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.

Steiner trades that give rise to completely decomposable latin interchanges

In this paper we focus on the representation of Steiner trades of volume less than or equal to nine and identify those for which the associated partial latin square can be decomposed into six disjoint latin interchanges.

Modelling High-Dimensional Data by Mixtures of Factor Analyzers

We focus on mixtures of factor analyzers from the perspective of a method for model-based density estimation from high-dimensional data, and hence for the clustering of such data. This approach enables a normal mixture model to be fitted to a sample of n data points of dimension p, where p is large relative to n. The number of free parameters is controlled through the dimension of the latent factor space. By working in this reduced space, it allows a model for each component-covariance matrix with complexity lying between that of the isotropic and full covariance structure models. We shall illustrate the use of mixtures of factor analyzers in a practical example that considers the clustering of cell lines on the basis of gene expressions from microarray experiments. (C) 2002 Elsevier Science B.V. All rights reserved.

Pseudotrypanosoma elphinstonae sp n., a trichomonad symbiotic in Schedorhinotermes (Isoptera : Rhinotermitidae)

A new species of Pseudotrypanosoma, P. elphinstonae sp. n., is described which is symbiotic within the hindguts of the rhinotermitid termites Schedorhinotermes secundus and S. intermedius. P. elphinstonae possesses most of the features of the genus: 4 anterior flagella, prominent costa and recurrent flagellum forming an undulating membrane and simple bean-shaped parabasal body. The mastigont complex is of similar composition and arrangement to other trichomonads but the pelto-axostylar complex is greatly simplified being composed of a single layer of microtubules which do not over lap and cannot be distinguished into separate structures. The undulating membrane is much smaller than in related species; the costa is smaller and simpler and there are no microtubular bundles connecting it to the recurrent flagellum. Comparison of the ultrastructure of P. elphinstonae sp. n. with that of P. giganteum demonstrated that P. elphinstonae sp. n. in addition to being much smaller in size had a correspondingly simper ultrastructural organisation lacking several organelles which characterise the latter species.

The tree cut and merge algorithm for estimation of network reliability

This article presents Monte Carlo techniques for estimating network reliability. For highly reliable networks, techniques based on graph evolution models provide very good performance. However, they are known to have significant simulation cost. An existing hybrid scheme (based on partitioning the time space) is available to speed up the simulations; however, there are difficulties with optimizing the important parameter associated with this scheme. To overcome these difficulties, a new hybrid scheme (based on partitioning the edge set) is proposed in this article. The proposed scheme shows orders of magnitude improvement of performance over the existing techniques in certain classes of network. It also provides reliability bounds with little overhead.

Avan??os desiguais e inten????es indefinidas: a reforma do estado do M??xico e a estrat??gia de gerenciamento

Este paper defende duas id??ias. A primeira, ?? apresentar os diferentes processos da reforma do Estado mexicano, analisados sob as prioridades diversas no decorrer do tempo. As reformas econ??mica, pol??tica, social e administrativa tiveram prioridades e objetivos divergentes. A reforma econ??mica foi sistem??tica e congruente, a pol??tica foi defensiva e pouco abrangente, e a social foi problem??tica e confusa. A reforma administrativa foi, comparativamente, limitada. Uma proposta para desenvolver um sistema administrativo respons??vel pelo servi??o p??blico foi postergada nos ??ltimos 12 anos at?? que, em maio de 1997, finalmente a atual administra????o prop??s um programa de moderniza????o. A segunda id??ia ?? que, mesmo que a atual administra????o tenha a inten????o de desenvolver um novo sistema de accountability e um plano de carreira para o servi??o p??blico, parece plaus??vel que a tradicional pol??tica de controle, atrav??s da estrutura administrativa, possa ser prejudicada se essas propostas realmente reduzirem o poder discricion??rio dos altos cargos p??blicos e submeterem reservas p??blicas a um esquema de controle social mais aberto e formal. Logo, ?? poss??vel dizer que a alternativa escolhida pelos reformistas foi usar uma abordagem gerenciadora, onde a melhoria dos procedimentos e a implementa????o de algumas t??cnicas administrativas avan??adas substituem, pelo menos at?? agora, uma transforma????o mais profunda da estrutura administrativa. Uma estrat??gia de gerenciamento permite, pelo menos at?? o momento, a melhoria dos servi??os atrav??s do aumento da participa????o de servidores p??blicos, sem prejudicar a atual administra????o, como um instrumento para implementar diferentes agendas pol??ticas usando recursos p??blicos. Nosso argumento ?? que, como o programa de moderniza????o est?? sendo implantado, ?? importante estudar minuciosamente as possibilidades de se implementar a reforma do servi??o p??blico e melhorar a responsabilidade do sistema, dada a particular rela????o que existe entre a administra????o p??blica e o sistema pol??tico no M??xico.

Toxicidade de óleo de mamona a Helicoverpa zea e a Trichogramma pretiosum

O objetivo deste trabalho foi avaliar os efeitos do óleo de mamona sobre a broca-grande do tomateiro, Helicoverpa zea, e sobre o parasitoide de ovos Trichogramma pretiosum. Foi determinada a mortalidade larval da broca, que foi submetida ao óleo de mamona por ingestão e contato às concentrações 0,5, 1,0, 1,5, 2,0, 2,5 e 3,0% (v v-1). A ação do óleo de mamona sobre T. pretiosum foi determinada mediante testes de seletividade e suscetibilidade. As maiores mortalidades de larvas foram observadas no tratamento por contato com as menores concentrações (0,5 e 1,0%), enquanto com as concentrações intermediárias (1,5; 2,0 e 2,5%), não houve diferença entre as vias de aplicação. À maior concentração testada (3,0%), o tratamento por ingestão proporcionou mortalidade superior àquela obtida por contato. O número de ovos parasitados por T. pretiosum, no teste de seletividade, foi afetado negativamente pelo óleo de mamona, contudo, os demais parâmetros avaliados quanto à seletividade e à suscetibilidade não foram afetados. O óleo de mamona reduz a sobrevivência de larvas de H. zea tanto por ingestão quanto por contato. Além disso, não prejudica o desenvolvimento de T. pretiosum, desde que as pulverizações sejam realizadas após as liberações do parasitoide.

Soybean growth and yield under cover crops

The use of cover crops in no-tillage systems can provide better conditions for the development of soybean plants with positive effects on grain yield and growth analysis techniques allow researchers to characterize and understand the behavior of soybean plants under different straw covers. Thus, the aim of this study was to characterize, using growth analysis, yield components and agronomic performance of soybean under common bean, Brachiaria brizantha and pearl millet straws. The experiment was performed on a soil under cerrado in the municipality of Santo Antônio de Goiás, GO. The experiment was arranged in a randomized complete block design with three treatments (cover crops) and five replications. Soybean grain yield was lower in the B. brizantha straw treatment (3,708 kg ha-1) than both in the pearl millet (4.772 kg ha-1) and common bean straw treatments (5,200 kg ha-1). The soybean growth analysis in B. brizantha, pearl millet and common bean allowed characterizing the variation in the production of dry matter of leaves, stems, pods and total and leaf area index that provided different grain yields. The cover crop directly affects the soybean grain yield.

Zinc supplementation, production and quality of coffee beans

Besides its importance in the coffee tree nutrition, there is almost no information relating zinc nutrition and bean quality. This work evaluated the effect of zinc on the coffee yield and bean quality. The experiment was conducted with Coffea arabica L. in "Zona da Mata" region, Minas Gerais, Brazil. Twelve plots were established at random with 4 competitive plants each. Treatments included plants supplemented with zinc (eight plots) and control without zinc supplementation (four plots). Plants were subjected to two treatments: zinc supplementation and control. Yield, number of defective beans, beans attacked by berry borers, bean size, cup quality, beans zinc concentration, potassium leaching, electrical conductivity, color index, total tritable acidity, pH, chlorogenic acids contents and ferric-reducing antioxidant activity of beans were evaluated. Zinc positively affected quality of coffee beans, which presented lower percentage of medium and small beans, lower berry borer incidence, lower potassium leaching and electrical conductivity, higher contents of zinc and chlorogenic acids and higher antioxidant activity in comparison with control beans.

Selection of anthracnose resistant common beans using detached leaves in partially controlled environment

The objectives of this study were to evaluate the possibility of selecting anthracnose resistant common bean plants using detached primary leaves in partially controlled environment of a greenhouse and identify differences in the reaction of genotypes to anthracnose. The common bean cultivars Ouro Negro, OuroVermelho, ManteigãoFosco 11, Rudá, Rudá-R, VP8, BRSMG Madrepérola, Pérola, MeiaNoite and BRSMG Talismãwere characterizedfor resistance to the races 65, 81 and 453 of Colletotrichum lindemuthianum and the method of detached primary leaves was compared to the method with the traditional inoculation of plants at the phenological stage V2. The lines Rudá, Rudá-R and Pérola were inoculated with the races 65 and 453 of C. lindemuthianum, aiming to assess the rate of coincidence of anthracnose severity by both inoculation methods. In general, the two methods presented similar results for the reaction of the cultivars. The use of detached primary leaves of common bean plants in the partially controlled environment was feasible for selection of plants resistant to anthracnose and has the advantages of low-needed infrastructure and reduction of resources, space and time.

Phytomass production and nutrient accumulation by green manure species

Green manuring is recognized as a viable alternative to improve nutrient cycling in soils. The aim of this study was to evaluate the phytomass production and nutrient accumulation in shoots of the summer green manures jack bean [Canavalia ensiformis (L.) DC.], dwarf pigeon pea (Cajanus cajanvar var. Flavus DC.), dwarf mucuna [Mucuna deeringiana (Bort) Merr] and sunn hemp (Crotalaria juncea L.), under nitrogen fertilization and/or inoculation with N-fixing bacteria. A split plot design was arranged with the four Fabaceae species as main plots and nitrogen fertilization (with and without) and inoculation with diazotrophic bacteria (with and without) as the subplots, in a 2² factorial. The experiment was arranged as a randomized complete block design with four replications. In the conditions of this trial, the sunn hemp had the highest production of shoot phytomass (12.4 Mg ha-1) and nutrient accumulation, while the dwarf mucuna had the lowest production of shoot phytomass (3.9 Mg ha-1) and nutrient accumulation. The results showed no effect of nitrogen fertilization or inoculation with N-fixing bacteria on the production of shoot phytomass and nutrient accumulation, except for inoculation without nitrogen fertilization, resulting in greater P accumulation (p <0.05) in the sunn hemp and greater Zn and Mn accumulation in the dwarf mucuna. These findings indicate that N fertilization or inoculation with N2-fixing bacteria for Fabaceae are low efficiency practices in the edaphoclimatic conditions of this study.

Decomposition of ground biomass of secondary forest and yield of annual crops in no tillage

ABSTRACT The objective of this work was to evaluate the dynamics of decomposition process of chopped secondary forest system, previously enriched with legumes Inga velutina Willd. and Stryphnodendron pulcherrimum (Willd.) Hochr. and the contribution of this process to the nutrient input to the cultivation of corn and bean under no-tillage. The experimental design was a randomized block, split plot with four replications. The plots were two species (I. velutina and S. pulcherrimum) and the subplots were seven times of evaluation (0, 7, 28, 63, 189, 252, 294 days after experiment installation). There was no difference (p ≥ 0.05) between the secondary forest systems enriched and no interaction with times for biomass waste, decomposition constant and half-life time. The waste of S. pulcherrimum trees had higher (p < 0.05) C/N ratio than that I. velutina. However, this one was higher (p < 0.05) in lignin content. Nevertheless, the dynamics of residue decomposition was similar. The corn yield was higher (p < 0.05) in cultivation under I.velutina waste. Meanwhile, the beans planted after corn, shows similar (p > 0.05) yield in both areas, regardless of the waste origin.

Application of continuous wavelet transform to the analysis of the modulus of the fractional Fourier transform bands for resolving two component mixture

In this paper, the fractional Fourier transform (FrFT) is applied to the spectral bands of two component mixture containing oxfendazole and oxyclozanide to provide the multicomponent quantitative prediction of the related substances. With this aim in mind, the modulus of FrFT spectral bands are processed by the continuous Mexican Hat family of wavelets, being denoted by MEXH-CWT-MOFrFT. Four modulus sets are obtained for the parameter a of the FrFT going from 0.6 up to 0.9 in order to compare their effects upon the spectral and quantitative resolutions. Four linear regression plots for each substance were obtained by measuring the MEXH-CWT-MOFrFT amplitudes in the application of the MEXH family to the modulus of the FrFT. This new combined powerful tool is validated by analyzing the artificial samples of the related drugs, and it is applied to the quality control of the commercial veterinary samples.

Acompanhamento da ampliação do restaurante mexicano "La Siesta", em Algés

Relatório de Estágio para obtenção do grau de Mestre em Engenharia Civil na Área de Especialização de Edificações