Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “multiple clustering”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8Linked to original sources
PubMed2003

Molecular characteristics of human immunodeficiency virus type 1 subtype C viruses from KwaZulu-Natal, South Africa: implications for vaccine and antiretroviral control strategies.

The KwaZulu-Natal region of South Africa is experiencing an explosive outbreak of human immunodeficiency virus type 1 (HIV-1) subtype C infections. Understanding the genetic diversity of C viruses and the biological consequences of this diversity is important for the design of effective control strategies. We analyzed the protease gene, the first 935 nucleotides of reverse transcriptase, and the C2V5 envelope region of a representative set of 72 treatment-naïve patients from KwaZulu-Natal and correlated the results with amino acid signature and resistance patterns. Phylogenetic analysis revealed multiple clusters or "lineages" of HIV-1 subtype C that segregated with other C viruses from southern Africa. The same pattern was observed for both black and Indian subgroups and for retrospective specimens collected prior to 1990, indicating that multiple sublineages of HIV-1 C have been present in KwaZulu-Natal since the early stages of the epidemic. With the exception of three nonnucleoside reverse transcriptase inhibitor mutations, no primary resistance mutations were identified. Numerous accessory polymorphisms were present in the protease, but none were located at drug-binding or active sites of the enzyme. One frequent polymorphism, I93L, was located near the protease/reverse transcriptase cleavage site. In the envelope, disruption of the glycosylation motif at the beginning of V3 was associated with the presence of an extra protein kinase C phosphorylation site at codon 11. Many polymorphisms were embedded within cytotoxic T lymphocyte or overlapping cytotoxic T-lymphocyte/T-helper epitopes, as defined for subtype B. This work forms a baseline for future studies aimed at understanding the impact of genetic diversity on vaccine efficacy and on natural susceptibility to antiretroviral drugs.

AIDS Vaccines↗
PubMed2004

Interaction of argon clusters with intense VUV-laser radiation: the role of electronic structure in the energy-deposition process.

The response of Ar clusters to intense vacuum-ultraviolet pulses is investigated with photoion spec-troscopy. By varying the laser wavelength, the initial excitation was either tuned to absorption bands of surface or bulk atoms of clusters. Multiple ionization is observed, which leads to Coulomb explosion. The efficiency of resonant 2-photon ionization for initial bulk and surface excitation is compared with that of the nonresonant process at different laser intensities. The specific electronic structure of clusters plays almost no role in the explosion dynamics at a peak intensity larger than 1.8 x 10(12) W/cm(2). The inner ionization of atoms for resonant and nonresonant excitation is then saturated and the energy deposition is mainly controlled by the plasma heating rate. Molecular dynamics simulations indicate that standard collisional heating cannot fully account for the strong energy absorption.

Journal Article↗
PubMed1979

Considerations in applying clustering techniques to speaker-independent word recognition.

Recent work at Bell Laboratories has demonstrated the utility of applying sophisticated pattern recognition techniques to obtain a set of speaker-independent word templates for an isolated word recognition system [Levinson et al.,IEEE Trans. Acoust. Speech Signal Process. ASSP-27 (2), 134--141 (1979); Rabiner et al., IEEE Trans. Acoust. Speech Signal Process.(in press)]. In these studies, it was shown that a careful experimenter could guide the clustering algorithms to choose a small set of templates that were representative of a large number of replications for each word in the vocabulary. Subsequent word recognition tests verified that the templates chosen were indeed representative of a fairly large population of talkers. Given the success of this approach, the next important step is to investigate fully automatic techniques for clustering multiple versions of a single word into a set of speaker-independent word templates. Two such techniques are described in this paper. The first method uses distance data (between replications of a word) to segment the population into stable clusters. The word template is obtained as either the cluster minimax, or as an averaged version of all the elements in the cluster. The second method is a variation of the one described by Rabiner [IEEE Trans. Acoust. Speech Signal Process. ASSP-26 (3), 34--42 (1978)] in which averaging techniques are directly combined with the nearest neighbor rule to simultaneously define both the word template (i.e., the cluster center) and the elements in the cluster. Experimental data show the first method to be superior to the second method when three or more clusters per word are used in the recognition task.

Humans↗
PubMed1993

Relationship between intrinsic connections and functional architecture revealed by optical imaging and in vivo targeted biocytin injections in primate striate cortex.

In primate primary visual cortex, neurons sharing similar response properties are clustered together forming functional domains that appear as a mosaic of patches or bands, often traversing the entire cortical depth from the pia to the white matter. Similarly, each cortical site connects laterally through an extensive network of intrinsic projections that are organized in multiple clusters (patches) and reach distances of up to a few millimeters. The relationship between the functional domains and these laterally connected patches has remained a controversial issue despite intensive research efforts. To investigate this relationship, we obtained high-resolution functional maps of the cortical architecture by in vivo optical imaging. Subsequently, extracellular injections of the sensitive anterograde tracer biocytin were targeted into selected functional domains. Within the ocular dominance system, we found that long-range intrinsic connections tended to link the monocular regions of same-eye ocular dominance columns. Furthermore, we discovered that binocular domains formed a separate set of connections in area V1; binocular regions were selectively connected among themselves but were not connected to strictly monocular regions, suggesting that they constitute a distinct columnar system. In the other subsystem subserving orientation preference, patches of intrinsic connections tended to link domains sharing similar orientation preferences. Analyses of the precision of these connections indicated that in both functional subsystems, < 15% of the connections were between domains having orthogonal response properties. However, their selectivity was limited; approximately 30% +/- 10% of the interconnected patches contained neurons exhibiting orientation tuning that differed from those found at the injection sites by at least 45 degrees. At short range (up to 400 microns from the injection site), this casual trend seemed markedly accentuated; the local, synaptic-rich axonal and dendritic arbors crossed freely through columns of diverse functional properties. These complex sets of connections can endow cortical neurons with a rich diversity of response properties and broad tuning.

Animals↗
PubMed2001

Basal cell carcinomas: association of allelic variants with a high-risk subgroup of patients with the multiple presentation phenotype.

Previous studies have shown that patients who present at first or a later presentation with a cluster of new basal cell carcinoma (BCC) comprise a subgroup, termed multiple presentation phenotype (MPP), that is at increased risk of developing further lesions. In this study, we examined the hypothesis that patients who develop multiple clusters are a high-risk subgroup. We found, in a total group of 926 BCC patients, 32 patients with 2-5 BCC clusters (multiple cluster MPP) and 113 cases with only one cluster (single cluster MPP). Multiple cluster MPP cases had mean of 11.3 BCC compared with 3.7 in single cluster MPP cases during similar follow-up. Ultraviolet (UV) exposure in these groups was similar. We determined whether the multiple cluster MPP was associated with characteristics associated with sensitivity to UV or glutathione S-transferase (GST) GSTT1, GSTM1, cytochrome P450 (CYP) CYP2D6, tumour necrosis factor (TNF)-alpha and vitamin D receptor (VDR) genotypes previously associated with BCC presentational phenotypes. While the frequencies of blue eyes and male gender were greater in multiple cluster than single cluster cases, these differences were not significant. In multiple cluster cases, mean age at first presentation with single tumours occurred earlier and the frequencies of CYP2D6 extensive metabolizer (EM) (94.4%) and GSTT1 null (41.2%) were significantly greater (P = 0.028 and P = 0.004) than in single cluster cases (67.1% and 14.3%, respectively). The odds ratios for the individual associations of CYP2D6 EM and GSTT1 null with the multiple cluster MPP were relatively larger; 15.5 and 7.39, respectively. TNF-alpha and VDR genotypes were not associated with multiple cluster MPP. We propose that the MPP is not the consequence of excessive UV exposure but rather reflects the presence of a distinct BCC subgroup which is defined by combinations of risk genes.

Alleles↗
PubMed2006

Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan.

BACKGROUND: Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards. RESULTS: Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations. CONCLUSION: The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species.

Conservation of Natural Resources↗
PubMed2003

Identification, structure and differential expression of novel pleurocidins clustered on the genome of the winter flounder, Pseudopleuronectes americanus (Walbaum).

Antimicrobial peptides form one of the first lines of defense against invading pathogens by killing the microorganisms and/or mobilizing the host innate immune system. Although over 800 antimicrobial peptides have been isolated from many different species, especially insects, few have been reported from marine fish. Sequence analysis of two genomic clones (15.6 and 12.5 kb) from the winter flounder, Pseudopleuronectes americanus (Walbaum) resulted in the identification of multiple clustered genes for novel pleurocidin-like antimicrobial peptides. Four genes and three pseudogenes (Psi) are encoded in these clusters, all of which have similar intron/exon boundaries but specify putative antimicrobial peptides differing in sequence. Pseudogenes are easily detectable but have incorrect initiator codons (ACG) and often contain a frameshift(s). Potential promoters and binding sites for transcription factors implicated in regulation of expression of immune-related genes have been identified in upstream regions by comparative genomics. Using reverse transcription-PCR assays, we have shown for the first time that each gene is expressed in a tissue-specific and developmental stage-specific manner. In addition, synthetic peptides based on the sequences of both genes and pseudogenes have been produced and tested for antimicrobial activity. These data can be used as a basis for prediction of antimicrobial peptide candidates for both human and nonhuman therapeutants from genomic sequences and will aid in understanding the evolution and transcriptional regulation of expression of these peptides.

Amino Acid Sequence↗
PubMed2005

Comparative genomic hybridizations reveal genetic regions within the Mycobacterium avium complex that are divergent from Mycobacterium avium subsp. paratuberculosis isolates.

Mycobacterium avium subsp. paratuberculosis is genetically similar to other members of the Mycobacterium avium complex (MAC), some of which are nonpathogenic and widespread in the environment. We have utilized an M. avium subsp. paratuberculosis whole-genome microarray representing over 95% of the predicted coding sequences to examine the genetic conservation among 10 M. avium subsp. paratuberculosis isolates, two isolates each of Mycobacterium avium subsp. silvaticum and Mycobacterium avium subsp. avium, and a single isolate each of both Mycobacterium intracellulare and Mycobacterium smegmatis. Genomic DNA from each isolate was competitively hybridized with DNA from M. avium subsp. paratuberculosis K10, and open reading frames (ORFs) were classified as present, divergent, or intermediate. None of the M. avium subsp. paratuberculosis isolates had ORFs classified as divergent. The two M. avium subsp. avium isolates had 210 and 135 divergent ORFs, while the two M. avium subsp. silvaticum isolates examined had 77 and 103 divergent ORFs. Similarly, 130 divergent ORFs were identified in M. intracellulare. A set of 97 ORFs were classified as divergent or intermediate in all of the nonparatuberculosis MAC isolates tested. Many of these ORFs are clustered together on the genome in regions with relatively low average GC content compared with the entire genome and contain mobile genetic elements. One of these regions of sequence divergence contained genes homologous to a mammalian cell entry (mce) operon. Our results indicate that closely related MAC mycobacteria can be distinguished from M. avium subsp. paratuberculosis by multiple clusters of divergent ORFs.

Conserved Sequence↗
PubMed2006

Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana.

We present MultiGO, a web-enabled tool for the identification of biologically relevant gene sets from hierarchically clustered gene expression trees (http://ekhidna.biocenter.helsinki.fi/poxo/multigo). High-throughput gene expression measuring techniques, such as microarrays, are nowadays often used to monitor the expression of thousands of genes. Since these experiments can produce overwhelming amounts of data, computational methods that assist the data analysis and interpretation are essential. MultiGO is a tool that automatically extracts the biological information for multiple clusters and determines their biological relevance, and hence facilitates the interpretation of the data. Since the entire expression tree is analysed, MultiGO is guaranteed to report all clusters that share a common enriched biological function, as defined by Gene Ontology annotations. The tool also identifies a plausible cluster set, which represents the key biological functions affected by the experiment. The performance is demonstrated by analysing drought-, cold- and abscisic acid-related expression data sets from Arabidopsis thaliana. The analysis not only identified known biological functions, but also brought into focus the less established connections to defense-related gene clusters. Thus, in comparison to analyses of manually selected gene lists, the systematic analysis of every cluster can reveal unexpected biological phenomena and produce much more comprehensive biological insights to the experiment of interest.

Abscisic Acid↗
PubMed2006

Fibrinolytic risk factor clustering and insulin resistance in healthy male relatives of men with intermittent claudication.

BACKGROUND: Raised fibrinolytic factors predict cardiovascular risk in healthy subjects. The aim of this study was to measure fibrinolytic factors and insulin resistance in healthy male first-degree relatives of men with intermittent claudication younger than 65 years. METHODS: The study compared 165 healthy first-degree relatives with 165 age-, sex- and race-matched control subjects free from a personal or family history of premature cardiovascular disease. Primary outcome measures were plasminogen activator inhibitor 1 (PAI-1), tissue plasminogen activator (tPA) and D-dimer levels. Insulin resistance was estimated by Homeostasis Model Assessment. Clinical and biochemical risk factors were measured and subjects genotyped for the PAI-1 4G/5G polymorphism. RESULTS: First-degree relatives had significantly higher mean PAI-1 (10.23 versus 7.85 ng/ml; P = 0.024), tPA (9.98 versus 8.29 ng/ml; P < 0.001) and D-dimer levels (56.6 versus 46.1 ng/ml; P = 0.004). They also had significantly higher insulin resistance (1.85 versus 1.53; P < 0.001) and clustered multiple atherogenic risk factors. On multivariate analysis the association between both tPA and D-dimer levels and relative status was independent of other variables. CONCLUSION: Raised levels of PAI-1, tPA, D-dimer and estimated insulin resistance were present in the healthy male first-degree relatives of men with intermittent claudication. These data support the hypothesis of fibrinolytic risk factor clustering in this high-risk population.

Cardiovascular Diseases↗
PubMed2004

Genogroup I and II noroviruses detected in stool samples by real-time reverse transcription-PCR using highly degenerate universal primers.

Genogroup I noroviruses from five genetic clusters and genogroup II noroviruses from eight genetic clusters were detected in stool extracts using degenerate primers and single-tube, real-time reverse transcription-PCR (RT-PCR) with SYBR Green detection. Two degenerate primer sets, designated MON 431-433 and MON 432-434, were designed from consensus sequences from the major clusters of norovirus based on the RNA-dependent RNA polymerase region of the norovirus genome. Viruses were extracted from stool samples within 20 min using a viral RNA extraction kit. Real-time RT-PCR for noroviruses generated semiquantitative results by means of the cycle threshold data and dilution endpoint standard curves. Presumptive product verification was achieved by evaluation of first-derivative melt graphs. Multiple clusters of noroviruses were identified simultaneously in a multiplex fashion by virtue of slight differences in melting temperature. The detection of 13 different genetic clusters suggests that the MON primers may serve as universal primers for most, if not all, of the noroviruses in a multiplex assay. Our technique provides a framework for broad application of real-time RT-PCR in clinical, environmental, and food testing laboratories for a wide range of noroviruses.

Caliciviridae Infections↗
PubMed1999

Unsupervised visual learning of three-dimensional objects using a modular network architecture.

This paper presents a modular network architecture that learns to cluster multiple views of multiple three-dimensional (3D) objects. The proposed network model is based on a mixture of non-linear autoencoders, which compete to encode multiple views of each 3D object. The main advantage of using a mixture of autoencoders is that it can capture multiple non-linear sub-spaces, rather than multiple centers for describing complex shapes of the view distributions. The unsupervised training algorithm is formulated within a maximum-likelihood estimation framework. The performance of the modular network model is evaluated through experiments using synthetic 3D wire-frame objects and gray-level images of real 3D objects. It is shown that the performance of the modular network model is superior to the performance of the conventional clustering algorithms, such as the K-means algorithm and the Gaussian mixture model.

Journal Article↗
PubMed1986

Comparison of sickness absence in Belgian, German, and Dutch firms.

International comparisons of sickness absence rates are difficult to make because of different national social security arrangements or recording procedures. Therefore a cross national study of sickness absence in Belgium, West Germany, and the Netherlands focused firstly on "contextual" aspects of sickness absence such as work incapacity benefit schemes, job security regulations, and the role of occupational physicians. Substantial differences were observed in regulations, local definitions, and available data. Those differences provide hypotheses for possibly divergent absence levels as well. For instance, Belgium shows the most diversified control procedures, the lowest level of sickness benefits, and the most rigid qualifying criteria for invalidity benefits. Sickness absence data were obtained from companies of four different clusters, each consisting of a comparable Belgian, German, and Dutch organisation. Conceptual, administrative, and statistical sources of bias were accounted for by selecting companies which resemble each other as to their product, production process, size, and geographical location: by using standardised definitions, absence data, and indices (observation period 1 January 1980 to 1 January 1982); and by measuring population variables to eliminate obvious explanations in terms of workforce composition. Controlled comparisons in these multiple clusters showed considerable and consistent differences in sickness absence rates. Whereas Belgian employees had 20.3 days of sickness absence (standardised for sex, age, and occupation) a year, German and Dutch employees had 28.5 and 39.1 days off a year respectively. Factors that might account for these differences are discussed.

Absenteeism↗
PubMed2005

Radical S-adenosylmethionine enzyme coproporphyrinogen III oxidase HemN: functional features of the [4Fe-4S] cluster and the two bound S-adenosyl-L-methionines.

The S-adenosylmethionine (AdoMet) radical enzyme oxygen-independent coproporphyrinogen III oxidase HemN catalyzes the oxidative decarboxylation of coproporphyrinogen III to protoporphyrinogen IX during bacterial heme biosynthesis. The recently solved crystal structure of Escherichia coli HemN revealed the presence of an unusually coordinated iron-sulfur cluster and two molecules of AdoMet. EPR spectroscopy of the reduced iron-sulfur center in anaerobically purified HemN in the absence of AdoMet has revealed a [4Fe-4S](1+) cluster in two slightly different conformations. Mössbauer spectroscopy of anaerobically purified HemN has identified a predominantly [4Fe-4S](2+) cluster in which only three iron atoms were coordinated by cysteine residues (isomer shift of delta = 0.43 (1) mm/s). The fourth non-cysteine-ligated iron exhibited a delta = 0.57 (3) mm/s, which shifted to a delta = 0.68 (3) mm/s upon addition of AdoMet. Substrate binding by HemN did not alter AdoMet coordination to the cluster. Multiple rounds of AdoMet cleavage with the formation of the reaction product methionine indicated AdoMet consumption during catalysis and identified AdoMet as a co-substrate for HemN catalysis. AdoMet cleavage was found to be dependent on the presence of the substrate coproporphyrinogen III. Two molecules of AdoMet were cleaved during one catalytic cycle for the formation of one molecule of protoporphyrinogen IX. Finally, the binding site for the unusual second, non iron-sulfur cluster coordinating AdoMet molecule (AdoMet2) was targeted using site-directed mutagenesis. All AdoMet2 binding site mutants still contained an iron-sulfur cluster and most still exhibited AdoMet cleavage, albeit reduced compared with the wild-type enzyme. However, all mutants lost their overall catalytic ability indicating a functional role for AdoMet2 in HemN catalysis. The reported significant correlation of structural and functional biophysical and biochemical data identifies HemN as a useful model system for the elucidation of general AdoMet radical enzyme features.

Bacterial Proteins↗
PubMed1999

Statistical evaluation of clusters derived by nonlinear mapping of EEG spatial patterns.

New methods were devised to improve the discrimination of EEG spatial amplitude patterns recorded from arrays of 64 electrodes placed on visual, auditory or somatic cortex. The 64 traces shared a spatially coherent, aperiodic carrier wave with a spatial pattern of amplitude modulation (AM). Previous observations on AM patterns from rabbits trained to discriminate conditioned stimuli with reinforcement (CS+) and without (CS-) had revealed epochs between the CS and the CR in which AM patterns on CS+ trials could be distinguished from AM patterns on CS- trials. The AM patterns were expressed by points in 64-space that formed clusters. Levels of CS-/CS+ pattern separation were quantified by a pair-wise Euclidean distance method with cross-validation. The present study documents use of the technique for nonlinear mapping (NLM) to project the 64-dimensional structure onto a plane while preserving the relative distances between all points. The goodness of classification by the Euclidean distance measure was the same or improved after projection. Whereas the Euclidean distance measure only gave pair-wise classifications, the planar displays showed the patterns for multiple clusters simultaneously. These NLM-based methods revealed previously unrecognized structures within distributions of AM patterns in sensory cortices in the time period between the CS and CR.

Animals↗
PubMed1998

[Multiple and unilateral angiofibromas of the face: forme fruste of Bourneville tuberous sclerosis].

BACKGROUND: Multiple facial angiofibromas are considered a characteristic and pathognomonic feature of tuberous sclerosis. In contrast, the observation of localized multiple angiofibromas limited to one side of the face is a uncommon. OBSERVATIONS: We cared for two patients with multiple clustered unilateral angiofibromas (although one patient also presented a few angiofibromas on the other side) without other features associated with the sclerosis tuberous complex. DISCUSSION: The possibility that these patients presented an independent disorder or a minor form of tuberous sclerosis is discussed.

Angiofibroma↗
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↗