Model-based clustering in gene expression microarrays: An application to breast cancer data

In microarray studies, the application of clustering techniques is often used to derive meaningful insights into the data. In the past, hierarchical methods have been the primary clustering tool employed to perform this task. The hierarchical algorithms have been mainly applied heuristically to these cluster analysis problems. Further, a major limitation of these methods is their inability to determine the number of clusters. Thus there is a need for a model-based approach to these. clustering problems. To this end, McLachlan et al. [7] developed a mixture model-based algorithm (EMMIX-GENE) for the clustering of tissue samples. To further investigate the EMMIX-GENE procedure as a model-based -approach, we present a case study involving the application of EMMIX-GENE to the breast cancer data as studied recently in van 't Veer et al. [10]. Our analysis considers the problem of clustering the tissue samples on the basis of the genes which is a non-standard problem because the number of genes greatly exceed the number of tissue samples. We demonstrate how EMMIX-GENE can be useful in reducing the initial set of genes down to a more computationally manageable size. The results from this analysis also emphasise the difficulty associated with the task of separating two tissue groups on the basis of a particular subset of genes. These results also shed light on why supervised methods have such a high misallocation error rate for the breast cancer data.

Visual Biology of Hawaiian Coral Reef Fishes. I. Ocular Transmission and Visual Pigments

The visual biology of Hawaiian reef fishes was explored by examining their eyes for spectral sensitivity of their visual pigments and for transmission of light through the ocular media to the retina. The spectral absorption curves for the visual pigments of 38 species of Hawaiian fish were recorded using microspectrophotometry. The peak absorption wavelength (lambda(max)) of the rods varied from 477-502 nm and the lambda(max) of individual species conformed closely to values for the same species previously reported using a whole retina extraction procedure. The visual pigments of single cone photoreceptors were categorized, dependent on their lambda(max)-values, as ultraviolet (347-376 nm), violet (398-431 nm) or blue (439-498 nm) sensitive cones. Eight species possessed ultraviolet-sensitive cones and 14 species violet-sensitive cones. Thus, 47% of the species examined displayed photosensitivity to the short-wavelength region of the spectrum. Both identical and nonidentical paired and double cones were found with blue sensitivity or green absorption peaks (> 500 nm). Spectrophotometry of the lens, cornea, and humors for 195 species from 49 families found that the spectral composition of the light transmitted to the retina was most often limited by the lens (73% of species examined). Except for two unusual species with humor-limited eyes, Acanthocybium solandri (Scombridae) and the priacanthid fish, Heteropriacanthus cruentatus, the remainder had corneal-limited eyes. The wavelength at which 50% of the light was blocked (T50) was classified according to a system modified from Douglas and McGuigan (1989) as Type I, T50 < = 355 nm, (32 species); Type IIa, 355 < T50 < = 380 nm (30 species); Type IIb, 380 < T50 405 nm (84 species). Possession of UV-transmitting ocular media follows both taxonomic and functional lines and, if the ecology of the species is considered, is correlated with the short-wavelength visual pigments found in the species. Three types of short-wavelength vision in fishes are hypothesized: UV-sensitive, UV-specialized, and violet-specialized. UV-sensitive eyes lack UV blockers (Type I and IIa) and can sense UV light with the secondary absorption peak or beta peak of their longer wavelength visual pigments but do not possess specialized UV receptor cells and, therefore, probably lack UV hue discrimination. UV-specialized eyes allow transmission of UV light to the retina (Type I and IIa) and also possess UV-sensitive cone receptors with peak absorption between 300 and 400 nm. Given the appropriate perceptual mechanisms, these species could possess true UV-color vision and hue discrimination. Violet-specialized eyes extend into Type IIb eyes and possess violet-sensitive cone cells. UV-sensitive eyes are found throughout the fishes from at least two species of sharks to modern bony fishes. Eyes with specialized short-wavelength sensitivity are common in tropical reef fishes and must be taken into consideration when performing research involving the visual perception systems of these fishes. Because most glass and plastics are UV-opaque, great care must be taken to ensure that aquarium dividers, specimen holding containers, etc., are UV-transparent or at least to report the types of materials in use.

Media Convergence's Third Wave Content Streaming

Movies, pieces of music, books, or newspapers can all be expressed in the same binary code. Discrete forms of analogue media are just different dialects of the language of computerese. Content is becoming a very liquid asset. To take Marshall McLuhan's famed dictum a step further: The message is now independent of the medium

Rates of electronic energy transfer in conformationally flexible bichromophoric macrocyclic complexes: a combined experimental and molecular modeling study

Electronic energy transfer (EET) rate constants between a naphthalene donor and anthracene acceptor in [ZnL4a](ClO4)(2) and [ZnL4b](ClO4)(2) were determined by time-resolved fluorescence where L-4a and L-4b are the trans and cis isomers of 6-((anthracen-9-yl-methyl)amino)-6,13-dimethyl-13-((naphthalen-1-yl-methyl)amino)-1,4,8,11-tetraazacyclotetradecane, respectively. These isomers differ in the relative disposition of the appended chromophores with respect to the macrocyclic plane. The trans isomer has an energy transfer rate constant (k(EET)) of 8.7 x 10(8) s(-1), whereas that of the cis isomer is significantly faster (2.3 x 10(9) s(-1)). Molecular modeling was used to determine the likely distribution of conformations in CH3CN solution for these complexes in an attempt to identify any distance or orientation dependency that may account for the differing rate constants observed. The calculated conformational distributions together with analysis by H-1 NMR for the [ZnL4a](2+) trans complex in the common trans-III N-based isomer gave a calculated Forster rate constant close to that observed experimentally. For the [ZnL4b](2+) cis complex, the experimentally determined rate constant may be attributed to a combination of trans-Ill and trans-I N-based isomeric forms of the complex in solution.

Contribui????es do governo eletr??nico para a reforma administrativa e a governan??a no Brasil

O artigo investiga as contribui????es da pol??tica de governo eletr??nico para a reforma administrativa e a governan??a no Brasil. A pesquisa baseou-se na opini??o de informantes-chave dos quatro setores que atuam no e-gov: setor p??blico, iniciativa privada, terceiro setor e academia. Concluiu-se que as tecnologias de informa????o e comunica????o (TIC) podem ser a principal ferramenta para as iniciativas de moderniza????o do Estado, sendo ressalvado que o e-governo n??o pode ser visto como panac??ia para as reformas: o uso de tecnologias deveria caminhar em paralelo com outras medidas governamentais, nos campos pol??tico e econ??mico, por exemplo. Embora tenha sido reconhecido o potencial das TIC, o governo eletr??nico ainda n??o se encontra inserido com a ??nfase necess??ria na agenda governamental brasileira, de modo a contribuir decisivamente para a reforma administrativa e a governan??a.

A reorganiza????o das retaguardas administrativas de governo para a melhoria dos servi??os p??blicos eletr??nicos

Este texto constitui parte do primeiro volume do relat??rio Reorganisation of government backoffices for better electronic public services European good practices (back-office reorganisation), apresentado ?? Comiss??o Europ??ia em janeiro de 2004. O estudo foi patrocinado pelo Directorate General for Information Society and Media (Diret??rio Geral para a Sociedade da Informa????o e M??dia) da Comiss??o Europ??ia.

Relações de trabalho em uma universidade : atividade dos servidores técnico-administrativos da Universidade Federal do Espírito Santo

Trata-se esta de uma pesquisa de intervenção realizada com servidores técnico-administrativos, da Universidade Federal do Espírito Santo, ocupantes do cargo de assistente em administração, cujo objetivo principal foi analisar o trabalho sob o ponto de vista da atividade. A metodologia utilizada se baseou no referencial teórico-metodológico da Clínica da atividade, proposta por Yves Clot e seus colaboradores. Nesse percurso, a oficina de fotos foi utilizada como um procedimento de análise da atividade. Para esse estudo foram também utilizados, como referência de pesquisa, autores que postulam esse mesmo enfoque teórico metodológico. Articulando-se a estes, foram alçados estudos de pesquisadores brasileiros que trabalham com a temática nos campos da psicologia, da saúde, da educação, das clínicas do trabalho, dentre outros. O grupo associado foi composto por 10 funcionários de diferentes setores da Universidade, entre os quais, três se dispuseram a fotografar cenas do cotidiano do trabalho. Tais fotos foram escolhidas, confrontadas e analisadas pelo grupo de trabalhadores. Os trabalhadores ao se confrontarem com as situações de trabalho fotografadas viabilizaram um debate profícuo, conduzindo o grupo a pensar criticamente as atividades e os processos de trabalho que desenvolvem. A pesquisa indica que os trabalhadores procuram se reinventar e elaborar maneiras outras para enfrentar situações de trabalho que os desafiam, buscando modos diversos de atuar, o que se faz a partir da ampliação do poder de agir.