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Results for “Clustering Algorithms”

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PubMed2004

Nocardia pigrifrangens sp. nov., a novel actinomycete isolated from a contaminated agar plate.

A polyphasic study was undertaken to establish the taxonomic position of an actinomycete strain isolated from a contaminated agar plate. The strain, designated 7031T, had morphological and chemotaxonomic properties typical of the genus Nocardia. An almost-complete 16S rRNA gene sequence determined for the strain was aligned with available sequences for nocardiae, and phylogenetic trees were inferred using three tree-generating algorithms. Strain 7031T clustered with the type strains of Nocardia carnea and Nocardia flavorosea, showing low 16S rRNA gene sequence similarities to these species (97.2 and 97.5 %, respectively). The strain was also distinguished from the closest species by a range of phenotypic properties. It is proposed that the strain be recognized as a novel species of Nocardia, Nocardia pigrifrangens sp. nov., the type strain of which is 7031T (= AS 4.1808T = JCM 11884T).

Bacterial Typing Techniques↗

PubMed1999

Calculation of ground states of four-dimensional +/-J Ising spin glasses.

Ground states of four-dimensional (d=4) Edwards-Anderson Ising spin glasses are calculated for sizes up to 7 x 7 x 7 x 7 using a combination of a genetic algorithm and cluster-exact approximation. The ground-state energy of the infinite system is extrapolated as e0(infinity)=-2.095(1). The ground-state stiffness (or domain wall) energy Delta is calculated. A delta approximately L(theta(S)) behavior with theta(S)=0.64(5) is found which confirms that the d=4 model has an equilibrium spin-glass-paramagnet transition for nonzero T(c).

Journal Article↗

PubMed2000

Three-dimensional ising model in the fixed-magnetization ensemble: A monte carlo study

We study the three-dimensional Ising model at the critical point in the fixed-magnetization ensemble, by means of the recently developed geometric cluster Monte Carlo algorithm. We define a magnetic-field-like quantity in terms of microscopic spin-up and spin-down probabilities in a given configuration of neighbors. In the thermodynamic limit, the relation between this field and the magnetization reduces to the canonical relation M(h). However, for finite systems, the relation is different. We establish a close connection between this relation and the probability distribution of the magnetization of a finite-size system in the canonical ensemble.

Journal Article↗

PubMed2001

Cluster Monte Carlo simulations of the nematic-isotropic transition.

We report the results of simulations of the three-dimensional Lebwohl-Lasher model of the nematic-isotropic transition using a single cluster Monte Carlo algorithm. The algorithm, first introduced by Kunz and Zumbach to study two-dimensional nematics, is a modification of the Wolff algorithm for spin systems, and greatly reduces critical slowing down. We calculate the free energy in the neighborhood of the transition for systems up to linear size 70. We find a double well structure with a barrier that grows with increasing system size. We thus obtain an upper estimate of the value of the transition temperature in the thermodynamic limit.

Journal Article↗

PubMed2005

Colloidal stabilization via nanoparticle halo formation.

We present a detailed numerical study of effective interactions between micrometer-sized silica spheres, induced by highly charged zirconia nanoparticles. It is demonstrated that the effective interactions are consistent with a recently discovered mechanism for colloidal stabilization. In accordance with the experimental observations, small nanoparticle concentrations induce an effective repulsion that counteracts the intrinsic van der Waals attraction between the colloids and thus stabilizes the suspension. At higher nanoparticle concentrations an attractive potential is recovered, resulting in reentrant gelation. Monte Carlo simulations of this highly size-asymmetric mixture are made possible by means of a geometric cluster Monte Carlo algorithm. A comparison is made to results obtained from the Ornstein-Zernike equations with the hypernetted-chain closure.

Journal Article↗

PubMed2002

Conformal invariance of the Ising model in three dimensions.

We investigate a critical Ising-like model in the curved geometry S2 x R1 obtained by a conformal mapping of the infinite 3D space R3. The incompatibility of regular lattices with this geometry is avoided by use of the anisotropic limit of the lattice Ising model, which renders one of the space coordinates continuous. We determine magnetic and energylike correlation lengths of this model by means of a cluster Monte Carlo algorithm. From these data, and the assumption of conformal invariance, we obtain the magnetic and temperature scaling dimensions as X(h) = 0.5178(12) and X(t) = 1.423(19), respectively. These numbers are in a good agreement with the existing results for the 3D Ising universality class.

Journal Article↗

PubMed2003

Complete identification of alkali sites in ion conducting lithium silicate glasses: a computer study of ion dynamics.

The available sites for ions in a typical disordered ionic conductor are determined. For this purpose we devised a straightforward algorithm which via cluster analysis identifies these sites from long time ionic trajectories below the glass transition. This is exemplified for a lithium silicate glass (Li2O)(x)(SiO2)((1-x)) for x=0.5 and x=0.1. We find for both concentrations that the number of sites is only slightly bigger than the number of ions. This result suggests a theoretical description of the dynamics in terms of mobile vacancies as most appropriate. Furthermore, identification of the ionic sites allows one to obtain detailed characteristics of the ionic motion, e.g., quantification of correlated forward-backward jumps.

Journal Article↗

PubMed2006

Simulating nanoscale dielectric response.

We introduce a constrained energy functional to describe dielectric response. We demonstrate that the local functional is a generalization of the long-ranged Marcus energy. Our reformulation is used to implement a cluster Monte Carlo algorithm for the simulation of dielectric media. The algorithm avoids solving the Poisson equation and remains efficient in the presence of spatial heterogeneity, nonlinearity, and scale dependent dielectric properties.

Journal Article↗

PubMed2006

Genotyping of measles virus in clinical specimens on the basis of oligonucleotide microarray hybridization patterns.

An oligonucleotide microarray hybridization method for identification of most known measles virus (MV) genotypes was developed. Like the conventional genotyping method, the microarray relied on detecting sequence differences in the 450-nucleotide region coding for the COOH-terminal 150 amino acids of the nucleoprotein (N). This region was amplified using PCR primers binding to all known MV genotypes. The microarray included 71 pairs of oligonucleotide probes (oligoprobes) immobilized on glass slides. Each pair consisted of a genotype-specific oligoprobe, which matched the sequence of only one target genotype, and a control oligoprobe, which contained mismatches at the nucleotide positions unique to this genotype. A pattern recognition algorithm based on cluster analysis of the ratios of hybridization signals from specific and control oligoprobes was used to identify the specific MV genotype. Following the initial validation, the method was used for rapid genotyping of two panels of coded samples. The results of this study showed good sensitivity (90.7%), specificity (100%), and genotype agreement (91.8%) for the new method compared to the results of genotyping conducted using phylogenetic analysis of viral sequences of the C terminus of the N gene. In addition, the microarray demonstrated the ability to identify potential new genotypes of MV based on the similarity of their hybridization patterns with those of known MV genotypes.

Genotype↗

PubMed2002

Increasing genetic diversity of Salmonella enterica serovar typhi isolates from papua new guinea over the period from 1992 to 1999.

Pulsed-field gel electrophoresis (PFGE) of XbaI-digested chromosomal DNA was performed on 133 strains of Salmonella enterica serovar Typhi obtained from Papua New Guinea, with the objective of assessing the temporal variation of these strains. Fifty-two strains that were isolated in 1992 and 1994 were of one phage type, D2, and only two predominant PFGE profiles, X1 and X2, were present. Another 81 strains isolated between 1997 and 1999 have shown divergence, with four new phage types, UVS I (n = 63), UVS (n = 5), VNS (n = 4), and D1 (n = 9), and more genetic variability as evidenced by the multiple and new PFGE XbaI profiles (21 profiles; Dice coefficient, F = 0.71 to 0.97). The two profiles X1 and X2 have remained the stable, dominant subtypes since 1992. Cluster analysis based on the unweighted pair group method using arithmetic averages algorithm identifies two main clusters (at 87% similarity), indicating that the divergence of the PFGE subtypes was probably derived from some genomic mutations of the X1 and X2 subtypes. The majority of isolates were from patients with mild and moderate typhoid fever and had various XbaI profiles. A single isolate from a patient with fatal typhoid fever had a unique X11 profile, while four of six isolates from patients with severe typhoid fever had the X1 pattern. In addition, 12 paired serovar Typhi isolates recovered from the blood and fecal swabs of individual patients exhibited similar PFGE patterns, while in another 11 individuals paired isolates exhibited different PFGE patterns. Three pairs of isolates recovered from three individuals had different phage types and PFGE patterns, indicating infection with multiple strains. The study reiterates the usefulness of PFGE in assessing the genetic diversity of S. enterica serovar Typhi for both long-term epidemiology and in vivo stability and instability within an individual patient.

Bacteriophage Typing↗

PubMed1990

Release of luteinizing hormone and growth hormone after recovery from maximal exercise.

Pulsatile properties of luteinizing hormone (LH) and growth hormone (GH) release were evaluated in 19 eumenorrheic untrained females [mean age 31.1 +/- 1.1 yr, height 165.2 +/- 1.4 cm, weight 64.8 +/- 2.1 kg, peak oxygen uptake (Vo2) 41.6 +/- 1.4 (SE) ml.kg-1.min-1] during the early follicular phase of the menstrual cycle (days 3-4 after the onset of menses). Each subject was studied during two consecutive menstrual cycles under each of two conditions in random order: 1) no formal exercise for 72 h (C) and 2) 12-24 h after two maximal exercise bouts (peak Vo2/lactate threshold treadmill evaluation and a 3,200-m time-trial run or a maximal Vo2 inclined treadmill test) performed on consecutive days (EX). Blood sampling was performed every 10 min for 12 h. LH and GH pulsatile parameters were identified and characterized by the Cluster pulse detection algorithm. No significant differences were noted in the number of peaks, peak amplitude, interpeak interval, peak increment, or 12-h integrated concentrations between C and EX for LH or GH. We conclude that maximal exercise protocols typically used for exercise evaluation do not have an effect on the pulsatile characteristics of LH or GH release in untrained women during the early follicular phase of the menstrual cycle if 12-24 h of recovery are allowed before evaluation of the pulsatile secretion of gonadotropins or GH.

Adult↗

PubMed1994

Growth hormone secretion in children with normal variants of short stature.

Pulsatile growth hormone (GH) secretion plays a central role in human growth during the prepubertal period of life. In order to investigate whether or not short stature in prepubertal children with normal variants of short stature (NVSS) may be explained, at least in part, by the presence of abnormalities in the pulsatile pattern of GH secretion, we have studied the spontaneous secretion of GH/24 h in 139 prepubertal children with short stature (< or = -2 SD) and normal growth velocity (> -1 SD) and in 37 prepubertal children with normal height and growth velocity. All of the subjects included in this study exhibited a body mass index (BMI) lower than 1 SD. The patients with short stature were divided into three groups according to their bone age and the existence of familial antecedents of short stature. These groups were: (1) familial short stature without bone age retardation (FSS-1); (2) constitutional, nonfamilial short stature, with bone age retardation suggesting further delay of puberty (possible constitutional delay of growth and puberty), and (3) familial short stature with bone age retardation (FSS-2). Spontaneous GH secretion was analyzed by using a computerized mathematical algorithm of pulsatility (Cluster). In addition, in all of the patients with short stature, the GH secretory response to three different pharmacological stimuli was evaluated, including: clonidine, growth hormone-releasing hormone (GHRH) and hypoglycemia after insulin administration. The mean values of GH/24 h exhibited a wide range of distribution (1.4-7.8ng/ml).(ABSTRACT TRUNCATED AT 250 WORDS)

Body Height↗

PubMed1979

Computer aided analysis of chromatin network and basophil color for differentiation of mononuclear peripheral blood cells.

Computer aided differentiation of plasmoblasts, Pfeiffer cells, immunoblasts, lymphocytes and centrocytes is achieved with the parameters of chromatin network arrangement and structure, and multispectral cytoplasm color. The digital methods involve: (a) segmenting the nuclear image into topographic sections and analyzing the optical density distribution from the chromatin in these sections; (b) determining the nuclear structure with a 7 x 7 median filter, gradient filter and contour following algorithms; and (c) clustering two-dimensional chromatic data from panoptically stained cellular components. The parameters reported here are a subset of those needed for the automated diagnosis of many hematologic diseases especially the leukemias.

Blood Cells↗

PubMed2004

ESTIMA, a tool for EST management in a multi-project environment.

BACKGROUND: Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs representative of putative genes. Usually, to be of value, ESTs and contigs must be associated with meaningful annotations, and made available to end-users. RESULTS: A web application, Expressed Sequence Tag Information Management and Annotation (ESTIMA), has been created to meet the EST annotation and data management requirements of multiple high-throughput EST sequencing projects. It is anchored on individual ESTs and organized around different properties of ESTs including chromatograms, base-calling quality scores, structure of assembled transcripts, and multiple sources of comparison to infer functional annotation, Gene Ontology associations, and cDNA library information. ESTIMA consists of a relational database schema and a set of interactive query interfaces. These are integrated with a suite of web-based tools that allow a user to query and retrieve information. Further, query results are interconnected among the various EST properties. ESTIMA has several unique features. Users may run their own EST processing pipeline, search against preferred reference genomes, and use any clustering and assembly algorithm. The ESTIMA database schema is very flexible and accepts output from any EST processing and assembly pipeline. ESTIMA has been used for the management of EST projects of many species, including honeybee (Apis mellifera), cattle (Bos taurus), songbird (Taeniopygia guttata), corn rootworm (Diabrotica vergifera), catfish (Ictalurus punctatus, Ictalurus furcatus), and apple (Malus x domestica). The entire resource may be downloaded and used as is, or readily adapted to fit the unique needs of other cDNA sequencing projects. CONCLUSIONS: The scripts used to create the ESTIMA interface are freely available to academic users in an archived format from http://titan.biotec.uiuc.edu/ESTIMA/. The entity-relationship (E-R) diagrams and the programs used to generate the Oracle database tables are also available. We have also provided detailed installation instructions and a tutorial at the same website. Presently the chromatograms, EST databases and their annotations have been made available for cattle and honeybee brain EST projects. Non-academic users need to contact the W.M. Keck Center for Functional and Comparative Genomics, University of Illinois at Urbana-Champaign, Urbana, IL, for licensing information.

Animals↗

PubMed2006

RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits.

BACKGROUND: Until today, analysis of 16S ribosomal RNA (rRNA) sequences has been the de-facto gold standard for the assessment of phylogenetic relationships among prokaryotes. However, the branching order of the individual phlya is not well-resolved in 16S rRNA-based trees. In search of an improvement, new phylogenetic methods have been developed alongside with the growing availability of complete genome sequences. Unfortunately, only a few genes in prokaryotic genomes qualify as universal phylogenetic markers and almost all of them have a lower information content than the 16S rRNA gene. Therefore, emphasis has been placed on methods that are based on multiple genes or even entire genomes. The concatenation of ribosomal protein sequences is one method which has been ascribed an improved resolution. Since there is neither a comprehensive database for ribosomal protein sequences nor a tool that assists in sequence retrieval and generation of respective input files for phylogenetic reconstruction programs, RibAlign has been developed to fill this gap. RESULTS: RibAlign serves two purposes: First, it provides a fast and scalable database that has been specifically adapted to eubacterial ribosomal protein sequences and second, it provides sophisticated import and export capabilities. This includes semi-automatic extraction of ribosomal protein sequences from whole-genome GenBank and FASTA files as well as exporting aligned, concatenated and filtered sequence files that can directly be used in conjunction with the PHYLIP and MrBayes phylogenetic reconstruction programs. CONCLUSION: Up to now, phylogeny based on concatenated ribosomal protein sequences is hampered by the limited set of sequenced genomes and high computational requirements. However, hundreds of full and draft genome sequencing projects are on the way, and advances in cluster-computing and algorithms make phylogenetic reconstructions feasible even with large alignments of concatenated marker genes. RibAlign is a first step in this direction and may be particularly interesting to scientists involved in whole genome sequencing of representatives of new or sparsely studied eubacterial phyla. RibAlign is available at http://www.megx.net/ribalign.

Algorithms↗

PubMed2004

Overview of commonly used bioinformatics methods and their applications.

Bioinformatics, in its broad sense, involves application of computer processes to solve biological problems. A wide range of computational tools are needed to effectively and efficiently process large amounts of data being generated as a result of recent technological innovations in biology and medicine. A number of computational tools have been developed or adapted to deal with the experimental riches of complex and multivariate data and transition from data collection to information or knowledge. These include a wide variety of clustering and classification algorithms, including self-organized maps (SOM), artificial neural networks (ANN), support vector machines (SVM), fuzzy logic, and even hyphenated techniques as neuro-fuzzy networks. These bioinformatics tools are being evaluated and applied in various medical areas including early detection, risk assessment, classification, and prognosis of cancer. The goal of these efforts is to develop and identify bioinformatics methods with optimal sensitivity, specificity, and predictive capabilities.

Computational Biology↗

PubMed1991

Small-cell carcinoma of the lung: derivation of a prognostic staging system.

Retrospective data on 22 pretreatment attributes were evaluated in 614 patients with small-cell carcinoma of the lung (SCCL). The series included 284 patients with limited disease (LD) and 328 patients with extensive disease (ED) managed between 1974 and 1986. Prognostic factors were evaluated by univariate analysis and by the Cox multivariate regression model. Recursive partition and amalgamation algorithm (RECPAM), two clustering methods well suited for obtaining strata and adapted for censoring survival data, were developed and used in the formulation of a new prognostic staging system. In univariate analysis, prognosis was significantly influenced by extent of disease (DE), the number of metastatic sites, and the detection of mediastinal spread in LD. Poor performance status (PS), male sex, and advanced age were negatively correlated with survival, as were increased serum levels of alkaline phosphates (AP), lactate dehydrogenase (LDH), carcinoembryonic antigen (CEA), total WBC count (WBCC), and low platelet count and low serum sodium. The Cox model identified plasma LDH and mediastinal spread as the only significant factors in LD; the influence of PS, number of metastatic sites, bone metastasis, brain metastasis, and platelet count were identified as significant in ED. The RECPAM model identified four distinct risk groups defined in a classification tree by the following eight attributes: DE, PS, serum AP, serum LDH, mediastinal spread, sex, WBCC, and liver metastasis. The four groups were distinguished by median survival times of 59, 49, 35, and 24 weeks, respectively (P = .0001). Interactions among prognostic factors are emphasized in the RECPAM classification model as evidenced by reassignment of patients across conventional staging barriers into alternate prognostic groups. The advantages of using RECPAM over the more conventional Cox regression techniques for a new staging system are discussed.

Adult↗

PubMed1993

Spontaneous gonadotropin and testosterone concentration profiles in prepubertal and pubertal boys: temporal relationship between luteinizing hormone and testosterone.

To investigate the detailed pattern of change in circulating gonadotropin and testosterone concentrations around the onset of puberty and to determine the temporal relationship between the gonadotropin and testosterone secretion, plasma gonadotropin and testosterone were measured at 20-min intervals for 24 h in 21 normal short boys. The obtained plasma hormone concentrations were analyzed by Cluster pulse detection algorithm, cosinor analysis, and cross-correlation analysis. The 21 subjects were divided into the prepubertal (n = 16) and early pubertal (n = 5) groups. All subjects showed nocturnal LH and FSH pulses and had significant circadian LH and FSH rhythms. Except for six boys of prepubertal group, all subjects showed nocturnal testosterone pulses and had significant circadian testosterone rhythms. The acrophase (clocktime of maximal value) of circadian testosterone rhythm was 0308-0428 h. Cross-correlation analysis demonstrated significant positive cross-correlations between LH and testosterone that were maximum at a testosterone lag of 60-120 min. Further, to eliminate intrinsic autocorrelations within the LH and testosterone time series, we filtered the data before subjecting them to the cross-correlation analysis. As a result, significant positive cross-correlations were found at a testosterone lag of 40 min in 10 peripubertal boys. We conclude that testosterone concentration profiles are pulsatile and show marked circadian rhythm well before the onset of puberty. LH and testosterone time series are significantly coupled when testosterone lags LH by about 40 min. This time lag might correspond to the time for synthesizing and secreting testosterone in Leydig cells after binding of LH to the Leydig cell receptors.

Adolescent↗