocellular dysplasia. Transcriptionally down-regulated genes in mice with liver lesions included those related to peroxisome proliferator, fatty acid, and steroid metabolism pathways. In conclusion, transcriptional profiling of hepatic genes documented gene expression signatures in the livers of H. hepaticus infected male A/JCr mice with chronic progressive hepatitis and preneoplastic liver lesions, complemented the histopathological diagnosis, and suggested molecular targets for the monitoring and intervention of disease progression prior to the onset of hepatocellular neoplasia.

Aging↗

PubMed2006

Behavioural changes after anaesthesia: validity and liability of the Post Hospitalization Behavior Questionnaire in a Swedish paediatric population.

AIM: To study the validity and liability of a Swedish translation of the Post Hospitalization Behavior Questionnaire (PHBQ) in children in Sweden. METHODS: The PHBQ was translated using a back-translation method. The subjects were 340 children, ages 2-13 y, admitted for elective surgery or diagnostic procedure with anaesthesia. The results were analysed using exploratory factor analysis with principal component analysis with Oblimin rotation. The fit to data was examined using confirmative factor analysis with a good measure of fit for the model (p>0.09 for all factors). RESULTS: Five factors emerged as being most consistent: general anxiety-withdrawal, eating disturbances, separation anxiety, regression-aggression and sleep anxiety. A panel of child psychologists confirmed the face validity of factors. Internal consistency (Chronbach's alpha) was adequate (0.75-0.87) for subscales and excellent for total score (0.93). Children less than 5 y old had higher scores than older children (mean 0.046+/-0.018 vs -0.0089+/-0.014, p<0.001). There were no gender differences. CONCLUSION: The results support a conclusion that a five-factor model better fits data from Swedish children than the original six-factor model.

Adolescent↗

PubMed2005

Measurement properties of the Activities-specific Balance Confidence Scale among individuals with stroke.

PURPOSE: To examine the reliability and validity of the Activities-specific Balance Confidence (ABC) scale among individuals with stroke. METHOD: Descriptive measurement study using a 4-week test-retest design. Data were collected at a tertiary rehabilitation centre form a community-dwelling sample of ambulatory older adults who sustained one stroke at least 1 year prior to the study. During the first measurement session, the total sample (n = 77) completed the ABC as well as the Berg Balance Scale (BBS) and gait speed. The reliability sample (n = 24), a subset of the larger data set, completed the ABC again 4 weeks later. RESULTS: Internal consistency of the ABC was 0.94 and test-retest reliability was ICC = 0.85 (95% CI, 0.68, 0.93). A moderate significant positive, linear correlation with both the BBS (rho = 0.36, P < 0.001) and gait speed (rho = 0.48, P < 0.001) was observed. A factor analysis using principal component analysis indicated that the ABC measures two components of balance self-efficacy (component 1 = perceived low-risk activities; component 2 = perceived high-risk activities). CONCLUSION: The ABC has acceptable measurement properties as demonstrated in this sample of individuals with stroke. This study provides further support for the use of the scale.

Aged↗

PubMed2002

A genomic schism in birds revealed by phylogenetic analysis of DNA strings.

The molecular systematics of vertebrates has been based entirely on alignments of primary structures of macromolecules; however, higher order features of DNA sequences not used in traditional studies also contain valuable phylogenetic information. Recent molecular data sets conflict over the phylogenetic placement of flightless birds (ratites - paleognaths), but placement of this clade critically influences interpretation of character change in birds. To help resolve this issue, we applied a new bioinformatics approach to the largest molecular data set currently available. We distilled nearly one megabase (1 million base pairs) of heterogeneous avian genomic DNA from 20 birds and an alligator into genomic signatures, defined as the complete set of frequencies of short sequence motifs (strings), thereby providing a way to directly compare higher order features of nonhomologous DNA sequences. Phylogenetic analysis and principal component analysis of the signatures strongly support the traditional hypothesis of basal ratites and monophyly of the nonratite birds (neognaths) and imply that ratite genomes are linguistically primitive within birds, despite their base compositional similarity to neognath genomes. Our analyses show further that the phylogenetic signal of genomic signatures are strongest among deep splits within vertebrates. Despite clear problems with phylogenetic analysis of genomic signatures, our study raises intriguing issues about the biological and genomic differences that fundamentally differentiate paleognaths and neognaths.

Animals↗

PubMedDate not supplied

Effects of feeding and body weight loss on the 1H-NMR-based urine metabolic profiles of male Wistar Han rats: implications for biomarker discovery.

For almost two decades, 1H-NMR spectroscopy has been used as an 'open' system to study the temporal changes in the biochemical composition of biofluids, including urine, in response to adverse toxic events. Many of these in vivo studies have reported changes in individual metabolites and patterns of metabolites that correlated with toxicological changes. However, many of the proposed novel biomarkers are common to a number of different types of toxicity. These may therefore reflect non-specific effects of toxicity, such as weight loss, rather than a specific pathology. A study was carried out to investigate the non-specific effects on urinary metabolite profiles by administering four hepatotoxic compounds, as a single dose, to rats at two dose levels: hydrazine hydrate (0.06 or 0.08 g kg (1)), 1,2-dimethylhydrazine (0.1 or 0.3 g kg (-1)), alpha-napthylisothiocyanate (0.1 or 0.15 g kg(-1)) and carbon tetrachloride (1.58 or 3.16 g kg(-1)). The study included weight-matched control animals along with those that were dosed, which were then 'pair-fed' with the treated animals so they achieved a similar weight loss. The urinary metabolite profiles were investigated over time using 1H-NMR spectroscopy and compared with the pathology from the same animals. The temporal changes were analysed statistically using multivariate statistical data analysis including principal component analysis, partial least squares, parallel factor analysis and Fisher's criteria. A number of metabolites associated with energy metabolism or which are partially dietary in origin, such as creatine, creatinine, tricarboxylic acid (TCA) cycle intermediates, phenylacetylglycine, fumarate, glucose, taurine, fatty acids and N-methylnicotinamide, showed altered levels in the urine of treated and pair-fed animals. Many of these changes correlated well with weight loss. Interestingly, there was no increase in ketone bodies (acetate and beta-hydroxybutyrate), which might be expected if energy metabolism was switched from glycolysis to fatty acid beta-oxidation. In some instances, the metabolites that changed were considered to be non-specific markers of toxicity, but were also identified as markers of a specific type of toxicity. For example, taurine was raised significantly in carbon tetrachloride-treated animals but reduced in the pair-fed group. However, raised urinary bile acid levels were only seen after alpha-napthylisothiocyanate treatment. The methodology, statistical analysis used and the data generated will help improve the identification of specific markers or patterns of urinary markers of specific toxic effects.

1,2-Dimethylhydrazine↗

PubMed2004

Development of biomarkers based on diet-dependent metabolic serotypes: practical issues in development of expert system-based classification models in metabolomic studies.

Dietary restriction (DR)-induced changes in the serum metabolome may be biomarkers for physiological status (e.g., relative risk of developing age-related diseases such as cancer). Megavariate analysis (unsupervised hierarchical cluster analysis [HCA]; principal components analysis [PCA]) of serum metabolites reproducibly distinguish DR from ad libitum fed rats. Component-based approaches (i.e., PCA) consistently perform as well as or better than distance-based metrics (i.e., HCA). We therefore tested the following: (A) Do identified subsets of serum metabolites contain sufficient information to construct mathematical models of class membership (i.e., expert systems)? (B) Do component-based metrics out-perform distance-based metrics? Testing was conducted using KNN (k-nearest neighbors, supervised HCA) and SIMCA (soft independent modeling of class analogy, supervised PCA). Models were built with single cohorts, combined cohorts or mixed samples from previously studied cohorts as training sets. Both algorithms over-fit models based on single cohort training sets. KNN models had >85% accuracy within training/test sets, but were unstable (i.e., values of k could not be accurately set in advance). SIMCA models had 100% accuracy within all training sets, 89 % accuracy in test sets, did not appear to over-fit mixed cohort training sets, and did not require post-hoc modeling adjustments. These data indicate that (i) previously defined metabolites are robust enough to construct classification models (expert systems) with SIMCA that can predict unknowns by dietary category; (ii) component-based analyses outperformed distance-based metrics; (iii) use of over-fitting controls is essential; and (iv) subtle inter-cohort variability may be a critical issue for high data density biomarker studies that lack state markers.

Algorithms↗

PubMed2002

The 'Medical Interview Satisfaction Scale' (MISS-21) adapted for British general practice.

BACKGROUND: The 29-item 'Medical Interview Satisfaction Scale' (MISS-29) was developed in the USA to assess patient satisfaction with individual doctor-patient consultations. It has been used in studies from British general practice. However, there is limited evidence for its psychometric properties in this population. OBJECTIVES: The present study was designed to examine the validity, reliability and applicability of the MISS-29 in British general practice populations. METHODS: The study was divided into two phases. The first investigated the properties of the MISS-29 in a UK general practice population and resulted in a modified MISS (MISS-21). The second investigated the properties of the MISS-21 in a wider UK general practice population. In phase 1, 150 patients over 16 years were recruited sequentially from patients attending a large group practice in suburban north London. Patients completed a questionnaire which collected demographic data and the MISS-29. In phase 2, 159 patients with a new problem were recruited from patients over 16 years consulting 18 GPs in north London, Essex and Suffolk. Patients completed a questionnaire while waiting to see the doctor; this collected demographic data and included six separate items, designed by the author, intended to measure patient satisfaction with previous consultations with the doctor. The patients completed the MISS-21 when they left the doctor's consulting room. RESULTS: The response rates for the phase 1 and phase 2 studies were 76.9 and 72.6%, respectively. Factor analysis, using principal component analysis with a varimax rotation, of the data collected in phase 1 resulted in a 21-item scale with the same four subscales as the original MISS-29. Correlations between subscales range from 0.46 to 0.65. Values of Cronbach's alpha between 0.67 and 0.92 suggest that the subscales are internally consistent under the conditions of the study. In phase 2, 92.1% completed all the items in the MISS-21 and there were no significant relationships between patients' demographic variables and the proportion of completed MISS-21 questionnaires, nor were there any differences in the proportion of completed MISS-21 questionnaires between type of practice or between practices serving different geographic populations, suggesting that the items were acceptable to patients. There were highly significant positive correlations (0.21-0.63) between scores on the MISS-21 and all aspects of satisfaction with previous consultations, providing supportive evidence for the construct validity of the MISS-21. CONCLUSION: This study has demonstrated that the use in British general practice of the 29-item MISS developed in the USA should be treated with caution. However, a new 21-item version with the same four subscales as the 29-item MISS was developed which has satisfactory internal reliability. The correlations between subscales suggest that they represent fairly discrete but overlapping aspects of satisfaction. Evidence is produced suggesting that patients have less difficulty completing the MISS-21 and that it is applicable for assessing satisfaction with the consultation in different practice types and populations in the UK. Limited data supporting the construct validity of the MISS-21 are presented. While this study does not provide a full assessment of the MISS-21, we believe it provides evidence for its psychometric properties, which suggests that it is a valid and reliable instrument for the assessment of patient satisfaction with individual consultations in British general practice.

Adult↗

PubMed1991

Comment on the statistical evaluation of data.

This paper represents a plea for a more professional approach to the statistical evaluation of data contained in biological research papers. On the one hand more attention needs to be given to ensuring that statistically rigorous methods are employed; the use of sophisticated methods is now a possibility due to the wide availability of statistical computer packages. Examples are presented of some interesting applications of the multivariate techniques Cluster Analysis and Principal Component Analysis, the data being drawn from early research work into in-vitro fertilization.

Statistics as Topic↗

PubMed2005

Determination of inter- and intra-species genetic relationships among six Eucalyptus species based on inter-simple sequence repeats (ISSR).

Eucalyptus is the most economically important hardwood plantation tree cultivated in tropical and subtropical countries. Inter-simple sequence repeat (ISSR) markers were used to evaluate genetic relationships within and between individuals of six Eucalyptus species. A total of 583 loci (265 to 1535 bp) were amplified from 149 individuals belonging to the six Eucalyptus species using seven ISSR primers (two to three nucleotide repeats anchored with one or two nucleotides at the 3' or 5' region). The ISSR fragments indicated significant polymorphism and genetic diversity among the individuals. Cluster analysis and principal component analysis revealed the occurrence of wide genetic diversity among populations of E. tereticornis Sm., E. camaldulensis Dehnh. and E. urophylla S.T. Blake and narrow genetic diversity among populations of E. citriodora Hook. and E. grandis W. Hill ex Maiden. Genetic diversity was high in E. tereticornis Sm. (47.27%) and low in E. citriodora (18.64%). Maximum Nei's genetic identity (0.897) was observed between E. camaldulensis and E. tereticornis species, whereas maximum genetic diversity (0.286) was found between individuals of E. citriodora and E. grandis.

Eucalyptus↗

PubMed1997

The Coping Strategies Questionnaire: a large sample, item level factor analysis.

OBJECTIVE: The Coping Strategies Questionnaire (CSQ), a measure of coping in chronic pain patients, was subjected to item-level exploratory factor analysis. SUBJECTS: A sample of 965 chronic pain patients were used in the analysis. RESULTS: Principal components analysis using a varimax rotation procedure identified nine factors that accounted for 54.5% of the variance. Of these nine factors, the first five represent subscales of the original CSQ subscales. The catastrophizing subscale replicated with significant loadings for all six original items, and ignoring sensations replicated with five of six items. Factors representing reinterpreting pain sensations, coping self-statements, and diverting attention subscales also appeared. The items from the praying and hoping subscale split into separate praying and hoping factors (factors 6 and 8). When reliability coefficients were calculated, factors 7 through 9 had unacceptably low internal consistency and thus were not considered stable factors. Correlations between factors 1 through 6 and other measures of psychological and physical functioning were calculated in the construct validation portion of this study. Previously found relationships were replicated in that the correlations between CSQ factor scores and measures of pain, depression, and disability were in the same direction in this data set as those previously reported.

Adaptation, Psychological↗

PubMed2004

Moral conflict, religiosity, and neuroticism in an outpatient sample.

Our sense of identity is inextricably connected to our sense of ourselves as moral beings. However, concerns about the rightness and wrongfulness of our own actions, and a range of emotions connected to moral worry, such as regret and remorse, rarely receive clinical attention. The present study sought to develop and operationalize the construct of moral concern or worry in a psychiatric outpatient sample and to investigate relationships between moral worry and age, gender, religiosity, and the tendency to worry in general. The Eysenck Personality Inventory, Duke Religiosity Scale, and a 20-item Worry Scale (containing eight moral worry items) were administered to 225 psychiatric outpatients. Data analysis included principal components analysis, repeated measures MANOVA to examine extent of worry among factor scales and interactions between age and sex, and multiple regression to identify significant correlates of each factor scale. Worry about moral issues emerged as a domain distinct from worry about practical matters. Although respondents reported more worry about practical matters than about moral concerns, worry about the former declined with age, whereas worry about the latter did not. Intrinsic religiosity was negatively correlated and neuroticism positively correlated with both scales. Because patients are concerned about the moral aspects of their character and behavior, this area deserves further research and consideration.

Adolescent↗

PubMed1984

Pencil and paper tests--sensitivity to psychotropic drugs.

The literature on pencil and paper tests and the effects of psychotropic drugs is reviewed. Performance at digit symbol substitution, symbol copying, letter cancellation, arithmetic, logic and cognitive processing with a relatively constant level of triazolam was compared with placebo. Analysis of variance, covariance analysis and principal component analysis were applied to the data. Pencil and paper tests which measure various skills are useful for detecting drug effects. Letter cancellation, arithmetic and DSST appear to be most sensitive, although logic and symbol copying may be useful.

Anti-Anxiety Agents↗

PubMed1992

Typing of Aeromonas strains from patients with diarrhoea and from drinking water.

Aeromonas strains (187) from human diarrhoeal stools and from drinking water (263) in The Netherlands were typed by three different methods. Biotyping alone was found to be of little value for epidemiological studies because 84% of all strains belonged to only 10 biotypes. Common biotypes could be further differentiated by serotyping. Gas-liquid chromatography of cell wall fatty acid methyl esters (FAME) was useful for species identification as well as for typing: 86% of all strains could be identified to the species level, and within this group 92% of all identifications corresponded with the biotype. Cluster analysis and principal component analysis of FAME profiles could be used for comparison of strains from different sources and gave the same general conclusions as bio- and serotyping. There was little overall similarity between Aeromonas strains from human (diarrhoeal) faeces and from drinking water, differences being most pronounced for Aeromonas caviae and least for A. sobria.

Aeromonas↗