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PubMed1986

A longitudinal study of the age dependence of human ocular refraction--II. Prediction of future trends in medium and high myopia by means of cluster analysis.

A sample population of myopes with an initial correction of 2 DS or more is extracted from the longitudinal sample of ametropes reported by Saunders (1986). The myopes are partitioned by means of cluster analysis and, as a result, three distinct groups of myopes are identified. The time/regression equations which best describe the groups are stated. It is concluded that meaningful long-term prognosis of medium and high myopes is unlikely and that reasonable prediction of short-term trends requires at least two consecutive refraction data to determine the group allocation of a myope.

Age Factors↗
PubMed1997

Evolutionary relationships among proteins probed by an iterative neighborhood cluster analysis (INCA). Alignment of bacteriorhodopsins with the yeast sequence YRO2.

PURPOSE: Searching the existing databases for homologous sequences is essential to understanding a protein's structure and function. For a query sequence, its nearest neighbors can be identified by BLAST (basic local alignment search tool). However, a single query sequence is sufficient to define the entire neighborhood of related sequences, and multiple BLAST queries are needed. We describe here a program which permits automated and iterative BLAST analysis of an entire neighborhood of sequences and apply this to search for homologs of the bacteriorhodopsins outside the archaea phylum. METHODS: We have developed a Java program, 'Iterative Neighborhood Cluster Analysis' (INCA), which performs iterative BLAST searches, beginning with a single starter sequence, and proceeding with any other sequence achieving a predefined minimum alignment score. This results in a cluster of sequences where each sequence is related to at least one other sequence by the cutoff score, additional lists of more distantly related sequences for each member of cluster. RESULTS: Bacteriorhodopsins had not been previously aligned with any other protein family with scores indicative of probable homology. Using INCA, we identified a probable homolog in yeast, YRO2_YEAST, also containing seven putative transmembrane domains. A finding of probable homology was supported by additional alignment strategies. CONCLUSIONS: INCA is a useful tool to assess complete protein neighborhoods. With an increasing database, INCA can serve to detect the emergence of evolutionary links between even the most distantly related protein families. Identifying a homolog of the bacteriorhodopsins in yeast illustrates this approach but at the same time highlights the vast evolutionary distances between polytopic membrane proteins, such as the bacteriorhodopsins.

Amino Acid Sequence↗
PubMed1997

[Risk profile: multivariate cluster analysis of urban small areas based on socioeconomic indicators - census tracts from the Greater Rio de Janeiro Metropolitan Area]

A method based on small area data analysis was developed to build a health risk classification for the Greater Rio de Janeiro Metropolitan Area. The approach uses 1991 census data and studies data pertaining to sanitation, ownership and type of housing, size and occupancy of the household, demography, schooling, and income. Principal component analysis applied over each dimension allowed for the choice of 15 variables, which summarized most of the observed variances. Additional analysis with these variables suggested that just six variables are sufficient for the construction of a classification using k-means method of multivariate cluster analysis. Five classes were obtained: (A) high income; (B) lower income; (C) poor; (D) low schooling and income; (E) low-level access to sanitation. The existing inequality in each of the geopolitical established areas was clearly identified. The proposed method allowed for the construction of compound indices to evaluate quality of life, based on widespread and easily obtained data (the census). Moreover, the method contributed to the detection of socioeconomic inequality, identifying, not only the larger poor regions but also the small excluded areas.

Journal Article↗
PubMed2006

Evidence of early childhood as the susceptibility period in multiple sclerosis: space-time cluster analysis in a Sardinian population.

The authors analyzed the natural history of multiple sclerosis (MS) before onset to identify the period of susceptibility and exogenous factors that might play a role in causing the disease. Space-time cluster analysis was performed among northern Sardinians, a genetically stable Italian population that showed an increasing risk of MS between 1965 and 1999. Residence changes from birth to clinical onset were recorded for all MS patients with clinical onset between 1965 and 1999 in the province of Sassari. Closeness in space and time was defined as living in the same municipality and differing in year of birth by 1, 2, or 5 years. Analyses were performed for the period from birth to age 25 years or MS onset and in demographic and clinical subgroups. Clustering was substantial in early childhood. Clustering was most marked in the most recent cases, among women, and among patients with early age at onset, a relapsing-remitting course, and in the eastern subarea. No clustering was found when closeness in time was defined as a fixed number of years before onset, which argues against a fixed latency period. Early childhood seemed to be a period of increased susceptibility to MS. This evidence and the increasing incidence of MS in northern Sardinia are compatible with a change in environmental exposure.

Adolescent↗
PubMedDate not supplied

[Cluster analysis of the classification of disseminated lupus erythematosus].

Using a grouping method the disease homogeneity within a group of 59 patients with systemic lupus erythematosus was studied. The mean observation period was 8 years and 10 months. By using a cluster analysis, the total group of patients could be divided into two subgroups which differed clearly in their symptomatology. One subgroup showed a higher incidence of hypertension, severe anaemia, oral ulceration, elevated serum creatinine values, and proteinuria. All 8 deaths occurred in this group. The second group was characterized by a more benign course of disease, a notably decreased incidence of symptoms characteristic for the first subgroup, and no deaths.

Adult↗
PubMed1994

Structural similarities in glucoamylase by hydrophobic cluster analysis.

The model of the catalytic domain of Aspergillus awamori var. X100 glucoamylase was related to 14 other glucoamylase protein sequences belonging to five subfamilies. Structural features of the different sequences were revealed by multisequence alignment following hydrophobic cluster analysis. The alignment agreed with the hydrophobic microdomains, normally conserved throughout evolution, evaluated from the 3-D model. Saccharomyces and Clostridium glucoamylases lack the alpha-helix exterior to the catalytic domain. A different catalytic base was found in the Saccharomyces glucoamylase subfamily. The starch binding domain of fungal glucoamylases has identical structural features and substrate interacting residues as the C-terminal domain of models of Bacillus circulans cyclodextrin glucosyltransferases. Three putative N-glycosylation sites were found in the same turns in glucoamylases of different subfamilies. O-Glycosylation is present at different levels in the catalytic domain and in the linker between the catalytic and starch binding domains.

Amino Acid Sequence↗
PubMed1985

[Cluster analysis of 109 patients with systemic lupus erythematosus].

Using a grouping method we studied the disease homogeneity within a group of 109 patients with systemic lupus erythematosus. The mean observation period was 6 years and 8 months. By using a cluster analysis, the total group of patients could be subdivided into two subgroups which differed clearly in their symptomatology. One subgroup (n = 42) showed higher incidence of elevated serum creatinine values, proteinuria, oral ulceration and severe anaemia. All 13 deaths occurred in this group. The second group (n = 67) was characterized by a more benign course of disease, a notably decreased incidence of renal involvement, and the Raynaud's Phenomenon was comparatively frequent.

Adult↗
PubMed2003

Cluster analysis of fMRI data using dendrogram sharpening.

The major disadvantage of hierarchical clustering in fMRI data analysis is that an appropriate clustering threshold needs to be specified. Upon grouping data into a hierarchical tree, clusters are identified either by specifying their number or by choosing an appropriate inconsistency coefficient. Since the number of clusters present in the data is not known beforehand, even a slight variation of the inconsistency coefficient can significantly affect the results. To address these limitations, the dendrogram sharpening method, combined with a hierarchical clustering algorithm, is used in this work to identify modality regions, which are, in essence, areas of activation in the human brain during an fMRI experiment. The objective of the algorithm is to remove data from the low-density regions in order to obtain a clearer representation of the data structure. Once cluster cores are identified, the classification algorithm is run on voxels, set aside during sharpening, attempting to reassign them to the detected groups. When applied to a paced motor paradigm, task-related activations in the motor cortex are detected. In order to evaluate the performance of the algorithm, the obtained clusters are compared to standard activation maps where the expected hemodynamic response function is specified as a regressor. The obtained patterns of both methods have a high concordance (correlation coefficient = 0.91). Furthermore, the dependence of the clustering results on the sharpening parameters is investigated and recommendations on the appropriate choice of these variables are offered. Hum. Brain Mapping 20:201-219, 2003.

Algorithms↗
PubMed2005

[K-mean cluster analysis for incisal jaw morphology of normal occlusion subjects among different vertical facial skeletal types].

OBJECTIVE: To study the incisal jaw morphology of subjects with normal occlusion and to discuss the relationship between different vertical facial skeletal types and different incisal jaw cluster types. METHODS: After studied by radiographic cephalometry, the incisal jaw morphology of 169 subjects with normal occlusion in early permanent dentition were analyzed by K-mean cluster analysis. RESULTS: Morphology of maxillary or mandibular incisal jaws could be divided into four types separately, including division I, division II, division III and division N. In maxilla or in mandible, the incisal jaw morphology of division I was characterized by wideness and shortness. In contrast, division II was characterized by thinness and length. As for division III and division IV, both of two were intermediate types between division I and division II . In maxilla, it was found that division II was the majority (86.49%) in the high-angle subjects, division III was the majority (47.67%) in the average-angle subjects, and division I and III were the majority (82.61%) in the low-angle subjects. In mandible, it was found that division II was the majority (51.35%) in the high-angle subjects, division IV was the majority (48.84%) in the average-angle subjects, and division III and IV were the majority (69.57%) in the low-angle subjects. CONCLUSION: Owing to the obvious characteristics of morphology in each cluster types and in each vertical facial skeletal types, different clinic considerations must be put forward when we want to move the incisor.

Cephalometry↗
PubMedDate not supplied

An alterative method for hospital partition determination using hierarchical cluster analysis.

The classification of short-term hospitals into homogeneous groups has become an integral part of many systems designed to abate continuing cost inflation in the hospital industry. This paper describes one approach which was developed to identify homogeneous groups of short-term hospitals. The approach, based on hierarchical cluster analysis, defines an objective measure (called expected distinctiveness) to evaluate any group of hospitals identified by a hierarchical grouping structure or dendrogram. Using this measure, an efficient algorithm is developed which finds the hospital partition from the identified groups which maximizes total expected distinctiveness. A numerical example illustrates the application and extensions.

Analysis of Variance↗
PubMed1976

Cluster analysis applied to symptom ratings of psychiatric patients: an evaluation of its predictive ability.

Rating on 39 symptoms were examined for patients admitted to the Neuropsychiatric Institute of the University of Michigan Medical Center. A detailed evaluation was made of the clusters derived by a hierarchical clustering algorithm, using complete linkage and a simple matching coefficient on the binary variables of presence or absence of symptoms. The four groups of patients suggested by the cluster analysis can be characterized as follows: (1) generalized multiplicity of symptoms; (2) capacity to cope except for orientation apart from generally held norms; (3) activity level and thought processes speeded up, intensified, and unselected; (4) inwardly punitive, slowed down and distressed. It is shown that these groups received significantly different treatment and that the effect of treatment was significantly different, while no such differences were noted for groups defined in terms of diagnoses. By means of linear discriminant functions, rules are suggested for assigning other psychiatric patients to one of these four groups.

Antipsychotic Agents↗
PubMed2003

Origin and evolution of transmembrane Chl-binding proteins: hydrophobic cluster analysis suggests a common one-helix ancestor for prokaryotic (Pcb) and eukaryotic (LHC) antenna protein superfamilies.

All chlorophyll (Chl)-binding proteins constituting the photosynthetic apparatus of both prokaryotes and eukaryotes possess hydrophobic domains, corresponding to membrane-spanning alpha-helices (MSHs). Hydrophobic cluster analysis of representative members of the different Chl protein superfamilies revealed that all Chl proteins except the five-helix reaction center II proteins and the small subunits of photosystem I possess related domains. As a major conclusion, we found that the eukaryotic antennae likely share a common precursor with the prokaryotic Chl a/b antennae from Chl-b-containing oxyphotobacteria. From these data, we propose a global scheme for the evolution of these proteins from a one-MSH ancestor.

Amino Acid Sequence↗
PubMed1998

Cluster analysis of HIV intervention outcomes among substance-abusing women.

The study described here presents an innovative approach to analyzing intervention outcomes among women substance abusers participating in a national HIV prevention research study funded by the National Institute on Drug Abuse. We used cluster analysis to divide the women in our sample (N=557) into four distinct subgroups predominantly characterized by differences in drug use, injecting risk, sexual behaviors, and drug and sexual risk combined. The four subgroups resulting from this process were primary crack-using women, primary needle-using women, high-frequency needle-using women, and women with multiple drug and sex risk behaviors. Our analysis focuses on changes in self-reported risk behaviors from baseline to 6-month follow-up. In general, the results clearly indicate that the women are heterogeneous; that is, the subgroups exhibit varying patterns of drug use, injecting risk, sexual behavior, and HIV seropositivity. Significant outcomes were found in many areas, indicating positive changes in risk behaviors. The two smaller subgroups of women--high-frequency needle users and those in the multiple-risk behavior subgroup--reported the highest rate of high-risk behaviors and seropositivity but also showed the greatest change at follow-up. A particularly important finding resulting from our analytical approach is that well over half the women in our sample were primary crack users (n=313). This finding is even more significant in light of the fact that the Cooperative Agreement specifically tried to include 70% or more participants who were injectors. Although the rate of HIV seropositivity is not as high for this crack-using subgroup as for the two smaller needle-using subgroups, a greater number of "women who are HIV positive" are in this primary crack-using subgroup than in all the other subgroups. Most of the crack-using women reported that they were not currently injecting drugs and never shared needles, but 10% were seropositive for HIV, suggesting that their risk comes primarily from sexual behaviors. Behaviors in this larger subgroup of women did not change as dramatically as those of women in the smaller subgroups; however, the women did show improvement in areas related to indirect risk (e.g., alcohol and crack use) and in several areas where change is most needed (e.g., trading sex for drugs and using condoms). The results demonstrate a promising alternative approach to analyzing substance abuse and HIV risk behaviors, and they suggest the need for further research on alternative interventions for women with different patterns of risk behaviors.

Community-Institutional Relations↗
PubMed1985

Cluster analysis of cognitive performance in elderly and demented subjects.

48 elderly normals, 14 demented subjects and 76 young controls were tested for basic cognitive functions. All the tests were quantified and could therefore be subjected to statistical analysis. The results show a difference in the speed of information processing and in memory load between the young controls and elderly normals but the age groups differed in quantitative terms only. Cluster analysis showed that the elderly and the demented formed two distinctly separate groups at the qualitative level, the basic cognitive processes being damaged in the demented group. Age thus appears to be only a risk factor for dementia and not its cause. It is concluded that batteries based on precise and measurable tasks are the most appropriate not only for the study of dementia but for rehabilitation purposes too.

Age Factors↗
PubMed1983

The use of cluster analysis in determining possible enzyme-substrate interactions with reference to nucleoside diphosphatase activity of Golgi membranes.

The relative effectiveness of deoxyribonucleoside diphosphates, ribonucleoside diphosphates and phosphorylated B vitamins as substrates of the nucleoside diphosphatase of Golgi membranes have been determined. The substrates have been classified by cluster analysis. These findings suggest that a base ketone group and the 3'-OH of the substrates are important in promoting catalytic effectiveness, possibly by promoting hydrogen bonding during enzyme-substrate complex formation.

Acid Anhydride Hydrolases↗
PubMed1990

Structural homology among the peroxidase enzyme family revealed by hydrophobic cluster analysis.

A number of peroxidase amino acid sequences show limited homology to short regions comprising the known active site cleft of yeast cytochrome c peroxidase. Otherwise no clear homology is visible in linear alignments between this enzyme and other peroxidases. We have subjected eight peroxidase sequences to hydrophobic cluster analysis. Our results suggest that these peroxidases are evolutionary related and that they share many folding characteristics.

Amino Acid Sequence↗
PubMed1984

Cluster analysis of chromatographic profiles of urine proteins.

A method to examine and classify the chromatograms of urinary proteins, separated on a fast protein liquid chromatography system, is presented. For the analyses a measure of similarity between chromatogram profiles is defined and this is used to implement a statistical cluster analysis technique for the identification of a system of classification. The resulting classification can be related to a clinical assessment of the proteinuria of the sample urines, which are from patients with various renal disorders.

Chromatography, High Pressure Liquid↗