Study of cerebral gene expression densities using Voronoi analysis

As the available public cerebral gene expression image data increasingly grows, the demand for automated methods to analyze such large amount of data also increases. An important study that can be carried out on these data is related to the spatial relationship between gene expressions. Similar spatial density distribution of expression between genes may indicate they are functionally correlated, thus the identification of these similarities is useful in suggesting directions of investigation to discover gene interactions and their correlated functions. In this paper, we describe the use of a high-throughput methodology based on Voronoi diagrams to automatically analyze and search for possible local spatial density relationships between gene expression images. We tested this method using mouse brain section images from the Allen Mouse Brain Atlas public database. This methodology provided measurements able to characterize the similarity of the density distribution between gene expressions and allowed the visualization of the results through networks and Principal Component Analysis (PCA). These visualizations are useful to analyze the similarity level between gene expression patterns, as well as to compare connection patterns between region networks. Some genes were found to have the same type of function and to be near each other in the PCA visualizations. These results suggest cerebral density correlations between gene expressions that could be further explored. (C) 2011 Elsevier B.V. All rights reserved.

Uma arqueologia de diagramas cibernéticos

This paper investigates the use of explicit structures of information in architectural design. Particularly, it approaches the use of diagrams related to cybernetics and information theory in experimental practices in the 1960’s and 1970’s. It analyses the diagram of cybernetic control proposed by the cybernetician Gordon Pask for the Fun Palace, the diagrams produced by the utopian architect Yona Friedman in the conceptual description of the Flatwriter program and Christopher Alexander’s diagrams and his theories of Synthesis of Form and Pattern Language. Finally it establishes a brief parallel between current domestication and use of dataflow programming with the cybernetic diagrams, highlighting differences in their complexity approach.

Identificação de ondas de Rossby a partir de diagramas de Hovmoller da concentração de clorofila entre as latitudes de 25o S e 45o S do Oceano Atlântico

Ondas de Rossby são ondas planetárias oceânicas de ocorrência quase global com comprimentos de onda da ordem de centenas a milhares de quilômetros, períodos da ordem de meses a anos e amplitudes superficiais da ordem de centímetros, causando anomalia da altura da superfície do mar (AASM). Transportando grandes quantidades de energia e influenciando diretamente a circulação de larga escala e o clima global, sua propagação de fase acontece sempre para oeste e sua velocidade é predominantemente uma função da latitude. É sabido que relações entre AASM e concentração de clorofila (CC) podem ser encontradas em todas as bacias oceânicas, evidenciando uma clara influência de fenômenos físicos em fenômenos biológicos. O presente trabalho visa a identificação de ondas de Rossby através da visualização de dados de CC, que, quando comparados a de AASM, apresentaram comprimento, período e velocidade de fase conforme previsto teoricamente para ondas de Rossby baroclínicas do primeiro modo vertical. A região de estudo, entre as latitudes de 25o S e 45o S, é caracterizada pela presença da Corrente do Atlântico Sul, da convergência subtropical e da faixa de rotacional nulo do vento e é, portanto, sede de importantes fenômenos oceanográficos de larga escala. Ambos os conjuntos de dados foram obtidos por sensoriamento remoto e submetidos a uma cadeia de filtros bidimensionais de resposta impulsiva finita (FIR2D) cujo funcionamento de baseia no princípio de convolução entre a série temporal e uma matriz-filtro. Os sinais filtrados foram decompostos em componentes propagantes e não-propagantes e entre os propagantes foi feita a separação das componentes em diversas bandas espectrais definidas por seus períodos centrais. Diagramas de Hovmoller foram confeccionados e as velocidades de fase foram obtidas através da transformada de Radon. A conclusão do trabalho evidenciou uma clara influência das ondas de Rossby sobre a distribuição de clorofila ao longo da região estudada.

Dos diagramas aos parâmetros: transformações no design digital

The article is part of an ongoing theoretical research about the emergence of parametric architecture. It discusses some of the last developments in digital design from the transition of the discourse and operativity by “diagrams” to the theories and processes derived from “parameters”. Centered in Peter Eisenman’s and Patrik Schumacher’s propositions, it is in its horizon to comprehend what relations are established between “diagram” and “parameter” -­‐ similarities, complementarities and differences -­‐, contributing for the critical contextualization of theoretical movements and design processes in contemporary architecture.

Identificação de ondas de Rossby a partir de diagramas de Hovmoller da concentração de clorofila entre as latitudes de 25o S e 45o S do Oceano Atlântico

Ondas de Rossby são ondas planetárias oceânicas de ocorrência quase global com comprimentos de onda da ordem de centenas a milhares de quilômetros, períodos da ordem de meses a anos e amplitudes superficiais da ordem de centímetros, causando anomalia da altura da superfície do mar (AASM). Transportando grandes quantidades de energia e influenciando diretamente a circulação de larga escala e o clima global, sua propagação de fase acontece sempre para oeste e sua velocidade é predominantemente uma função da latitude. É sabido que relações entre AASM e concentração de clorofila (CC) podem ser encontradas em todas as bacias oceânicas, evidenciando uma clara influência de fenômenos físicos em fenômenos biológicos. O presente trabalho visa a identificação de ondas de Rossby através da visualização de dados de CC, que, quando comparados a de AASM, apresentaram comprimento, período e velocidade de fase conforme previsto teoricamente para ondas de Rossby baroclínicas do primeiro modo vertical. A região de estudo, entre as latitudes de 25o S e 45o S, é caracterizada pela presença da Corrente do Atlântico Sul, da convergência subtropical e da faixa de rotacional nulo do vento e é, portanto, sede de importantes fenômenos oceanográficos de larga escala. Ambos os conjuntos de dados foram obtidos por sensoriamento remoto e submetidos a uma cadeia de filtros bidimensionais de resposta impulsiva finita (FIR2D) cujo funcionamento de baseia no princípio de convolução entre a série temporal e uma matriz-filtro. Os sinais filtrados foram decompostos em componentes propagantes e não-propagantes e entre os propagantes foi feita a separação das componentes em diversas bandas espectrais definidas por seus períodos centrais. Diagramas de Hovmoller foram confeccionados e as velocidades de fase foram obtidas através da transformada de Radon. A conclusão do trabalho evidenciou uma clara influência das ondas de Rossby sobre a distribuição de clorofila ao longo da região estudada

Análise climatológica da precipitação e do transporte de umidade na região da ZCAS através da nova geração de reanálises

O conhecimento do desempenho das reanálises e dos erros associados a elas apresenta um papel fundamental na compreensão dos processos físicos que ocorrem na atmosfera. Este trabalho tem por objetivo documentar as principais características da precipitação associada à Zona de Convergência do Atlântico Sul (ZCAS), baseado em seis conjuntos de reanálises atmosféricas (MERRA, ERA-Interim, ERA-40, NCEP 1, NCEP 2 e NCEP CFSR) e cinco conjuntos de produtos observados de precipitação (SALDAS, CPC, CMAP, GPCP e GLDAS). Através destes dados também foi analisado o transporte de umidade sobre a região da ZCAS, para os anos de 1979 a 2007. Em resumo, este trabalho evidencia o avanço das novas reanálises na tentativa de representar de forma mais adequada a variável precipitação acumulada. Os diagramas de Taylor mostram que os produtos de precipitação estão bem correlacionados com o ponto de referência (CPC), com coeficientes entre 0,6 e 0,9. Somente a reanálise do NCEP CFSR possui correlações próximas as dos produtos de precipitação. Os conjuntos mais antigos de reanálises apresentam correlações menores, abaixo de 0,6. O Oceano Atlântico é a fonte principal do fluxo de umidade para a direção da ZCAS, que diminui na direção do continente. Na Região SE do Brasil, a topografia tem um papel importante para a convergência de umidade. Já na parte noroeste da ZCAS, este fator deve estar associado a processos termodinâmicos.

Contribution to assessing the stiffness reduction of structural elements in the global stability analysis of precast concrete multi-storey buildings

This study deals with the reduction of the stiffness in precast concrete structural elements of multi-storey buildings to analyze global stability. Having reviewed the technical literature, this paper present indications of stiffness reduction in different codes, standards, and recommendations and compare these to the values found in the present study. The structural model analyzed in this study was constructed with finite elements using ANSYS® software. Physical Non-Linearity (PNL) was considered in relation to the diagrams M x N x 1/r, and Geometric Non-Linearity (GNL) was calculated following the Newton-Raphson method. Using a typical precast concrete structure with multiple floors and a semi-rigid beam-to-column connection, expressions for a stiffness reduction coefficient are presented. The main conclusions of the study are as follows: the reduction coefficients obtained from the diagram M x N x 1/r differ from standards that use a simplified consideration of PNL; the stiffness reduction coefficient for columns in the arrangements analyzed were approximately 0.5 to 0.6; and the variation of values found for stiffness reduction coefficient in concrete beams, which were subjected to the effects of creep with linear coefficients from 0 to 3, ranged from 0.45 to 0.2 for positive bending moments and 0.3 to 0.2 for negative bending moments.

Mechanical Alterations in airway smooth muscle after interaction with indoor pollutant – A mathematical model.

The viscoelasticity of mammalian lung is determined by the mechanical properties and structural regulation of the airway smooth muscle (ASM). The exposure to polluted air may deteriorate these properties with harmful consequences to individual health. Formaldehyde (FA) is an important indoor pollutant found among volatile organic compounds. This pollutant permeates through the smooth muscle tissue forming covalent bonds between proteins in the extracellular matrix and intracellular protein structure changing mechanical properties of ASM and inducing asthma symptoms, such as airway hyperresponsiveness, even at low concentrations. In the experimental scenario, the mechanical effect of FA is the stiffening of the tissue, but the mechanism behind this effect is not fully understood. Thus, the aim of this study is to reproduce the mechanical behavior of the ASM, such as contraction and stretching, under FA action or not. For this, it was created a two-dimensional viscoelastic network model based on Voronoi tessellation solved using Runge-Kutta method of fourth order. The equilibrium configuration was reached when the forces in different parts of the network were equal. This model simulates the mechanical behavior of ASM through of a network of dashpots and springs. This dashpot-spring mechanical coupling mimics the composition of the actomyosin machinery of ASM through the contraction of springs to a minimum length. We hypothesized that formation of covalent bonds, due to the FA action, can be represented in the model by a simple change in the elastic constant of the springs, while the action of methacholine (MCh) reduce the equilibrium length of the spring. A sigmoid curve of tension as a function of MCh doses was obtained, showing increased tension when the muscle strip was exposed to FA. Our simulations suggest that FA, at a concentration of 0.1 ppm, can affect the elastic properties of the smooth muscle ¯bers by a factor of 120%. We also analyze the dynamic mechanical properties, observing the viscous and elastic behavior of the network. Finally, the proposed model, although simple, incorporates the phenomenology of both MCh and FA and reproduces experimental results observed with in vitro exposure of smooth muscle to FA. Thus, this new mechanical approach incorporates several well know features of the contractile system of the cells in a tissue level model. The model can also be used in different biological scales.

Mechanical alterations in airway smooth muscle after interaction with indoor pollutant - A mathematical model

The viscoelasticity of mammalian lung is determined by the mechanical properties and structural regulation of the airway smooth muscle (ASM). The exposure to polluted air may deteriorate these properties with harmful consequences to individual health. Formaldehyde (FA) is an important indoor pollutant found among volatile organic compounds. This pollutant permeates through the smooth muscle tissue forming covalent bonds between proteins in the extracellular matrix and intracellular protein structure changing mechanical properties of ASM and inducing asthma symptoms, such as airway hyperresponsiveness, even at low concentrations. In the experimental scenario, the mechanical effect of FA is the stiffening of the tissue, but the mechanism behind this effect is not fully w1derstood. Thus, the aim of this study is to reproduce the mechanical behavior of the ASM, such as contraction and stretching, under FA action or not. For this, it was created a two-dimensional viscoelastic network model based on Voronoi tessellation solved using Runge-Kutta method of fourth order. The equilibrium configuration was reached when the forces in different parts of the network were equal. This model simulates the mechanical behavior of ASM through of a network of dashpots and springs. This dashpot-spring mechanical coupling mimics the composition of the actomyosin machinery of ASM through the contraction of springs to a minimum length. We hypothesized that formation of covalent bonds, due to the FA action, can be represented in the model by a simple change in the elastic constant of the springs, while the action of methacholinc (MCh) reduce the equilibrium length of the spring. A sigmoid curve of tension as a function of MCh doses was obtained, showing increased tension when the muscle strip was exposed to FA. Our simulations suggest that FA, at a concentration of 0.1 ppm, can affect the elastic properties of the smooth muscle fibers by a factor of 120%. We also analyze the dynamic mechanical properties, observing the viscous and elastic behavior of the network. Finally, the proposed model, although simple, ir1corporates the phenomenology of both MCh and FA and reproduces experirnental results observed with ir1 vitro exposure of smooth muscle to .FA. Thus, this new mechanical approach incorporates several well know features of the contractile system of the cells ir1 a tissue level model. The model can also be used in different biological scales.