A mixture model-based approach to the clustering of microarray expression data

Motivation: This paper introduces the software EMMIX-GENE that has been developed for the specific purpose of a model-based approach to the clustering of microarray expression data, in particular, of tissue samples on a very large number of genes. The latter is a nonstandard problem in parametric cluster analysis because the dimension of the feature space (the number of genes) is typically much greater than the number of tissues. A feasible approach is provided by first selecting a subset of the genes relevant for the clustering of the tissue samples by fitting mixtures of t distributions to rank the genes in order of increasing size of the likelihood ratio statistic for the test of one versus two components in the mixture model. The imposition of a threshold on the likelihood ratio statistic used in conjunction with a threshold on the size of a cluster allows the selection of a relevant set of genes. However, even this reduced set of genes will usually be too large for a normal mixture model to be fitted directly to the tissues, and so the use of mixtures of factor analyzers is exploited to reduce effectively the dimension of the feature space of genes. Results: The usefulness of the EMMIX-GENE approach for the clustering of tissue samples is demonstrated on two well-known data sets on colon and leukaemia tissues. For both data sets, relevant subsets of the genes are able to be selected that reveal interesting clusterings of the tissues that are either consistent with the external classification of the tissues or with background and biological knowledge of these sets.

A simulated annealing algorithm for finding consensus sequences

Motivation: A consensus sequence for a family of related sequences is, as the name suggests, a sequence that captures the features common to most members of the family. Consensus sequences are important in various DNA sequencing applications and are a convenient way to characterize a family of molecules. Results: This paper describes a new algorithm for finding a consensus sequence, using the popular optimization method known as simulated annealing. Unlike the conventional approach of finding a consensus sequence by first forming a multiple sequence alignment, this algorithm searches for a sequence that minimises the sum of pairwise distances to each of the input sequences. The resulting consensus sequence can then be used to induce a multiple sequence alignment. The time required by the algorithm scales linearly with the number of input sequences and quadratically with the length of the consensus sequence. We present results demonstrating the high quality of the consensus sequences and alignments produced by the new algorithm. For comparison, we also present similar results obtained using ClustalW. The new algorithm outperforms ClustalW in many cases.

Geographical variation in the penetrance of CDKN2A mutations for melanoma

Background: Germline mutations in the CDKN2A gene, which encodes two proteins (p16INK4A and p14ARF), are the most common cause of inherited susceptibility to melanoma. We examined the penetrance of such mutations using data from eight groups from Europe, Australia and the United States that are part of The Melanoma Genetics Consortium Methods: We analyzed 80 families with documented CDKN2A mutations and multiple cases of cutaneous melanoma. We modeled penetrance for melanoma using a logistic regression model incorporating survival analysis. Hypothesis testing was based on likelihood ratio tests. Covariates included gender, alterations in p14APF protein, and population melanoma incidence rates. All statistical tests were two-sided. Results: The 80 analyzed families contained 402 melanoma patients, 320 of whom were tested for mutations and 291 were mutation carriers. We also tested 713 unaffected family members for mutations and 194 were carriers. Overall, CDKN2A mutation penetrance was estimated to be 0.30 (95% confidence interval (CI) = 0.12 to 0.62) by age 50 years and 0.67 (95% CI = 0.31 to 0.96) by age 80 years. Penetrance was not statistically significantly modified by gender or by whether the CDKN2A mutation altered p14ARF protein. However, there was a statistically significant effect of residing in a location with a high population incidence rate of melanoma (P = .003). By age 50 years CDKN2A mutation penetrance reached 0.13 in Europe, 0.50 in the United States, and 0.32 in Australia; by age 80 years it was 0.58 in Europe, 0.76 in the United States, and 0.91 in Australia. Conclusions: This study, which gives the most informed estimates of CDKN2A mutation penetrance available, indicates that the penetrance varies with melanoma population incidence rates. Thus, the same factors that affect population incidence of melanoma may also mediate CDKN2A penetrance.

Youth unemployment outflow rates and labor market programs: Australian evidence

A matching function methodology is used to investigate the macroeconomic effects of labor market program (LMP) commencements on youth unemployment outflows in Australia using unpublished data that classify commencements and outflows by duration of unemployment. The results indicate that LMPs have had significant effects on outflows from short-term unemployment. There is a net positive effect from LMP commencements on short-term unemployed female outflow rates. However; females experienced negative spillover effects from male LMP commencements. These spillover effects appear to be associated with wage subsidy programs and suggest the net impact Of such programs may have been overstated in previous studies.

Explicit evidence-based prescribing criteria - an important step in achieving quality therapeutics in nursing homes

Reaction between 5-(4-amino-2-thiabutyl)-5-methyl-3,7-dithianonane-1, 9-diamine (N3S3) and 5- methyl-2,2-bipyridine-5-carbaldehyde and subsequent reduction of the resulting imine with sodium borohydride results in a potentially ditopic ligand (L). Treatment of L with one equivalent of an iron( II) salt led to the monoprotonated complex [Fe(HL)](3+), isolated as the hexafluorophosphate salt. The presence of characteristic bands for the tris( bipyridyl) iron( II) chromophore in the UV/vis spectrum indicated that the iron( II) atom is coordinated octahedrally by the three bipyridyl (bipy) groups. The [Fe( bipy) 3] moiety encloses a cavity composed of the N3S3 portion of the ditopic ligand. The mononuclear and monomeric nature of the complex [Fe(HL)](3+) has been established also by accurate mass analysis. [Fe(HL)](3+) displays reduced stability to base compared with the complex [Fe(bipy)(3)](2+). In aqueous solution [Fe(HL)](3+) exhibits irreversible electrochemical behaviour with an oxidation wave ca. 60 mV to more positive potential than [Fe(bipy)(3)](2+). Investigations of the interaction of [Fe(L)](2+) with copper( II), iron( II), and mercury( II) using mass spectroscopic and potentiometric methods suggested that where complexation occurred, fewer than six of the N3S3 cavity donors were involved. The high affinity of the complex [Fe(L)](2+) for protons is one reason suggested to contribute to the reluctance to coordinate a second metal ion.

Petrology and geochemistry of the Bandas del Sur Formation, Las Canadas Edifice, Tenerife (Canary Islands)

The Bandas del Sur Formation preserves a Quaternary extra-caldera record of central phonolitic explosive volcanism of the Las Canadas volcano at Tenerife. Volcanic rocks are bimodal in composition, being predominantly phonolitic pyroclastic deposits, several eruptions of which resulted in summit caldera collapse, alkali basaltic lavas erupted from many fissures around the flanks. For the pyroclastic deposits, there is a broad range of pumice glass compositions from phonotephrite to phonolite. The phonolite pyroclastic deposits are also characterized by a diverse, 7-8-phase phenocryst assemblage (alkali feldspar + biotite + sodian diopside + titanomagnetite + ilmenite + nosean-hauyne + titanite + apatite) with alkali feldspar dominant, in contrast to interbedded phonolite lavas that typically have lower phenocryst contents and lack hydrous phases. Petrological and geochemical data are consistent with fractional crystallization (involving the observed phenocryst assemblages) as the dominant process in the development of phonolite magmas. New stratigraphically constrained data indicate that petrological and geochemical differences exist between pyroclastic deposits of the last two explosive cycles of phonolitic volcanism. Cycle 2 (0.85-0.57 Ma) pyroclastic fall deposits commonly show a cryptic compositional zonation indicating that several eruptions tapped chemically, and probably thermally stratified magma systems. Evidence for magma mixing is most widespread in the pyroclastic deposits of Cycle 3 (0.37-0.17 Ma), which includes the presence of reversely and normally zoned phenocrysts, quenched mafic glass blebs in pumice, banded pumice, and bimodal to polymodal phenocryst compositional populations. Syn-eruptive mixing events involved mostly phonolite and tephriphonolite magmas, whereas a pre-eruptive mixing event involving basaltic magma is recorded in several banded pumice-bearing ignimbrites of Cycle 3. The periodic addition and mixing of basaltic magma ultimately may have triggered several eruptions. Recharge and underplating by basaltic magma is interpreted to have elevated sulphur contents (occurring as an exsolved gas phase) in the capping phonolitic magma reservoir. This promoted nosean-hauyne crystallization over nepheline, elevated SO3 contents in apatite, and possibly resulted in large, climatologically important SO2 emissions.

Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human

By spliced alignment of human DNA and transcript sequence data we constructed a data set of transcript-confirmed exons and introns from 2793 genes, 796 of which (28%) were seen to have multiple isoforms. We find that over one-third of human exons can translate in more than one frame, and that this is highly correlated with G+C content. Introns containing adenosine at donor site position +3 (A3), rather than guanosine (G3), are more common in low G+C regions, while the converse is true in high G+C regions. These two classes of introns are shown to have distinct lengths, consensus sequences and correlations among splice signals, leading to the hypothesis that A3 donor sites are associated with exon definition, and G3 donor sites with intron definition. Minor classes of introns, including GC-AG, U12-type GT-AG, weak, and putative AG-dependant introns are identified and characterized. Cassette exons are more prevalent in low G+C regions, while exon isoforms are more prevalent in high G+C regions. Cassette exon events outnumber other alternative events, while exon isoform events involve truncation twice as often as extension, and occur at acceptor sites twice as often as at donor sites. Alternative splicing is usually associated with weak splice signals, and in a majority of cases, preserves the coding frame. The reported characteristics of constitutive and alternative splice signals, and the hypotheses offered regarding alternative splicing and genome organization, have important implications for experimental research into RNA processing. The 'AltExtron' data sets are available at http://www.bit.uq.edu.au/altExtron/ and http://www.ebi.ac.uk/similar tothanaraj/altExtron/.

Refinements in stress echocardiographic techniques improve inter-institutional agreement in interpretation of dobutamine stress echocardiograms

Aims To determine the degree of inter-institutional agreement in the assessment of dobutamine stress echocardiograms using modern stress echo cardiographic technology in combination with standardized data acquisition and assessment criteria. Method and Results Among six experienced institutions, 150 dobutamine stress echocardiograms (dobutamine up to 40 mug.kg(-1) min(-1) and atropine up to I mg) were performed on patients with suspected coronary artery disease using fundamental and harmonic imaging following a consistent digital acquisition protocol. Each dobutamine stress echocardiogram was assessed at every institution regarding endocardial visibility and left ventricular wall motion without knowledge of any other data using standardized reading criteria. No patients were excluded due to poor image quality or inadequate stress level. Coronary angiography was performed within 4 weeks. Coronary angiography demonstrated significant coronary artery disease (less than or equal to50% diameter stenosis) in 87 patients. Using harmonic imaging an average of 5.2+/-0.9 institutions agreed on dobutamine stress echocardiogram results as being normal or abnormal (mean kappa 0.55; 95% CI 0.50-0.60). Agreement was higher in patients with no (equal assessment of dobutamine stress echocardiogram results by 5.5 +/- 0.8 institutions) or three-vessel coronary artery disease (5.4 +/- 0.8 institutions) and lower in one- or two- vessel disease (5.0 +/- 0.9 and 5.2 +/- 1.0 institutions, respectively-, P=0.041). Disagreement on test results was greater in only minor wall motion abnormalities. Agreement on dobutamine stress echocardiogram results was lower using fundamental imaging (mean kappa 0.49; 95% CI 0.44-0.54; P

Urbanization, population transition, and growth

This paper analyzes a dual economy consisting of urban market areas and less developed rural areas with or without local markets. Urban areas have better opportunities for earnings and education than rural areas. Rural families choose whether to move to urban areas at costs that differ from location to location. As per capita output grows relative to the moving cost, urbanization proceeds, leading to lower fertility, more investments in human and physical capital per child relative to output per worker, and faster economic growth. These impacts are stronger if rural areas have no access to markets.

A new preventive maintenance strategy for items sold under warranty

When products are sold under warranty, the manufacturer incurs additional costs for warranty servicing. Preventive maintenance actions can be used to reduce this cost and these are worthwhile only if the extra cost incurred is less than the reduction achieved. In this paper we propose a new preventive maintenance policy where the parameters are selected optimally to minimize the total warranty servicing cost.