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PubMedDate not supplied

Cluster analysis with constraints: its use with breast cancer mortality rates in Argentina.

One approach to analyse geographic variations of a disease within a country is through mortality rates in administrative areas. In some geographical areas the rates can be unstable due to their low population. Thus, the statistical analysis of the rate could be not significant due to low population, not because of the real value. An alternative approach to this problem is to set a minimum level of population that enables valid statistical comparisons with the national rate to be made. It is decided to apply an algorithm that groups neighbouring geographical units that reach the minimum population. In the resulting regions, mortality rates are calculated, and the geographic patterns are analysed through the Moran's I coefficient of spatial clustering. This paper presents an application of this approach to mortality rates from breast cancer by Argentine departments, political administrative units into which a province is divided. Applying this procedure, 217 regions were obtained. In two of the regions the rates were significantly higher than the national rate, while in 40 regions they were significantly lower. Significant spatial grouping, reflected by a Moran I coefficient of O-47, was observed.

Algorithms↗

PubMed1995

Four-cluster analysis: a simple method to test phylogenetic hypotheses.

A simple statistical test for comparing three alternative phylogenetic hypotheses for four monophyletic groups is presented. This test is based on the minimum-evolution principle, and it does not require any information regarding the branching order within each monophyletic group. It is computationally efficient and can be easily extended to five or more monophyletic groups.

Animals↗

PubMed1998

Molecular identification and cluster analysis of homofermentative thermophilic lactobacilli isolated from dairy products.

Twenty-five strains of thermophilic lactobacilli isolated from yoghurt and from semi-hard and hard cheeses (in parallel with nine type or reference strains) were identified and grouped according to their genetic relatedness. Strains were identified by sugar fermentation patterns using the "API 50 CHL" galleries, by species-specific DNA probes in dot-blot hybridization experiments, by amplification and restriction analysis of the 16S rRNA gene (ARDRA) and by polymerase chain reaction (PCR) using species-specific oligonucleotide primers. Strains were classified as Lactobacillus delbrueckii subsp. lactis and subsp. bulgaricus, L. helveticus, and L. acidophilus. Strains which were atypical by sugar fermentation patterns were also identified. Most of the strains could not be grouped using carbohydrate fermentation profiles. PCR fingerprinting was used to identify DNA profiles for the 25 lactobacilli. Experimentally obtained PCR profiles enabled discrimination of all strains, which were grouped according to the similarities in their combined patterns. In general, the clustering of the strains corresponded well with species delineation obtained by molecular identification. The dendrogram of genetic relatedness enabled the unambiguous identification of most of the strains which were shown to be atypical by the sugar fermentation profile, except for a discrepancy in one L. delbrueckii subsp. lactis strain and one atypical Lactobacillus sp. strain.

Bacterial Typing Techniques↗

PubMed2006

[The application of infrared spectra and clustering analysis in the discrimination of geographical origin of Flos Chrysanthemi].

OBJECTIVE: To identify the origin of Flos Chrysanthemi. METHODS: FTIR (Fourier transform infrared spectroscopy) and SIMCA (sofe independent modeling of class analogy). RESULTS: The correctness of every classification was higher than 60%. CONCLUSION: This approach was proved to be a reliable and practicable method for the discrimination of geographical origin of Chrysanthemum.

Chrysanthemum↗

PubMed2005

Cluster analysis of S100 gene expression and genes correlating to psoriasin (S100A7) expression at different stages of breast cancer development.

Gene expression patterns in ductal carcinoma in situ (DCIS) and invasive and metastatic breast tumors have been determined using serial analysis of gene expression (SAGE). The purpose of this approach was to identify biologically and clinically meaningful subgroups of DCIS with a high risk of progression to invasive disease. The analyses have led to the identification of several differentially expressed genes, such as HIN-1, dermcidin and S100A7 (psoriasin). The aim of the present study was further to delineate the expression profile of S100 genes using information from 22 breast epithelial SAGE libraries. We demonstrated the down-regulation of S100A6 and S100A10 in breast cancer, irrespective of pathological stage. S100P and S100Z were both up-regulated in cancer; whereas S100A7, S100A8 and S100A9 were strongly up-regulated only in DCIS. The hierarchical clustering of S100 gene expression in these 22 libraries revealed two major groups with distinguishable S100 gene expression profiles. One of them was characterized by the high concomitant expression of S100A7, S100A8 and S100A9. Using SAGE informatics, we found 21 genes with a high positive correlation to S100A7 expression in libraries representing different categories of tissues archived at SAGE Genie, suggesting a function of psoriasin that is not tissue specific. Like S100A7, several of these genes displayed cation-binding properties. We also report the strong correlation in the breast epithelial SAGE libraries between the expression of S100A7 and genes reported as being up-regulated in DCIS, as well as in the inflammatory skin disorder, psoriasis; including RGS5, UPK1A, TMPRSS3, S100A9, p53, SCCA1, SCCA2 and KRT17.

Base Sequence↗

PubMed1996

Classification of RNA secondary structures using the techniques of cluster analysis.

An RNA molecule has a lot of suboptimal secondary structures. Some of these suboptimal structures are very similar and some are entirely different. In some cases, the free energy of these suboptimal structures does not differ much from that of the optimal structure. In order to characterize this relationship more clearly, we defined a metric among the secondary structures by the unweighted pair group method, using the arithmetic average and extended this metric to the sets of secondary structures. We report two applications of this metric. First, we developed a method for the classification of these suboptimal secondary structures of a given RNA sequence. Results of classification are presented with the secondary structures of cadang-cadang coconut viroid, potato spindle tuber viroid and polio virus as examples. Second, we applied this metric to the classification of the secondary structures derived from a set of mutant RNA sequences. We discuss that the mutation of a given RNA sequence changes not only the optimal secondary structure, but also the population of the cluster of the secondary structures.

Animals↗

PubMed2001

[Identification of red kojic from different habitats with clustering analysis by near-infrared diffuse reflectance spectrometry].

OBJECTIVE: To provide a new method for identifying Red kojic. METHODS: Being controled with the Aspergillus terreus, near-infrared diffuse reflectance spectroscopy combining with clusering analysis was used in the identification of Red Kojic made by M. purpureus fermentation from 18 different habitats. RESULTS: We can easily distinguish the Red Kojic from different habitats and the Aspergillus terreus. The results are consistent in some degree with that of morphologic study. CONCLUSION: This method is a new, rapid, simple and low cost assay technique being able to be used in the quality control of Red Kojic.

Cluster Analysis↗

PubMed2006

Patterns of presentations of dizziness in primary care--a cross-sectional cluster analysis study.

OBJECTIVES: Dizziness is a common symptom in adults in primary care. We explored in a sample of people recruited from general practice the existence of patterns of presentations, their characteristics, and clinical and health service predictors. METHOD: We assessed in a cross-sectional random sample of people registered at London general practices in the United Kingdom the following: subtypes of dizziness, effect on personal activity and physical function, relevant medical and drug history, level of anxiety or depression, treatments received, and information on whether help was sought from their general practitioners. RESULTS: Of 1820 subjects, 442 (24.3%) reported symptoms of dizziness. We identified three clinical presentations. Group 1 was a "nonspecific" presentation experienced by 113 (25.5%) people and characterized by true vertigo, presyncope, disequilibrium, and other types of dizziness with severe impact on all aspects of function. The other two groups were characterized by true vertigo and presyncope. In Group 2 [193 (43.7%)], these symptoms had some impact on personal and daily function, whereas in Group 3 [136 (30.7%)], there was no impact. Eighty-four percent of the people in Group 1 consulted their family practitioner on account of their symptoms, 61% did so in Group 2, and only 38% in Group 3. On multinomial logistic regression analysis, current depression, unemployment, and use of prescribed medication were predictors of the Group 1 compared with Group 2, whereas increasing anxiety and depression scores on the Hospital Anxiety and Depression Scale were predictors of the Group 2 compared with the Group 3. CONCLUSIONS: This is the first step in classifying dizziness from a symptomatic and functional point of view. Further research is required on the natural progression of these presentations and their relationship to each other.

Anxiety↗

PubMed1995

Differentiation of normal and pathologic brain structures in MRI using exact T1 and T2 values followed by a multidimensional cluster analysis.

A new method to differentiate and classify normal and pathologic brain tissue in Magnetic Resonance Imaging (MRI) is introduced. With a special pulse sequence, exact T1 and T2 values are simultaneously acquired, where the T2 values may show a biexponential decay behavior. The automatic segmentation of the tissue is based on a histogram analysis of the multidimensional parameters. The tissue-characterizing parameters are stored in a database, which serves as an objective classification of different tissues. A pilot study with 15 healthy volunteers and 100 patients showed a good differentiation between normal tissue like white and gray matter, cerebrospinal fluid, muscle, and fat, thereby revealing a biexponential decay behavior of fat. Pathologic tissue-like edema and meningioma could be classified with high accuracy, while glioblastoma or astrocytoma were difficult to classify because of their non-homogeneous structures.

Adipose Tissue↗

PubMed2003

A mixture model-based cluster analysis of DNA microarray gene expression data on Brahman and Brahman composite steers fed high-, medium-, and low-quality diets.

The objective of this study is to explore aspects of the statistical analysis of gene expression response at the muscle tissue level to varying levels of energy and protein in the diet. Eleven Brahman and Brahman composite steers (weighing 302 +/- 9.8 kg, on average) were allocated randomly into high- (HIGH), medium- (MED), and low- (LOW) quality forage diets for 27 d. After this period, a biopsy of the longissimus dorsi muscle was taken from each animal and total RNA was extracted to generate the labeled target for microarray experimentation. These targets were hybridized to a complementary DNA (cDNA) microarray of 9,274 probes from cattle muscle and subcutaneous fat cDNA libraries. After edits, 151,904 expression intensity levels of 4,747 genes were analyzed. Emphasis was given to the choice of power transformation of the intensity channel readings and to the consistency of readings within each diet quality group. The statistical approach to isolate differentially expressed genes was based on model-based clustering via a mixture of normal distributions estimated through maximal likelihood. The base-2 logarithm was found to be the optimal power transformation to normalize gene intensity levels. A two-sample t-statistic was defined as a measure of possible differential expression. For each of the three diet contrasts, HIGH vs. LOW, HIGH vs. MED, and MED vs. LOW, three clusters were found, two of which contained more than 94% genes with almost no altered gene expression levels, whereas the third cluster contained the remaining genes with a differential expression. Results from the HIGH vs. LOW contrast identified 27 genes with a greater than 95% posterior probability of belonging to the cluster of differentially expressed genes.

Animal Feed↗

PubMed2005

Cluster analysis of multiple experimental pain modalities.

Identifying individual differences in pain is an important topic; however, little is known regarding patterns of responses across various experimental pain modalities. This study evaluated subgroups emerging from multiple experimental pain measures. One hundred and eighty-eight individuals (59.0% female) completed several psychological instruments and underwent ischemic, pressure, and thermal pain assessments. Thirteen separate pain measures were obtained by using three experimental pain modalities with several parameters tested within each modality. The pain ratings and scores were submitted to factor analysis that identified four pain factors from which Pain Sensitivity Index (PSI) scores were computed: heat pain (HP), pressure pain (PP), ischemic pain (IP), and temporal summation of heat pain (TS). Cluster analyses of PSI scores revealed four distinct clusters. The first cluster demonstrated high overall pain sensitivity, the second cluster revealed high TS, the third cluster showed particular insensitivity to IP and low sensitivity across pain modalities except PP, and the fourth cluster demonstrated low sensitivity to PP. Significant correlations were found between psychological measures and Index scores and those differed by sex. Cluster membership was associated with demographic variables of ethnicity and sex as well as specific psychosocial variables, although cluster differences were only partially explained by such factors. These analyses revealed that groups respond differently across varied pain stimuli, and this was not related solely to demographic or psychosocial factors. These findings highlight the need for future investigation to identify patterns of responses across different pain modalities in order to more accurately characterize individual differences in responses to experimental pain.

Adolescent↗

PubMed2001

[Cluster analysis of Dendrobium by RAPD and design of specific primer for Dendrobium candidum].

OBJECTIVE: To analyze the genetic relationship of Dendrobium and design a specific primer to differentiate Dendrobium candidum effectively. METHOD: Random amplified polymorphic DNA (RAPD) technique was used to analyze the genetic relationships of 26 species of Dendrobium and one species of Ephemerantha. Dendrogram was constructed by UPGMA. According to the sequence of DNA fragment selected, Sangon 18 primer had been extended from 3' extreme to 20 bp in order to form a specific primer. RESULT AND CONCLUSION: This primer can be used to distinguish Dendrobium candidum from other Dendrobium effectively. Such a technique provides a new way for the identification of Chinese traditional medicines.

Cluster Analysis↗

PubMedDate not supplied

[An assessment of the clinical status of patients with alveolar echinococcosis by using statistical processing methods. 1. An assessment of the stage of the disease by cluster analysis].

The clinical condition was assessed in 44 patients with alveolar echinococcosis, using methods of mathematical analysis of 10 basic routine laboratory parameters reflecting protein-forming liver function and immune disturbances. The data were processed on a "NOVA-2" [correction of "HOBA-2"] computer using Fortran software on taxonomy 7 classes of conditions were determined, which reflect the progressing severity of the pathological process and correspond to three stages of the disease: uncomplicated, complicated and terminal. A high clinical value of the method has been demonstrated for the evaluation of the patient's condition and determination of the treatment tactics as well as its importance for the creation of a clinical data bank in the invasion focus.

Algorithms↗

PubMedDate not supplied

Bayesian small area cluster analysis of neural tube defects in Newfoundland.

BACKGROUND: The incidence of neural tube defects (NTDs) is declining worldwide due to the implementation of folic acid supplementation programs. Such a program was implemented over 1996-97 in Newfoundland and Labrador, Canada. The geographical distribution of birth incidence was studied prior to and after the implementation of the program to identify regions of residual high incidence. Excess residual cases may potentially be due to genetic causes or incomplete supplementation program implementation. METHODS: Maternal place of residence for all provincial live birth and stillbirth notifications, provincial maternal-fetal medicine referrals, provincial rehabilitation referrals, and all provincial hospitals with NTDs or terminations for NTDs was obtained from 1975 to 2002 for near complete case ascertainment. Bayesian small area analysis was separately performed on cases from 1975-1996 and 1997-2002. The two time periods were compared. RESULTS: Birth incidence of NTDs was noted to decline after 1996, from 5.54/1000 live births to 1.08/1000 live births. 592 cases were found from 1975-1996 and 34 cases from 1997-2002. Relative risk of birth incidence was 0.93-1.18 (95% CI) for 1975-1996 and 0.97-1.02 for 1997-2002 after Bayesian smoothing. One region had an excess of residual cases greater than 34%. CONCLUSIONS: The implications of this observation to the management of the public health initiative imply that overall response to the decrease in cases tends to be uniform across the province, with potentially one area of interest where extra efforts may be devoted.

Bayes Theorem↗

PubMed1994

Redox mechanism for the chaperone activity of heat shock proteins HSPs 60, 70 and 90 as suggested by hydrophobic cluster analysis: hypothesis.

We have recently shown that the N-terminal ATPase fragment of hsp70 (1-375, composed of domains I and II) as well as the subsequent domain III (376-520) may share three-dimensional similarities with hsp60. In this study, we propose that domain III, common to the hsp60s and hsp70s is also found in the hsp90s and adopts a beta-alpha-beta Rossmann-folded structure which is encountered in the NAD-binding domain of dehydrogenases. Consequently, with the help of the domain IV (in hsp70s and hsp90s) or of hsp10/GroES (in hsp60s) and possibly that of auxilliary partners, the hsp molecules could act as "unfoldases" or "reset systems" by disrupting secondary structures through redox reactions on the main polypeptidic chain with which they interact. The models built on this hypothesis may open up a new way for understanding the chaperone functions within the folding/unfolding processes.

Chaperonin 60↗

PubMed2002

Increased prevalence of scleroderma in southwestern Ontario: a cluster analysis.

OBJECTIVE: To estimate the prevalence of scleroderma (systemic sclerosis, SSc) in 3 cities, Windsor, Sarnia, and Woodstock, Ontario, within our referral area, which has a referral base population of 1 million. METHODS: To compare the addresses and exposures of referrals with SSc, we performed a case control study using our patients with scleroderma and 2 age and sex matched controls from the same rheumatologist's practice. RESULTS: Sixty-seven of 91 patients with SSc and 87 of 154 controls responded. The mean age of patients with SSc was 53.2 years versus 52.8 years in controls. There was no statistically significant increase in the number of SSc patients from Windsor (population 197,694): 14 patients (15.4%) with SSc versus 18 controls (11.6%) (p < 0.41); or Sarnia (population 72,738): 7 patients (7.7%) with SSc versus 7 controls (4.5%) (p < 0.31). However, there were 9 cases (9.9%) from Woodstock (population 32,086) versus one control (0.64%) (p < 0.0004). The point prevalence of scleroderma was at least 0.71/10,000 in Windsor, 0.96/10,000 in Sarnia, and 2.8/10,000 in Woodstock. There were no significant between-group differences in exposure to industrial toxins or chemicals including vinyl chloride, silica, and benzene, but exposure rates in both groups were low. Occupations and proportion of those who were work disabled were not different. Patients with SSc were not more likely to have smoked cigarettes (p < 0.43); however, they were more likely to drink at least 6 drinks of alcohol per week (p < 0.04) and had more dental fillings (p < 0.05). Patients with SSc knew on average 3.2 others with this disease, and controls knew only 0.25 others with scleroderma (p < 0.00001). Two patients with SSc knew someone with SSc in their workplace versus none of the controls. CONCLUSION: Our a priori expected higher prevalence of scleroderma in Windsor and Sarnia did not reach significance, but the cluster in Woodstock seems statistically validated, and the exact reason for this cluster remains unclear. It is unlikely that all patients with SSc in Woodstock were seen by us, so the prevalence of scleroderma is at least 2.8/10,000, which is a medium to high prevalence compared to other studies. Associations with alcohol and dental fillings require further study.

Adult↗

PubMedDate not supplied

A cluster analysis study of acetyl-L-carnitine effect on NMDA receptors in aging.

Aging is associated with a reduction in the maximum density of n-methyl-d-aspartate (NMDA)-sensitive glutamate binding sites in the hippocampus of Fischer 344 rats. This study was designed to investigate the effect of acetyl-l-carnitine (ALCAR) on NMDA receptors in the old rat (24 months) after chronic or single-dose treatments. The number of NMDA receptors was significantly decreased in the old rat hippocampus by 19.5% compared with the young rat. A six-month treatment with ALCAR in the old rat attenuated the loss of NMDA binding sites in the hippocampus. A single-dose treatment with ALCAR in the old rat increased the Bmax value by 35%, while no change was observed in the young group. We conclude that ALCAR can exert two actions: a trophic/neuro-preserving one when chronically administered during aging, and a stimulatory one when given at a single dose in the aged rat.

Acetylcarnitine↗

PubMedDate not supplied

[Cancer cluster analysis. The case of the Campdorà District in Girona, Spain].

A conglomerate of cases may be defined as the onset of a number of cases of a disease larger than would be expected for a certain population group, geographical area or a certain timeframe. In the case of cancer, the study of conglomerates entails a number of specific characteristics as compared to other groups of diseases. This work is aimed at proposing a protocol affording the possibility of conducting the study of cancer conglomerates in time and/or space. This article is illustrated with a practical application in the case of the Campdorà District in Girona. Following a proposed protocol for the study of conglomerates, a description is provided of several statistical tools making it possible to draw a comparison among the existence of time-related groupings, as well as the related risk. During the period studied (1994-2002), no excessive statistically significant number of cancer cases seemed to have occurred in the Campdorà District in Girona.

Cluster Analysis↗