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PubMedDate not supplied

[Inheritance of grain esterase genes in rye populations (Secale cereale L.)].

Genetic analysis of four tow straw rye populations has been carried out basing on the trait electrophoretic spectrum of grain esterase isozymes. Expression of seven independent Est genes has been shown. Three of them are clustered and their intrapopulation polymorphism exceeds two alleles. Comparative analysis of the frequences of different genes in parental populations and in F2 with literature data about localization of Est genes makes it possible to carry out chromosomal localization of the genes identified according to the fact of presence or absence of linking with the genes of rye self-incompatibility.

Algorithms↗

PubMed2002

Projective ART for clustering data sets in high dimensional spaces.

A new neural network architecture (PART) and the resulting algorithm are proposed to find projected clusters for data sets in high dimensional spaces. The architecture is based on the well known ART developed by Carpenter and Grossberg, and a major modification (selective output signaling) is provided in order to deal with the inherent sparsity in the full space of the data points from many data-mining applications. This selective output signaling mechanism allows the signal generated in a node in the input layer to be transmitted to a node in the clustering layer only when the signal is similar to the top-down weight between the two nodes and, hence, PART focuses on dimensions where information can be found. Illustrative examples are provided, simulations on high dimensional synthetic data and comparisons with Fuzzy ART module and PROCLUS are also reported.

Algorithms↗

PubMed1990

Form perception and visual acuity in a chimpanzee.

A 6.5-year-old female chimpanzee learned to distinguish perfectly every letter of the alphabet in a matching-to-sample task with 26 letters as choice alternatives. Confusion of letters during the initial training was used to scale them in a multidimensional similarity space and to associate them in hierarchical clusters. The results resembled those obtained from similarity judgements by humans. Using letters of various sizes, a visual acuity test revealed that the chimpanzee's acuity was about 1.5, comparable to that in normal humans. The chimpanzee also readily learned to use letters as names of individual humans and chimpanzees. A species-typical feature was identified in the perceptual processes associated with complex forms, such as those involved in individual recognition.

Algorithms↗

PubMed2006

AMIGOS: a method for the inspection of genomic organisation or structure and its application to characterise conserved gene arrangements.

In order to identify and to characterise gene clusters conserved in microbial genomes, the algorithm AMIGOS was developed. It is based on a categorisation of genes using a predefined set of gene functions (GFs). After the categorisation of all genes of a genome and based on their location on a replicon, distances between GFs were determined and stored in genome-specific matrices. These matrices were used to identify GF clusters like those strictly conserved in 13 archaeal, in 47 bacterial genomes and in the combination of the sets. Within the combined set of these 60 microbial genomes, there exist only two strictly conserved clusters harbouring two ribosomal genes each, namely those for L4, L23 and L22, L29. In order to characterise less strictly conserved GF clusters, content of genomes i.e. matrices were analysed pairwise. Resulting clusters were merged to (meta-) clusters if their content overlapped. A scoring system named cons(CL) was developed. It quantifies conservedness of cluster membership for individual GFs. For the genome of Escherichia coli it was shown that a grouping of cluster elements on cons(CL) values dissected the clusters into smaller sets. These sets were frequently overlapped by known transcriptional units (TUs). This finding justifies the usage of cons(CL) scores to predict TU membership of genes. In addition, cons(CL) values provide a sound basis for non-homologous gene annotation. Based on cons(CL) values, examples of conserved clusters containing annotated genes and single ones with unknown function are given.

Algorithms↗

PubMed1992

Selection of representative protein data sets.

The Protein Data Bank currently contains about 600 data sets of three-dimensional protein coordinates determined by X-ray crystallography or NMR. There is considerable redundancy in the data base, as many protein pairs are identical or very similar in sequence. However, statistical analyses of protein sequence-structure relations require nonredundant data. We have developed two algorithms to extract from the data base representative sets of protein chains with maximum coverage and minimum redundancy. The first algorithm focuses on optimizing a particular property of the selected proteins and works by successive selection of proteins from an ordered list and exclusion of all neighbors of each selected protein. The other algorithm aims at maximizing the size of the selected set and works by successive thinning out of clusters of similar proteins. Both algorithms are generally applicable to other data bases in which criteria of similarity can be defined and relate to problems in graph theory. The largest nonredundant set extracted from the current release of the Protein Data Bank has 155 protein chains. In this set, no two proteins have sequence similarity higher than a certain cutoff (30% identical residues for aligned subsequences longer than 80 residues), yet all structurally unique protein families are represented. Periodically updated lists of representative data sets are available by electronic mail from the file server "netserv@embl-heidelberg.de." The selection may be useful in statistical approaches to protein folding as well as in the analysis and documentation of the known spectrum of three-dimensional protein structures.

Algorithms↗

PubMed1991

Interstitial lung disease associated with connective tissue diseases. The use of statistical structure analysis in model development.

Interstitial lung disorders associated with the connective tissue diseases are thought to be quite common, but their precise analysis is fraught with difficulty because of the absence of a Gold Standard that, short of open lung biopsy, is not available. Analysis is hampered by the biologic variability in test results, large overlap between the normal and the disease population for individual tests, the confounding effect of smoking, and the complexities of viewing multidimensional data. In order to better define the pattern of the lung involvement, an entirely different approach has been adopted that is based on the use of graphic and clustering techniques to define the multivariate structure inherent in the data, then discriminant analysis to assign patients into distinct clusters. Using this approach it has been possible to group patients into four distinct clusters based on the result of respiratory function studies, gallium lung scan, bronchoalveolar lavage, and smoking status. These clusters are a normal smoking cluster and a normal nonsmoking cluster, a cluster of patients with active ILD, and a cluster with bronchiolitis. The validity of this method has been verified, and an algorithm has been developed that allows the assignment of any new patient entering the study into one of these clusters. This type of analysis offers a valuable new approach to the categorization of patients into distinct groups based on the results of multiple investigations.

Algorithms↗

PubMed1997

Data-dependent interval partition of naturally ordered individuals by complete cluster analysis in epidemiological and cardiac data processing.

Cluster analysis cannot usually examine every possible clustering. However, some external constraint may reduce the number of clusterings to a practical amount. In this paper, we consider naturally ordered individuals and calculate the number of interval partitions among them, if a minimal width for each interval is demanded. Two examples illustrate the application of the method. We first determine optimal information preserving age intervals due to the frequencies of some diseases. In the second example, we find a subinterval of the intraventricular blood pressure curve suitable to determine the time constant of heart relaxation.

Adolescent↗

PubMed2002

Global gene expression patterns during differentiation of F9 embryonal carcinoma cells into parietal endoderm.

Expression levels of over 8,900 murine genes were examined, using cDNA microarrays, during the differentiation of F9 cells into parietal endoderm following exposure to retinoic acid/dibutyryl cAMP. Gene induction and repression over the time course exhibited a biphasic pattern consistent with a transition from undifferentiated F9 cells to primitive endoderm and finally parietal endoderm. A 6-h induction with retinoic acid/cAMP/cycloheximide resulted in 109 candidate immediate response genes. During a 9-day time course 516 genes were selected as being significantly induced/repressed. Several of these genes had been previously identified as having altered expression patterns in F9 cells undergoing differentiation by retinoic acid/cAMP. Functional characterization of these genes demonstrated that the majority were transcription factors while others included surface antigens and genes involved in intracellular transport. Cluster analysis, utilizing both a hierarchical algorithm and self-organizing map, resulted in very similar gene clusters. Our studies revealed an extremely complex set of interacting signals that decide between cell death, differentiation, cell cycle withdrawal, and ultimately the traits associated with the terminal differentiated parietal endoderm cell type. The sets of genes identified here can now be modulated in a rational way to try to understand their role in differentiation.

Animals↗

PubMed2005

Long-term memory: a natural mechanism for the clustering of extreme events and anomalous residual times in climate records.

We study the statistics of the return intervals between extreme events above a certain threshold in long-term persistent records. We find that the long-term memory leads (i) to a stretched exponential distribution of the return intervals, (ii) to a pronounced clustering of extreme events, and (iii) to an anomalous behavior of the mean residual time to the next event that depends on the history and increases with the elapsed time in a counterintuitive way. We present an analytical scaling approach and demonstrate that all these features can be seen in long climate records. The phenomena should also occur in heartbeat records, Internet traffic, and stock market volatility and have to be taken into account for an efficient risk evaluation.

Algorithms↗

PubMed2004

CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology.

SUMMARY: Analysis of microarray data most often produces lists of genes with similar expression patterns, which are then subdivided into functional categories for biological interpretation. Such functional categorization is most commonly accomplished using Gene Ontology (GO) categories. Although there are several programs that identify and analyze functional categories for human, mouse and yeast genes, none of them accept Arabidopsis thaliana data. In order to address this need for A.thaliana community, we have developed a program that retrieves GO annotations for A.thaliana genes and performs functional category analysis for lists of genes selected by the user. AVAILABILITY: http://www.personal.psu.edu/nhs109/Clench

Abstracting and Indexing↗

PubMed1991

MCS/SEL/BAS program--an overlapping clustering method with examples from mating type interactions of ciliated protozoa.

The MCS/SEL/BAS program provides a method for group recognition, based on a criterion of homogeneity within the groups. The basic aim of this clustering method is not to 'force' data into a number of separate groups, as it allows the possibility that a given element in the data set can be assigned to more than one group. Moreover, a parsimonious path through the groups is sought by selecting groups on the basis of two suitably chosen, peak-ordered criteria. This selection continues until a covering of the data set is obtained (i.e., until each element in the data set is assigned to at least one group). Then relationships occurring among the set of selected groups are investigated by means of two coefficients, called overlapping and cohesion coefficient, respectively. The utility of this program has been demonstrated here in elaborating large sets of data derived from mating type interactions of ciliates, but it can be used also for analyzing data derived from a wide spectrum of compatibility phenomena exhibited by other living organisms. Algorithms of this program are written in BASIC and formulated in a conversational mode for processing on a Macintosh. A computer program (MCS/SEL/BAS) is available from G. Mancini upon request.

Algorithms↗

PubMed2004

A structure-odour relationship study using EVA descriptors and hierarchical clustering.

Structure-odour relationship analyses using hierarchical clustering were carried out on a diverse dataset of 47 molecules. These molecules were divided into seven odour categories: ambergris, bitter almond, camphoraceous, rose, jasmine, muguet, and musk. The alignment-independent descriptor EVA (EigenVAlue) was used as the molecular descriptor. The results were compared with those of another kind of descriptor, the UNITY 2D fingerprint. The dendrograms obtained with these descriptors were compared with the seven odour categories using the adjusted Rand index. The dendrograms produced by EVA consistently outperformed those from UNITY 2D in reproducing the experimental odour classifications of these 47 molecules.

Algorithms↗

PubMed2004

Classification of primary headaches.

Given the range of disorders that produce headache, a systematic approach to classification and diagnosis is an essential prelude to clinical management. For the last 15 years, the diagnostic criteria of the International Headache Society (IHS) have been the accepted standard. The second edition of The International Classification of Headache Disorders (January 2004) reflects our improved understanding of some disorders and the identification of new disorders. Neurologists who treat headache should become familiar with the revised criteria. Like its predecessor, the second edition of the IHS classification separates headache into primary and secondary disorders. The four categories of primary headaches include migraine, tension-type headache, cluster headache and other trigeminal autonomic cephalalgias, and other primary headaches. There are eight categories of secondary headache. Important changes in the second edition include a restructuring of these criteria for migraine, a new subclassification of tension-type headache, introduction of the concept of trigeminal autonomic cephalalgias, and addition of previously unclassified primary headaches. Several disorders were eliminated or reclassified. In this article, the authors present an overview of the revised IHS classification, highlighting the primary headache disorders and their diagnostic criteria. They conclude by presenting an approach to headache diagnosis based upon these criteria.

Adult↗

PubMed2006

bioNMF: a versatile tool for non-negative matrix factorization in biology.

BACKGROUND: In the Bioinformatics field, a great deal of interest has been given to Non-negative matrix factorization technique (NMF), due to its capability of providing new insights and relevant information about the complex latent relationships in experimental data sets. This method, and some of its variants, has been successfully applied to gene expression, sequence analysis, functional characterization of genes and text mining. Even if the interest on this technique by the bioinformatics community has been increased during the last few years, there are not many available simple standalone tools to specifically perform these types of data analysis in an integrated environment. RESULTS: In this work we propose a versatile and user-friendly tool that implements the NMF methodology in different analysis contexts to support some of the most important reported applications of this new methodology. This includes clustering and biclustering gene expression data, protein sequence analysis, text mining of biomedical literature and sample classification using gene expression. The tool, which is named bioNMF, also contains a user-friendly graphical interface to explore results in an interactive manner and facilitate in this way the exploratory data analysis process. CONCLUSION: bioNMF is a standalone versatile application which does not require any special installation or libraries. It can be used for most of the multiple applications proposed in the bioinformatics field or to support new research using this method. This tool is publicly available at http://www.dacya.ucm.es/apascual/bioNMF.

Algorithms↗

PubMed2004

Clustered-minority-pixel error diffusion.

We present a clustered-minority-pixel error-diffusion halftoning algorithm for which the quantizer threshold is modified on the basis of the past output and a dot activation map. Dot area, dot shape, and dot distribution are more controllable than with other clustered-dot halftone algorithms such as Levien's algorithm. This method also effectively reduces structured mazelike artifacts in midtones that occur in Levien's algorithm. The dot distribution is further improved by using different error-diffusion weights for different input gray levels.

Journal Article↗

PubMedDate not supplied

Uniform remeshing with an adaptive domain: a new scheme for view-dependent level-of-detail rendering of meshes.

We present a new algorithm for view-dependent level-of-detail rendering of meshes. Not only can it effectively resolve complex geometry features similar to edge collapse-based schemes, but it also produces meshes that modern graphics hardware can render efficiently. This is accomplished through a novel hybrid approach: For each frame, we view-dependently refine the progressive mesh (PM) representation of the original mesh and use the output as the base domain of uniform regular refinements. The algorithm exploits frame-to-frame coherence and only updates portions of the output mesh corresponding to modified domain triangles. The PM representation is built using a custom volume preservation-based error function. A simple k-d tree enhanced jump-and-walk scheme is used to quickly map from the dynamic base domain to the original mesh during regular refinements. In practice, the PM refinement provides a view-optimized base domain for later regular refinements. The regular refinements ensure almost-everywhere regularity of output meshes, allowing optimization for vertex cache coherence and caching of geometry data in high-performance graphics memory. Combined, they also have the effect of allowing our algorithm to operate on uniform clusters of triangles instead of individual ones, reducing CPU workload.

Algorithms↗

PubMed2006

Identifying units for conservation using molecular systematics: the cautionary tale of the Karner blue butterfly.

The federally endangered North American Karner blue butterfly (Lycaeides melissa samuelis) and the closely related Melissa blue butterfly (L. m. melissa) can be distinguished based on life history and morphology. Western populations of L. m. samuelis share mitochondrial haplotypes with L. m. melissa populations, while eastern populations of L. m. samuelis have divergent haplotypes. Here we test two hypotheses concerning the presence of L. m. melissa mitochondrial haplotypes in western L. m. samuelis populations: (i) mitochondrial introgression has occurred from L. m. melissa populations into western L. m. samuelis populations, or (ii) western populations of the nominal L. m. samuelis are more closely related to L. m. melissa than to eastern L. m. samuelis populations, yet are phenotypically similar to the latter. A Bayesian algorithm was used to cluster 190 L. melissa individuals based on 143 informative amplified fragment length polymorphism (AFLP) loci. This method clearly differentiated L. m. samuelis and L. m. melissa. Thus, genomic divergence was greater between western L. m. samuelis populations and L. m. melissa populations than it was between western and eastern populations of L. m. samuelis. This supports the hypothesis that the presence of L. m. melissa mitochondrial haplotypes in western L. m. samuelis populations is the result of mitochondrial introgression. These data provide valuable information for conservation and management plans for the endangered L. m. samuelis, and illustrate the risks of using data from a single locus for diagnosing significant units of biodiversity for conservation.

Algorithms↗

PubMed1999

Limited functional grouping of neurons in the motor cortex hand area during individuated finger movements: A cluster analysis.

Primary motor cortex (M1) hand area neurons show patterns of discharge across a set of individuated finger and wrist movements so diverse as to preclude classifying the neurons into functional groups on the basis of simple inspection. We therefore applied methods of cluster analysis to search M1 neuronal populations for groups of neurons with similar patterns of discharge across the set of movements. Populations from each of three monkeys showed a large group of neurons the discharge of which increased for many or all of the movements and a second small group the discharge of which decreased for many or all movements. Two to three other small groups of neurons that discharged more specifically for one or two movements also were found in each monkey, but these groups were less consistent than the groups with broad movement fields. The limited functional grouping of M1 hand area neurons suggests that M1 neurons act as a network of highly diverse elements in controlling individuated finger movements.

Algorithms↗