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PubMed2005

The fuzzy clustering analysis based on AFS theory.

In the framework of axiomatic fuzzy sets theory, we first study how to impersonally and automatically determine the membership functions for fuzzy sets according to original data and facts, and a new algorithmic framework of determining membership functions and their logic operations for fuzzy sets has been proposed. Then, we apply the proposed algorithmic framework to give a new clustering algorithm and show that the algorithm is feasible. A number of illustrative examples show that this approach offers a far more flexible and effective means for the intelligent systems in real-world applications. Compared with popular fuzzy clustering algorithms, such as c-means fuzzy algorithm and k-nearest-neighbor fuzzy algorithm, the new fuzzy clustering algorithm is more simple and understandable, the data types of the attributes can be various data types or subpreference relations, even descriptions of human intuition, and the distance function and the class number need not be given beforehand.

Algorithms↗
PubMedDate not supplied

[Return of immigrants: a cluster analysis of mesotheliomas among residents of the Veneto region who used to work at the ETERNIT AG factory at Niederurnen, Switzerland].

We identified 5 mesotheliomas among Italian migrant workers who returned home and settled in the Veneto Region, after employment at the ETERNIT AG factory in Switzerland. During the 1970s the factory employed about 1000 workers and the presence of Italian migrants was relevant. The cluster confirms that migration for work has caused exposures to carcinogenic substances and confirms that neoplastic diseases are occurring among those resettled in Italy and helps explaining the high occurrence of mesotheliomas in this country.

Catchment Area, Health↗
PubMed2003

A cluster analysis of road traffic-related childhood knee injuries.

BACKGROUND: Knee injuries represent an important category of road traffic injuries among children, and they are heterogeneous in their aetiology. The aims of this study were to estimate the incidence of road traffic childhood knee injuries in Greece by age and gender, point out their time, place and person co-ordinates and identify clusters with distinct characteristics with a view to potential preventive interventions. METHODS: During a 3-year period, 305 children with knee injuries resulting from a road traffic accident were identified among the 66,870 children with injuries recorded in the Emergency Department Injury Surveillance System (EDISS) of Greece. Using previously derived sampling ratios and national data on childhood population, incidence data by age and gender were estimated. Hierarchical analysis was undertaken for cluster identification. RESULTS: The incidence of road traffic knee injuries was 97.5 per 100,000 children-years. The incidence increased with age and was higher among boys than among girls. Most childhood knee injuries (50.2%) occur among pedestrians, and the majority (90.9%) of the children or their guardians admitted responsibility in crossing the road. Of the 31 children injured as car passengers, the vast majority (87.1%) were unrestrained, and a large fraction (38.7%) were front seat passengers. Two clusters were identified: the first consisted of younger children who resided mostly in the Athens area and suffered less serious knee injuries as pedestrians or car passengers during the colder months; the second consisted of older children, frequently tourists, who suffered more serious injuries as cyclists while vacationing. CONCLUSIONS: Many of the children who suffered road traffic knee injuries as pedestrians admitted responsibility in road crossing, whereas a large proportion of children who were injured as car passengers were injured while improperly seated in the front and without seatbelt protection. Older children, frequently tourists, were at high risk of knee injuries while using motorcycles and bicycles.

Accidents, Traffic↗
PubMedDate not supplied

[The occurrence of Echinococcus multilocularis in red foxes in lower Saxony: identification of a high risk area by spatial epidemiological cluster analysis].

There is considerable interest in the spatial distribution of Echinococcus multilocularis in red foxes (Vulpes vulpes L.), because this parasite causes the zoonoses of alveolar echinococcosis which is potentially of high fatality rate. High risk areas are known from France, Switzerland and the Swabian Alb in Germany for a long time. In this work, the spatial scan statistic is introduced as an instrument for identification and localisation of high risk areas, so called disease clusters in spatial epidemiology. The use of the spatial scan statistic along with data about the distribution of the parasite in 5365 red foxes in Lower Saxony, that were collected during 1991 to 1997, led to the identification of another high risk area. The relative risk for this disease cluster is approximated by RR = 5.03 (CI0.95(RR) = [4.27; 6.58]) for the period of 1991 to 1994 and by RR = 4.45 (CI0.95(RR) = [3.53; 5.59]) for the period of 1994 to 1997, respectively.

Animals↗
PubMed2001

Cluster analysis of Neisseria meningitidis type 22 strains isolated in Poland.

The aim of this study was to investigate the genetic relationships among strains belonging to Neisseria meningitidis serotype 22 recovered in Poland from 1995 to 1998. Phenotypical characterisation of meningococcal strains isolated from patients with meningococcal disease has been performed since 1995. Strains belonging to Neisseria meningitidis type 22 were most frequently recovered from severe cases of meningitis and septicaemia. The type 22 strains were separated into clusters by serosubtyping and DNA analyses by pulsed-field gel electrophoresis and ribotyping. However, the grouping according to serosubtypes was quite different from that obtained by ribotyping and pulsed-field gel electrophoresis. Furthermore, the two genotyping methods seldom identified the same clusters, nor were clusters identified among 26 Neisseria meningitidis type 22 strains recovered from patients hospitalised in five cities. Determination of the susceptibility to penicillin showed that a single strain was resistant (MIC, 2 mg/l) and that one-third (24/71) of the strains tested had reduced susceptibility (MIC range, 0.1-1 mg/l).

Adult↗
PubMed1997

Using cluster analysis to develop a healing typology in vascular ulcers.

A clinically meaningful typology of healing was developed to assist nurses in assessing patients' healing potential. A descriptive correlational design was used to determine similarities in healing characteristics of older people with venous, venous-arterial, and arterial leg ulcers (n = 156). Hierarchical clustering techniques dendrogram using Ward's method suggested that three clusters existed based on the ankle/brachial pressure index, liposclerosis (hardening and induration of the skin of the lower limb), edema and wound characteristics: thus a healing typology was potentially formed. Nonhierarchical techniques such as analysis of variance examined cluster differences for the initial ulcer area (p < 0.013) and suggested that these groupings were reflective of differing ulcer areas. However, significant differences in the rate of healing (difference between ulcer surface area in week 4 and week 1) (measured by topographic mapping) group comparisons were not significant at the 0.05 level. Clinical differences in the healing rate were apparent, and three individual profiles of leg ulcer sufferers based on the three differing clusters of factors were outlined: rapid healers, slow healers, and nonhealers. Further research into the clustering of these factors and their application to longer healing times or time to complete healing may be significant and support the utility of this typology.

Aged↗
PubMed1998

Mining the National Cancer Institute Anticancer Drug Discovery Database: cluster analysis of ellipticine analogs with p53-inverse and central nervous system-selective patterns of activity.

The United States National Cancer Institute conducts an anticancer drug discovery program in which approximately 10,000 compounds are screened every year in vitro against a panel of 60 human cancer cell lines from different organs. To date, approximately 62,000 compounds have been tested in the program, and a large amount of information on their activity patterns has been accumulated. For the current study, anticancer activity patterns of 112 ellipticine analogs were analyzed with the use of a hierarchical clustering algorithm. A dramatic coherence between molecular structures and their activity patterns could be seen from the cluster tree: the first subgroup (compounds 1-66) consisted principally of normal ellipticines, whereas the second subgroup (compounds 67-112) consisted principally of N2-alkyl-substituted ellipticiniums. Almost all apparent discrepancies in this clustering were explainable on the basis of chemical transformation to active forms under cell culture conditions. Correlations of activity with p53 status and selective activity against cells of central nervous system origin made this data set of special interest to us. The ellipticiniums, but not the ellipticines, were more potent on average against p53 mutant cells than against p53 wild-type ones (i.e., they seemed to be "p53-inverse") in this short term assay. This study strongly supports the hypothesis that "fingerprint" patterns of activity in the National Cancer Institute in vitro cell screening program encode incisive information on the mechanisms of action and other biological behaviors of tested compounds. Insights gained by mining the activity patterns could contribute to our understanding of anticancer drugs and the molecular pharmacology of cancer.

Antineoplastic Agents↗
PubMed2006

RAPD cluster analysis and chlorate sensitivity of some Indian isolates of Macrophomina phaseolina from sorghum and their relationships with pathogenicity.

Charcoal rot caused by Macrophomina phaseolina is an economically important disease in sorghum grown during the post rainy season in India. Variations in random amplified polymorphic DNA (RAPD) polymorphisms, chlorate sensitivity and pathogenicity were studied among sorghum isolates of M. phaseolina collected from different parts of India. RAPD data based on 14 random primers of Kit A and C (OPA and OPC) on 20 isolates showed a high degree of polymorphism (98.1%) in different isolates. UPGMA dendrogram on RAPD data produced 7 clusters at the level of 37% similarity. Isolates from the same locations showed a tendency to group closer, substantiating closer genetic relatedness. Sorghum infecting Macrophomina isolates showed a mixed response for sensitivity to potassium chlorate (120 mM). Chlorate-resistant isolates were predominant (>65% of the isolates) over sensitive isolates. Chlorate-sensitive isolates were found to be genetically closer among them than the resistant ones. For the first time it was shown that chlorate sensitivity in Macrophomina had some relations with charcoal rot severity in sorghum.

Ascomycota↗
PubMed2003

Cluster analysis of structural stage classes to map wildland fuels in a Madrean ecosystem.

Geospatial information technology is changing the nature of fire mapping science and management. Geographic information systems (GIS) and global positioning system technology coupled with remotely sensed data provide powerful tools for mapping, assessing, and understanding the complex spatial phenomena of wildland fuels and fire hazard. The effectiveness of these technologies for fire management still depends on good baseline fuels data since techniques have yet to be developed to directly interrogate understory fuels with remotely sensed data. We couple field data collections with GIS, remote sensing, and hierarchical clustering to characterize and map the variability of wildland fuels within and across vegetation types. One hundred fifty six fuel plots were sampled in eight vegetation types ranging in elevation from 1150 to 2600 m surrounding a Madrean 'sky island' mountain range in the southwestern US. Fuel plots within individual vegetation types were divided into classes representing various stages of structural development with unique fuel load characteristics using a hierarchical clustering method. Two Landsat satellite images were then classified into vegetation/fuel classes using a hybrid unsupervised/supervised approach. A back-classification accuracy assessment, which uses the same pixels to test as used to train the classifier, produced an overall Kappa of 50% for the vegetation/fuels map. The map with fuel classes within vegetation type collapsed into single classes was verified with an independent dataset, yielding an overall Kappa of 80%.

Cluster Analysis↗
PubMed2002

Multiple sclerosis distribution in northern Sardinia: spatial cluster analysis of prevalence.

BACKGROUND: A heterogeneous geographic distribution of MS has been reported among different ethnic groups, and also within small communities. Epidemiologic studies conducted over the past two decades using repeated assessments clearly show that Sardinia is at high risk for MS, with a prevalence of 150 per 100,000 in 1997. OBJECTIVE: To present spatial analysis of the disease prevalence to disclose possible "hot" or "cold" spots of disease, further allowing correlations with risk factors. METHODS: A spatial analysis of the whole province of Sassari, in northern Sardinia, at a microgeographic level (i.e., in the 89 administrative communes and 6 linguistic areas) was conducted. Because of the small number of cases per commune and to overcome random variability, a hierarchical Bayesian approach was adopted. The distribution of prevalent cases by commune of residence on December 31, 1997 and from age 5 to 15 years was analyzed. RESULTS: A clustering pattern was found in the southwestern communes of the province based on geographic distribution by both prevalence and residence at age 5 to 15 years. A west-to-east gradient also was observed. CONCLUSIONS: This study highlights a hot spot of MS in the southwestern part of Sassari province, bordering with the commune of Macomer, where MS was once hypothesized as having occurred as an epidemic. Interestingly, these areas of MS clustering comprise the Common Logudorese linguistic domain. The Catalan area, linguistically and genetically distant from the remaining Sardinian domains, does not show such high estimates. Because MS is not a single-source infectious disease, this study may help test the hypothesis that a widely and evenly spread environmental (infectious?) agent may produce disease in subgroups of genetically more susceptible individuals in areas at higher inbreeding rates, wherein a disease mode of inheritance could be better investigated.

Adolescent↗
PubMed2000

Using cluster analysis of alcohol use disorders to investigate 'diagnostic orphans': subjects with alcohol dependence symptoms but no diagnosis.

The purpose of this paper is to examine the characteristics of community subjects with one or two alcohol dependence symptoms who did not satisfy the criteria for Diagnostic and Statistical Manual of Mental Disorders-Fourth Edition (DSM-IV) alcohol dependence or abuse (sub-diagnostic group or diagnostic orphans). Variables not included in the DSM-IV alcohol abuse and dependence criteria are used to compare the different alcohol statuses. The results indicate that the sub-diagnostic group 'diagnostic orphans' formed a cluster distinct from that of the non-problem drinkers group, and appeared to be closer to those with alcohol abuse than to those with alcohol dependence. The diagnosis of DSM-IV alcohol dependence (with three, four, or five or more symptoms) appeared to be its own entity. The findings lend credence to the requirement of three symptoms (in any 12 months) for the diagnosis of alcohol dependence in DSM-IV. However, those with one or two symptoms of alcohol dependence should be considered along with alcohol abuse as an entity in future DSM classifications.

Adult↗
PubMed1998

Tissue viability by multispectral near infrared imaging: a fuzzy C-means clustering analysis.

Clinically, skin color, temperature, and capillary perfusion are used to assess tissue viability following microvascular tissue transfer. However, clinical signs that arise as a consequence of poor perfusion become evident only after several hours of compromised perfusion. This study demonstrates the potential usefulness of optical/infrared multispectral imaging in the prognosis of tissue viability immediately post-surgery. Multispectral images of a skin flap model acquired within 1 h of surgical elevation are analyzed in comparison to the final 72-h clinical outcome with a high degree of correlation. Regional changes in tissue perfusion and oxygenation present immediately following surgery are differentiated using fuzzy clustering and image processing algorithms. These methodologies reduce the intersubject variability inherent in infrared imaging methods such that the changes in perfusion are reproducible and clearly distinguishable across all subjects. Clinically, an early prognostic indicator of viability such as this would allow for a more timely intervention following surgery in the event of compromised microvasculature.

Algorithms↗
PubMed2003

How does Trypanosoma equiperdum fit into the Trypanozoon group? A cluster analysis by RAPD and multiplex-endonuclease genotyping approach.

The pathogenic trypanosomes Trypanosoma equiperdum, T. evansi as well as T. brucei are morphologically identical. In horses, these parasites are considered to cause respectively dourine, surra and nagana. Previous molecular attempts to differentiate these species were not successful for T. evansi and T. equiperdum; only T. b. brucei could be differentiated to a certain extent. In this study we analysed 10 T. equiperdum, 8 T. evansi and 4 T. b. brucei using Random Amplified Polymorphic DNA (RAPD) and multiplex-endonuclease fingerprinting, a modified AFLP technique. The results obtained confirm the homogeneity of the T. evansi group tested. The T. b. brucei clustered out in a heterogenous group. For T. equiperdum the situation is more complex: 8 out of 10 T. equiperdum clustered together with the T. evansi group, while 2 T. equiperdum strains were more related to T. b. brucei. Hence, 2 hypotheses can be formulated: (1) only 2 T. equiperdum strains are genuine T. equiperdum causing dourine; all other T. equiperdum strains actually are T. evansi causing surra or (2) T. equiperdum does not exist at all. In that case, the different clinical outcome of horse infections with T. evansi or T. b. brucei is primarily related to the host immune response.

Animals↗
PubMed2004

High-resolution single-nucleotide polymorphism array and clustering analysis of loss of heterozygosity in human lung cancer cell lines.

Chromosomal loss of heterozygosity (LOH) is a common mechanism for the inactivation of tumor suppressor genes in human epithelial cancers. Hybridization to single-nucleotide polymorphism (SNP) arrays is an efficient method to detect genome-wide cancer LOH. Here, we survey LOH patterns in a panel of 33 human lung cancer cell lines using SNP array hybridization containing 1500 SNPs. We compared the LOH patterns generated by SNP array hybridization to those previously obtained by 399 microsatellite markers and find a high degree of concordance between the two methods. A novel informatics platform, dChipSNP, was used to perform hierarchical tumor clustering based on genome-wide LOH patterns. We demonstrate that this method can separate non-small-cell and small-cell lung cancer samples based on their shared LOH. Furthermore, we analysed seven human lung cancer cell lines using a novel 10 000 SNP array and demonstrate that this is an efficient and reliable method of high-density allelotyping. Using this array, we identified small regions of LOH that were not detected by lower density SNP arrays or by standard microsatellite marker panels.

Biomarkers, Tumor↗
PubMed2000

Cluster analysis of antinuclear autoantibodies in the prognosis of SLE nephropathy: are anti-extractable nuclear antibodies protective?

To investigate the possible role of anti-ENA autoantibodies in the pathogenesis of SLE nephropathy, we performed a cross sectional clustering study of 91 SLE patients using 75 clinical and laboratory variables examining the presence of anti-dsDNA and ENA autoantibodies by ELISA and Western blot. We applied principal component, hierarchical cluster, multiple correspondence and logistical regression analysis. Two polar forms of SLE nephropathy and five clinical groups were identified: group 1 without overt nephropathy (n = 37), group 2 with nephropathy and only proteinuria (n = 19), group 3 nephropathy and only hematuria (n = 11), group 4 with hematuria and proteinuria (n = 14) and group 5 on renal failure (n = 10). When analyzed individually, levels of anti-dsDNA and single anti-ENA antibodies did not allow us to differentiate between renal and non-renal groups. However, when the anti-ENA autoantibodies were analyzed as a cluster, a high predictive value for clinical nephropathy was obtained. Thus, the absence of ENA antibodies (ENA ve or Venezuelan cluster) increased eleven-fold the odds ratio to develop SLE nephropathy. We suggested that the ENA ve cluster may predict development of the most severe forms of renal lupus while the ENA Sm/RNP and the ENA Ro/La/Sm/RNP clusters could be associated with the absence and the most benign form of SLE nephropathy. It must be interesting to apply similar cluster methodology in an SLE population with different ethnic background.

Adolescent↗
PubMed2006

Gene cluster analysis method identifies horizontally transferred genes with high reliability and indicates that they provide the main mechanism of operon gain in 8 species of gamma-Proteobacteria.

The formation mechanism of operons remains unresolved: operons may form by rearrangements within a genome or by acquisition of genes from other species, that is, horizontal gene transfer (HGT). One hindrance to its elucidation is the unavailability of a method to accurately identify HGT, although it is generally considered to occur. It is critically important first to select horizontally transferred (HT) genes reliably and then to determine the extent to which HGT is involved in operon formation. For this purpose, we considered indels in terms of gene clusters instead of individual genes and chose candidates of HT genes in 8 species of Escherichia, Shigella, and Salmonella based on the minimization of indels. To select a benchmark set of positively HT genes against which we can evaluate the candidate set, we devised another procedure using intergenetic alignments. Comparison with the benchmark set demonstrated the absence of a significant number of false positives in the candidate set, showing the high reliability of the method. Analyses of Escherichia coli K-12 operons revealed that although approximately 20 operons were probably gained from the last common ancestor of the 8 gamma-proteobacteria, deletion of intervening genes accounts for the formation of no operons, whereas horizontal transfer expanded 2 operons and introduced 4 entire operons. Based on these observations and reasoning, we suggest that the main mechanism of operon gain is HGT rather than intragenomic rearrangements. We propose that genes with related essential functions tend to reside in conserved operons, whereas genes in nonconserved operons mostly confer slight advantage to the organisms and frequently undergo horizontal transfer and decay. HT genes constitute at least 5.5% of the genes in the 8 species and approximately 45% of which originate from other gamma-proteobacteria. Genes involved in viral functions and mobile and extrachromosomal element functions are HT more often than expected. This finding indicates frequent mediation of HGT by bacteriophages. On the other hand, not only informational genes (those involved in transcription, translation, and related processes) but also operational genes (those involved in housekeeping) are HT less frequently than expected.

Cluster Analysis↗
PubMed2003

Spike cluster analysis in neocortical localization related epilepsy yields clinically significant equivalent source localization results in magnetoencephalogram (MEG).

OBJECTIVE: In magnetoencephalogram (MEG) recordings of patients with epilepsy several types of sharp transients with different spatiotemporal distributions are commonly present. Our objective was to develop a computer based method to identify and classify groups of epileptiform spikes, as well as other transients, in order to improve the characterization of irritative areas in the brain of epileptic patients. METHODS: MEG data centered on selected spikes were stored in signal matrices of C channels by T time samples. The matrices were normalized and euclidean distances between spike representations in vector space R(CxT) were input to a Ward's hierarchical clustering algorithm. RESULTS: The method was applied to MEG data from 4 patients with localization-related epilepsy. For each patient, distinct spike subpopulations were found with clearly different topographical field maps. Inverse computations to selected spike subaverages yielded source solutions in agreement with seizure classification and location of structural lesions, if present, on magnetic resonance images. CONCLUSIONS: With the proposed method a reliable categorization of epileptiform spikes is obtained, that can be applied in an automatic way. Computation of subaverages of similar spikes enhances the signal-to-noise ratio of spike field maps and allows for more accurate reconstruction of sources generating the epileptiform discharges.

Adult↗