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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↗

PubMed2002

Environmetric approaches to estimate pollution impacts on a coastal area by sediment and river water studies.

This paper represents an effort to demonstrate the opportunities of some environmetric methods like regression analysis, cluster analysis and principal components analysis. Their role for data modeling is stressed and the basic theoretical principles are given. The application of the multivariate statistical methods is illustrated by two major examples: Assessment of metal pollution based on multivariate statistical modeling of "hot spot" sediments from the Black Sea; and a trend study of Kamchia River water quality. In the first part of the study the environmetric approach makes it possible to separate three zones of the marine environment with different levels of pollution (Bourgas gulf, Varna gulf and lake buffer zone). Further, the extraction of four latent factors offers a specific interpretation of the possible pollution sources and separates the natural factors from the anthropogenic ones, the latter originating from contamination by chemical and steel-works and an oil refinery. In the second part of the study nine sampling sites along Kamchia River were considered as sources for water quality monitoring data. Trends for all parameters are calculated by the use of linear regression analysis and special attention is paid to a specific coastal site. Then five latent factors were extracted from the monitoring data set in order to gain information about some structural characteristics of the set.

Cluster Analysis↗

PubMed2005

Genotypic analysis of Nomuraea rileyi collected from various noctuid hosts.

The genetic diversity of 79 Nomuraea rileyi isolates from various lepidopteran hosts in Asia, North America, and South America was evaluated using amplified fragment length polymorphism (AFLP) analysis. Cluster analysis separated the N. rileyi isolates into two major groups and seven subgroups. The resulting dendrogram generally classified the N. rileyi isolates based on insect host and geographical region. The haplotypic diversity index of N. rileyi subpopulations from each location and host origin was ranging from 0.8788 to 1.000. However, analysis of molecular variance (AMOVA) demonstrated no significant differences (p =0.3421) among N. rileyi isolates from different continents. Whereas the genetic variation among the N. rileyi populations from the different host insects within each continent was significantly different (p <0.0001).

Animals↗

PubMed2003

[Identification of the habitat of Ligusticum chuangxiong with chromatographic fingerprinting].

OBJECTIVE: To establish the chromatographic fingerprinting for identifying the habitat of Ligusticum chuangxiong. METHOD: HPLC system was applied to obtain the chromatograms of L. chuangxiong samples from different areas, and 15 peaks were measured from the chromatograms. Then some computer-based methods including principle component analysis, clustering analysis, similarity calculation and fisher factor analysis were applied for data analysis. RESULT: There was obvious difference among chromatographic fingerprints of L. chuangxiong samples from different areas. The 15 measured peaks could be used as the fingerprint features. CONCLUSION: Chromatographic fingerprinting can be used for identifying the habitat of L. chuangxiong.

China↗

PubMed2004

Intra-specific variability of ozone sensitivity in Centaurea jacea L., a potential bioindicator for elevated ozone concentrations.

Brown knapweed (Centaurea jacea L.) has been suggested as a potential bioindicator for tropospheric ozone (O3), but little is known about the intra-specific variation in O3 sensitivity in this wild species. The aim of this study was to quantify the differences in O3 sensitivity among and within five populations, and to relate the differences to morphological, phenological, and genetic characteristics. These parameters were periodically recorded in two consecutive experiments on a total of 357 plants from five different European countries (Norway, Hungary, Switzerland, Italy, Slovenia). They were grown from seed in natural soil under ambient conditions at a site with seasonally elevated O3 concentrations (Cadenazzo, southern Switzerland). The populations differed significantly both in frequency and extent of O3 injury, as well as in phenological development. The observed degree of O3 injury was highest in the Slovenian and the Swiss populations, while only few Hungarian and Norwegian plants showed slight symptoms of injury. Plants were generally most sensitive to O3 when reaching the reproductive stage, and insensitive at the rosette stage. Amplified fragment length polymorphism analysis (AFLP) demonstrated genetic distinctiveness of the five C. jacea populations. All individuals of four of the five populations were correctly assigned to the respective populations based on principal component analysis. Cluster analysis quite accurately reflected the geographic origin of each population. Overall, the analysis revealed a high degree of intra-specific variability in O3 sensitivity in C. jacea, and underlined the important influence of the climate-dependent population-specific plant development on O3 sensitivity. These observations may constrain the development of a standardized biomonitoring system.

Air Pollutants↗

PubMed1995

In vivo proton MR spectroscopy of human gliomas: definition of metabolic coordinates for multi-dimensional classification.

Several multi-dimensional statistical evaluation methods were applied to single-voxel proton MR spectra of glial brain tumors and of healthy volunteers. Metabolic coordinates with histological relevance for future diagnosis were found by which spectra from controls, low-grade tumors, and high-grade tumors were completely separated. Significant differences between low-grade and high-grade glioma patients and controls were found for several metabolic ratios by variance analysis. Cluster analysis both with and without principal component analysis was applied. The outcome of these two approaches depended mainly on the lipid-to-creatine ratio. Two other approaches, discriminant factor analysis and the orthonormal discriminant vector method were then used to find discriminatory metabolic coordinates. It turned out that a linear combination of all evaluable metabolic ratios made it possible to separate the three groups completely. On the basis of these results, a classification method that uses the entire proton MRS spectrum is proposed.

Adult↗

PubMed2005

Pulmonary hemodynamics in advanced COPD candidates for lung volume reduction surgery or lung transplantation.

STUDY OBJECTIVES: To assess the pulmonary hemodynamic characteristics in COPD candidates for lung volume reduction surgery (LVRS) or lung transplantation (LT). DESIGN: Retrospective study. SETTING: One center in France. PATIENTS: Two hundred fifteen patients with severe COPD who underwent right-heart catheterization before LVRS or LT. RESULTS: Mean age was 54.6 years. Pulmonary function test results were as follows: FEV(1), 24.3% predicted; total lung capacity, 128.3% predicted; residual volume, 259.7% predicted. Mean pulmonary artery pressure (PAPm) was 26.9 mm Hg. Pulmonary hypertension (PAPm > 25 mm Hg) was present in 50.2% and was moderate (PAPm, 35 to 45 mm Hg) or severe (PAPm > 45 mm Hg) in 9.8% and in 3.7% of patients, respectively. Cardiac index was low normal. PAPm was related to Pao(2) and alveolar-arterial oxygen gradient in multivariate analysis. Cluster analysis identified a subgroup of atypical patients (n = 16, 7.4%) characterized by moderate impairment of the pulmonary mechanics (mean FEV(1), 48.5%) contrasting with high level of pulmonary artery pressure (PAPm, 39.8 mm Hg), and severe hypoxemia (mean Pao(2), 46.2 mm Hg). CONCLUSION: While pulmonary hypertension is observed in half of the COPD patients with advanced disease, moderate-to-severe pulmonary hypertension is not a rare event in these patients. We individualized a subgroup of patients presenting with a predominant vascular disease that could potentially benefit from vasodilators.

Adult↗

PubMed2007

Assessing the effect of underreporting energy intake on dietary patterns and weight status.

OBJECTIVES: To identify misreporting among older rural adults using a prediction algorithm and to compare dietary patterns of underreporters and plausible reporters. DESIGN: In this cross-sectional study, diet information was assessed by five 24-hour recalls collected over 10 months. All foods were classified into 24 food subgroups. Demographic, health, and anthropometric data were collected via home visit. SETTING: Rural Pennsylvania. SUBJECTS: One hundred seventy-nine community-dwelling adults, aged 66 to 87 years. STATISTICAL ANALYSIS: Cluster analysis. RESULTS: Underreporters (n=43) were more likely than plausible reporters (n=133) to be overweight and less educated but did not differ by sex. Underreporters consumed fewer servings across the majority of food groups. Two dietary patterns were determined for all and plausible reporters, in both cases one of higher and one of lower nutrient density. Using only plausible reporters to determine dietary patterns was very similar to using all reporters. The correlation between energy intake and weight status was improved for plausible-reporting women, but not men. CONCLUSIONS: Dietary patterns of plausible reporters were generally similar to that of all reporters; however, correlations with energy intake and weight status improved for women using only plausible reporters. Individuals may not accurately report dietary intake. Those obtaining diet reports should be aware of reporting errors before making decisions about dietary adequacy.

Aged↗

PubMed2002

Vibrios isolated from the cultured manila clam (Ruditapes philippinarum): numerical taxonomy and antibacterial activities.

AIMS: A numerical taxonomic study of halophilic Vibrio isolated from healthy and brown ring disease (BRD) affected manila clams (Ruditapes philippinarum), harvested from the Atlantic coast of south-western Spain, was performed. METHODS AND RESULTS: Characterization of 123 presumptive Vibrio spp. was carried out using 94 phenotypic tests. Simple matching and Jaccard similarity coefficients were used for numerical analysis. Cluster analysis by the unweighted pair group method with arithmetic averages yielded 15 phena defined at 0.81 similarity. Large phena corresponded to Vibrio tubiashii, V. splendidus biotype I and V. harveyi (phena 1, 5 and 9, respectively). The species V.splendidus biotype II, V. natriegens, V. mediterranei and V. alginolyticus were also represented. The inhibitory effect of diffusible extracellular products of the isolates against 27 strains of V.tapetis, the aetiological agent of BRD, was also investigated. Only five V. tubiashii isolates inhibited the growth of V. tapetis strains. The antimicrobial effect was inhibited by heating and depended on the culture medium. CONCLUSIONS: The main Vibrio species associated with manila clams were V. tubiashii, V.spendidus and V. harveyi. The antagonistic relationship established between V. tapetis and the Vibrio spp. clam microbiota may explain the failure of isolation in plating medium of V.tapetis from BRD-affected clams on the south Atlantic coast of Spain. SIGNIFICANCE AND IMPACT OF THE STUDY: Some of the strains isolated from manila clams correspond to agarolytic strains that constitute phenon 7 and they do not fit into any of the currently described Vibrio species.

Animals↗

PubMed2006

Individual variation in cortisol responses to acute "on-back" restraint in an outbred hamster.

An outbred species of dwarf hamster (Phodopus campbelli) was used to assess between-individual variability in the response to, and recovery from, a one-time stressor of 6 min of physical restraint in a subordinate, on-back, position. Four repeated plasma samples were drawn under home-cage isoflurane anesthesia from 33 males and 38 females 50 min before, and then 10, 60, and 120 min after the stress onset. Plasma cortisol concentrations were higher in females than males, but there was no evidence for a sex difference in response to the stressor. The expected cross-sectional increase ( approximately 50 ng/ml) in response to the stressor, followed by recovery, was seen. However, there was extensive individual variation, ranging from no reaction to continuous decline from the initial to the final sample. Results were expressed in four ways (absolute concentration, relative concentration, and area under the curve relative to ground and relative to the stress-induced increase) and also standardized and subjected to hierarchical cluster analysis. Clusters failed to effectively partition the between-individual variation and did not cluster by sex, age, or housing conditions. The current study cautions against ignoring individual differences and suggests that outbred animal models might be particularly relevant to understanding stress-related pathological conditions.

Aging↗

PubMed1997

Analysis of alcohol use clusters among subcritically injured emergency department patients.

OBJECTIVES: 1) To cluster patients according to self-reported drinking patterns using cluster analysis; 2) to externally validate clustered groups on variables related to drinking but not used in the cluster analysis; and 3) to use the clustered patients' responses to alcohol consumption questions to develop a brief screening tool emergency physicians can use to identify patients in need of referral or intervention related to potentially hazardous alcohol consumption. METHODS: A self-report battery was administered to 95 subcritically injured patients. Patients also were saliva alcohol-tested upon arrival to the ED. Using the patients' self-reported quantity, frequency of alcohol consumption, and frequency of having > or = 6 drinks on a drinking occasion, patients were categorized into 3 groups using cluster analysis. The 3 clusters were externally validated using injury-related variables, alcohol-related consequences, and the patients' reported readiness to change drinking. A screening tool was developed using cutoff values reported by the patients' answers to drinking pattern questions. RESULTS: Fifty-nine patients were alcohol-negative, and 36 tested alcohol-positive (i.e., > 4 mmol/L [> 20 mg/dL]) or had elevated scores on an alcohol problem screening instrument. Three distinct drinking pattern clusters were found. Clusters were validated using discriminant function analysis and multivariate analyses of variance to confirm cluster classifications. Steady and high-intensity drinkers reported more alcohol-related negative consequences, and high-intensity drinkers indicated they would consider changing their drinking. The screening tool correctly classified 97% of the patient sample into their respective clusters. CONCLUSIONS: Using the drinking pattern questions in the clustering procedure was effective for grouping injured patients into clusters that could be differentiated on other drinking-related variables. The resulting screening tool can be used in the ED setting to screen patients for further assessment and intervention. The readiness-to-change results support the assertion that the injury event provides a "teachable moment" for subcritically injured patients whose injury may be related to their alcohol consumption.

Alcohol Drinking↗

PubMed1990

Positive and negative symptoms in schizophrenia. A cluster-analytic approach.

The relationships between positive and negative symptoms of schizophrenia and between negative symptoms and social dysfunction were investigated using cluster analysis. Clustering across schizophrenic subjects produced three distinct groups, each characterized by some mix of positive and negative symptoms. Clustering across symptoms and behavioral variables produced a cluster comprising negative symptoms and measures of social adjustment and an additional cluster comprising only measures of social skill. A series of correlations revealed a positive relationship between positive and negative symptom measures. chi 2 analysis revealed a significant relationship between the cluster solution across subjects and classification of patients according to negative symptoms based on previously published criteria. Results are discussed in terms of the implications for the further development and refinement of subclassification schemes for schizophrenia.

Adult↗

PubMed2004

Food habits are related to glycemic control among people with type 2 diabetes mellitus.

OBJECTIVE: To investigate the food habits of people with type 2 diabetes and to identify those habits related to glycemic control. DESIGN: The purposive sampling plan targeted people (40 to 65 years old) living in two urban communities in the Southeastern United States with type 2 diabetes for >1 year (60% women, 50% African Americans and low-income individuals). In-depth interviews were used to identify food habits. Glycated hemoglobin (HbA(1c)) was measured to assess glycemic control. SUBJECTS: The final sample contained 89 participants (62% women, 48% African American, and 43% below 200% of the poverty level). STATISTICAL ANALYSES PERFORMED: Analysis of variance, principal component/factor analysis, cluster analysis, and multiple regression were used to relate food habits to glycemic control. RESULTS: A four-factor solution derived from 15 food habits explained 51.5% of the total variance in HbA(1c) values. High factor scores for three factors (Basic Eating Practices, Meal Planning, and Carbohydrate/Vegetable Strategies) and low factor scores for a fourth factor (Challenges of Dining Out) were related to lower HbA(1c) values. Based on similar patterns across the 15 food habits, participants were clustered into four groupings. The clusters differing on HbA(1c) (mean+/-standard deviation) were Healthful Eating Lifestyle (6.25+/-0.25), Disciplined Eating Approach (7.31+/-0.35), Limited Dietary Focus (8.28+/-0.33), and Poor Dietary Management (9.05+/-0.24). These groupings reflected different food habit factor profiles. CONCLUSIONS: Knowledge of the specific food habits of people with diabetes can offer a way to structure a meaningful dialog with clients about dietary self-management and guide the collaborative development of relevant dietary goals.

Adult↗

PubMed2006

Identification of new flagellar genes of Salmonella enterica serovar Typhimurium.

RNA levels of flagellar genes in eight different genetic backgrounds were compared to that of the wild type by DNA microarray analysis. Cluster analysis identified new, potential flagellar genes, three putative methyl-accepting chemotaxis proteins, STM3138 (McpA), STM3152 (McpB), and STM3216(McpC), and a CheV homolog, STM2314, in Salmonella, that are not found in Escherichia coli. Isolation and characterization of Mud-lac insertions in cheV, mcpB, mcpC, and the previously uncharacterized aer locus of S. enterica serovar Typhimurium revealed them to be controlled by sigma28-dependent flagellar class 3 promoters. In addition, the srfABC operon previously isolated as an SsrB-regulated operon clustered with the flagellar class 2 operon and was determined to be under FlhDC control. The previously unclassified fliB gene, encoding flagellin methylase, clustered as a class 2 gene, which was verified using reporter fusions, and the fliB transcriptional start site was identified by primer extension analysis. RNA levels of all flagellar genes were elevated in flgM or fliT null strains. RNA levels of class 3 flagellar genes were elevated in a fliS null strain, while deletion of the fliY, fliZ, or flk gene did not affect flagellar RNA levels relative to those of the wild type. The cafA (RNase G) and yhjH genes clustered with flagellar class 3 transcribed genes. Null alleles in cheV, mcpA, mcpB, mcpC, and srfB did not affect motility, while deletion of yhjH did result in reduced motility compared to that of the wild type.

Artificial Gene Fusion↗

PubMed2004

Evaluation of a simple carrier molecule to enhance drug penetration of dermal layers by utilizing multivariate methods, structure property correlations, and continuous system modeling.

Nicotinic acid is shown to be comparable to dihydropyridine in its capacity to facilitate penetration of an attached antibacterial drug through dermal layers. Antibacterial drugs examined with nicotinic acid or dihydropyridine carriers were beta-lactam antibiotics: methicillin, oxacillin, benzylpenicillin, penicillin F, penicillin dihydro F, propicillin, carbenicillin, penicillin K, penicillin X, and ampicillin. An oxymethyl (-O-CH2-) group is inserted as the linker between the antibiotic and the carrier group. Structure Property Correlations and multivariate methods such as regression analysis, cluster analysis, principal component analysis, discriminate analysis, self-organizing tree algorithm, and factor analysis clearly showed that nicotinic acid performs as an effective carrier drug and is comparable to dihydropyridine. The skin penetration constant Kp was calculated for all 10 antibiotics having either dihydropyridine or nicotinic acid as carrier, and was found to have a mean of 5.13E-05 cm/hour and 1.83E-05 cm/hour, respectively. The standard deviation for each group showed the numerical values overlap as did the 90% confidence interval for each group. A hierarchical tree organization of skin shows the overlapped dermal layers as they exist in normal skin and for the model utilized in this work. A Deming-Regression analysis also shows the nicotinic acid and dihydropyridine structures to have similar and correlated water solubility. Plotting Kp of the dihydropyridine structures as independent variable versus Kp of the nicotinic acid structures show good correlation (Pearson correlation r = 0.6606) and no significant departure from linearity. Connected box plots showed the majority of Kp values for each group of modified antibiotics to exist in a tight cluster. Polar graph of the Log Kow values showed the two groups of modified antibiotics to be correlated and numerically adjacent in trend. ChemSketch property calculations and modeling demonstrates the affects of structural oxygens, nitrogens, carbonyl groups, amide groups, and aromatic rings that are important in understanding the pervasiveness through dermal layers. Continuous model analysis by acslXtreme is utilized and demonstrates three models of the dispersion of drugs through dermal layers based on diffusivity constant (D), Log Kp from Log Kow and formula weight, and Kp as a function of time.

Administration, Topical↗

PubMed1996

Improved method of detection of testosterone abuse by gas chromatography/combustion/isotope ratio mass spectrometry analysis of urinary steroids.

The current approach to detection of doping with testosterone is based on measuring the testosterone to epitestosterone ratio (T/E) in urine by gas chromatography/mass spectrometry. The median T/E for healthy males who have not used T is about 1.0. In a single urine, a T/E lower than six leads to a negative report even though it does not exclude T administration. A value greater than six indicates possible T administration or a naturally elevated ratio. It has been shown previously that the carbon isotope ratio of urinary T changes after T administration. In this study a potential confirmation method for T abuse was optimized. Gas chromatography/combustion/carbon isotope ratio mass spectrometry (GC/C/IRMS) was used to analyze two T precursors (cholesterol and 5-androsten-3 beta, 17 beta-diol) and two T metabolites (5 alpha- and 5 beta-androstane-3 alpha, 17 beta-diol) in addition to T itself in each of 25 blind urines collected from eight healthy men before, during or after T administration. The carbon isotope ratios of T and the metabolites were lower after T administration. The relationships among the variables were studied using multivariate analysis and beginning with principal components analysis; cluster analysis revealed that the data are composed of two clusters, and classified the samples obtained after T administration in one cluster and the remainder in the other; discriminant analysis correctly identified T users. The measurement of carbon isotope ratios of urinary androgens is comparable to the T/E > 6 test and continues to show promise for resolving cases where doping with T is suspected.

Adult↗

PubMed2006

Statistical, computational and visualization methodologies to unveil gene primary structure features.

OBJECTIVES: Gene sequence features such as codon bias, codon context, and codon expansion (e.g. trinucleotide repeats) can be better understood at the genomic scale level by combining statistical methodologies with advanced computer algorithms and data visualization through sophisticated graphical interfaces. This paper presents the ANACONDA system, a bioinformatics application for gene primary structure analysis. METHODS: Codon usage tables using absolute metrics and software for multivariate analysis of codon and amino acid usage are available in public databases. However, they do not provide easy computational and statistical tools to carry out detailed gene primary structure analysis on a genomic scale. We propose the usage of several statistical methods--contingency table analysis, residual analysis, multivariate analysis (cluster analysis)--to analyze the codon bias under various aspects (degree of association, contexts and clustering). RESULTS: The developed solution is a software application that provides a user-guided analysis of codon sequences considering several contexts and codon usage on a genomic scale. The utilization of this tool in our molecular biology laboratory is focused on particular genomes, especially those from Saccharomyces cerevisiae, Candida albicans and Escherichia coli. In order to illustrate the applicability and output layouts of the software these species are herein used as examples. CONCLUSIONS: The statistical tools incorporated in the system are allowing to obtain global views of important sequence features. It is expected that the results obtained will permit identification of general rules that govern codon context and codon usage in any genome. Additionally, identification of genes containing expanded codons that arise as a consequence of erroneous DNA replication events will permit uncovering new genes associated with human disease.

Algorithms↗

PubMed1988

An interactive multivariate analysis of FCM data.

The procedure and results of the interactive multivariate analysis of FCM data are described. Using principal-components analysis, cluster analysis, and interactive maneuvers, this procedure facilitates an effective data compression from a four-dimensional space into two-dimensional space, then allows cluster separation. The procedure is especially effective for separating clusters, which are degenerated in the usual scattergrams. Programs were mostly written in C language on MS-DOS and were tested on four-dimensional analysis of the blood cells, which resulted in a successful separation of the degenerated clusters.

Cell Separation↗