Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis

The molecular mechanisms of pulmonary fibrosis are poorly understood. We have used oligonucleotide arrays to analyze the gene expression programs that underlie pulmonary fibrosis in response to bleomycin, a drug that causes lung inflammation and fibrosis, in two strains of susceptible mice (129 and C57BL/6). We then compared the gene expression patterns in these mice with 129 mice carrying a null mutation in the epithelial-restricted integrin β6 subunit (β6−/−), which develop inflammation but are protected from pulmonary fibrosis. Cluster analysis identified two distinct groups of genes involved in the inflammatory and fibrotic responses. Analysis of gene expression at multiple time points after bleomycin administration revealed sequential induction of subsets of genes that characterize each response. The availability of this comprehensive data set should accelerate the development of more effective strategies for intervention at the various stages in the development of fibrotic diseases of the lungs and other organs.

Spatially independent activity patterns in functional MRI data during the Stroop color-naming task

A method is given for determining the time course and spatial extent of consistently and transiently task-related activations from other physiological and artifactual components that contribute to functional MRI (fMRI) recordings. Independent component analysis (ICA) was used to analyze two fMRI data sets from a subject performing 6-min trials composed of alternating 40-sec Stroop color-naming and control task blocks. Each component consisted of a fixed three-dimensional spatial distribution of brain voxel values (a “map”) and an associated time course of activation. For each trial, the algorithm detected, without a priori knowledge of their spatial or temporal structure, one consistently task-related component activated during each Stroop task block, plus several transiently task-related components activated at the onset of one or two of the Stroop task blocks only. Activation patterns occurring during only part of the fMRI trial are not observed with other techniques, because their time courses cannot easily be known in advance. Other ICA components were related to physiological pulsations, head movements, or machine noise. By using higher-order statistics to specify stricter criteria for spatial independence between component maps, ICA produced improved estimates of the temporal and spatial extent of task-related activation in our data compared with principal component analysis (PCA). ICA appears to be a promising tool for exploratory analysis of fMRI data, particularly when the time courses of activation are not known in advance.

Análise da influência de variáveis meteorológicas e da hidrodinâmica sobre os padrões espaciais e temporais da qualidade da água e de florescimentos de cianobactérias e macrófitas em um reservatório urbano

Os reservatórios urbanos estão suscetíveis a uma variedade de interferências antropogênicas que acarretam grande variabilidade espacial e temporal. Contudo, possuem uma dinâmica própria na qual o hidroclima e micro e macro-eventos meteorológicos atuam sobre os processos físicos, químicos e biológicos resultando em respostas particulares de cada corpo de água. No presente estudo a existência de padrões espaciais e temporais na formação de florescimentos de algas, cianobactérias e macrófitas no reservatório Guarapiranga, São Paulo, SP, foi avaliada por meio de experimento de curta escala de tempo durante o evento da entrada de uma frente fria. Foram amostrados 64 pontos em todo o reservatório, e o estudo intensivo de florescimento algal e de cianobactérias em dois ciclos nictemerais, em um ponto selecionado no reservatório. Um modelo tridimensional de hidrodinâmica foi aplicado ao estudo compartimentalizado dos tempos de residência e imagens de satélite foram analisadas para determinação de padrões temporais e espaciais durante períodos de tempo mais amplos. Os resultados revelaram que os períodos mais favoráveis ao surgimento de florescimentos de cianobactérias são geralmente os meses mais quentes, de dezembro e janeiro, ou aqueles em que ocorrem estratificações mais fortes como no fim do inverno, em julho, e após as primeiras chuvas nos meses de setembro e outubro. Existem padrões espaciais recorrentes na formação dos florescimentos, controlados em grande parte pela ação do vento, que no reservatório Guarapiranga é predominantemente nas direções leste e sudeste empurrando os florescimentos na direção da foz dos tributários Embu Mirim e Embu Guaçu e ocasionalmente na direção da foz do rio Parelheiros. As simulações hidrodinâmicas evidenciam as forçantes que determinam os padrões observados e reforçam a importância de se discretizarem os tempos de residência de diferentes compartimentos do reservatório. As séries temporais amplas permitiram a determinação da qualidade da água em cada região e fornecem subsídios para o futuro manejo do reservatório. Como esse comportamento não se restringe ao reservatório Guarapiranga, o tipo de modelagem aqui utilizada pode ser útil para obter informações importantes no processo de planejamento e seleção de medidas para o gerenciamento de reservatórios urbanos tropicais polimíticos, em geral.

Characterization of spatial–temporal patterns in dynamic speckle sequences using principal component analysis

Abstract. Speckle is being used as a characterization tool for the analysis of the dynamics of slow-varying phenomena occurring in biological and industrial samples at the surface or near-surface regions. The retrieved data take the form of a sequence of speckle images. These images contain information about the inner dynamics of the biological or physical process taking place in the sample. Principal component analysis (PCA) is able to split the original data set into a collection of classes. These classes are related to processes showing different dynamics. In addition, statistical descriptors of speckle images are used to retrieve information on the characteristics of the sample. These statistical descriptors can be calculated in almost real time and provide a fast monitoring of the sample. On the other hand, PCA requires a longer computation time, but the results contain more information related to spatial–temporal patterns associated to the process under analysis. This contribution merges both descriptions and uses PCA as a preprocessing tool to obtain a collection of filtered images, where statistical descriptors are evaluated on each of them. The method applies to slow-varying biological and industrial processes.

Response of Catch-Per-Unit-Effort to Spatial and Environmental Factors: an Exploratory Data Analysis Using Generalized Additive Models

Understanding spatial distributions and how environmental conditions influence catch-per-unit-effort (CPUE) is important for increased fishing efficiency and sustainable fisheries management. This study investigated the relationship between CPUE, spatial factors, temperature, and depth using generalized additive models. Combinations of factors, and not one single factor, were frequently included in the best model. Parameters which best described CPUE varied by geographic region. The amount of variance, or deviance, explained by the best models ranged from a low of 29% (halibut, Charlotte region) to a high of 94% (sablefish, Charlotte region). Depth, latitude, and longitude influenced most species in several regions. On the broad geographic scale, depth was associated with CPUE for every species, except dogfish. Latitude and longitude influenced most species, except halibut (Areas 4 A/D), sablefish, and cod. Temperature was important for describing distributions of halibut in Alaska, arrowtooth flounder in British Columbia, dogfish, Alaska skate, and Aleutian skate. The species-habitat relationships revealed in this study can be used to create improved fishing and management strategies.

A Spatial Analysis of Agricultural Land Prices in Bavaria. Factor Markets Working Document No. 50, June 2013

This paper empirically analyses a dataset of more than 7,300 agricultural land sales transactions from 2001 and 2007 to identify the factors influencing agricultural land prices in Bavaria. We use a general spatial model, which combines a spatial lag and a spatial error model, and in addition account for endogeneity introduced by the spatially lagged dependent variable as well as other explanatory variables. Our findings confirm the strong influence of agricultural factors such as land productivity, of variables describing the regional land market structure, and of non-agricultural factors such as urban pressure on agricultural land prices. Moreover, the involvement of public authorities as a seller or buyer increases sales prices in Bavaria. We find a significant capitalisation of government support payments into agricultural land, where a decrease of direct payments by 1% would decrease land prices in 2007 and 2001 by 0.27% and 0.06%, respectively. In addition, we confirm strong spatial relationships in our dataset. Neglecting this leads to biased estimates, especially if aggregated data is used. We find that the price of a specific plot increases by 0.24% when sales prices in surrounding areas increase by 1%.

Bifurcation Analysis of Reaction Diffusion Systems on Arbitrary Surfaces

In this article we present a computational framework for isolating spatial patterns arising in the steady states of reaction-diffusion systems. Such systems have been used to model many different phenomena in areas such as developmental and cancer biology, cell motility and material science. Often one is interested in identifying parameters which will lead to a particular pattern. To attempt to answer this, we compute eigenpairs of the Laplacian on a variety of domains and use linear stability analysis to determine parameter values for the system that will lead to spatially inhomogeneous steady states whose patterns correspond to particular eigenfunctions. This method has previously been used on domains and surfaces where the eigenvalues and eigenfunctions are found analytically in closed form. Our contribution to this methodology is that we numerically compute eigenpairs on arbitrary domains and surfaces. Here we present various examples and demonstrate that mode isolation is straightforward especially for low eigenvalues. Additionally we see that if two or more eigenvalues are in a permissible range then the inhomogeneous steady state can be a linear combination of the respective eigenfunctions. Finally we show an example which suggests that pattern formation is robust on similar surfaces in cases that the surface either has or does not have a boundary.

Homogeneous Spatial Units (HSU) - a Pan-European geographical basis for environmental and socio-economic modelling

The spatial data set delineates areas with similar environmental properties regarding soil, terrain morphology, climate and affiliation to the same administrative unit (NUTS3 or comparable units in size) at a minimum pixel size of 1km2. The scope of developing this data set is to provide a link between spatial environmental information (e.g. soil properties) and statistical data (e.g. crop distribution) available at administrative level. Impact assessment of agricultural management on emissions of pollutants or radiative active gases, or analysis regarding the influence of agricultural management on the supply of ecosystem services, require the proper spatial coincidence of the driving factors. The HSU data set provides e.g. the link between the agro-economic model CAPRI and biophysical assessment of environmental impacts (updating previously spatial units, Leip et al. 2008), for the analysis of policy scenarios. Recently, a statistical model to disaggregate crop information available from regional statistics to the HSU has been developed (Lamboni et al. 2016). The HSU data set consists of the spatial layers provided in vector and raster format as well as attribute tables with information on the properties of the HSU. All input data for the delineation the HSU is publicly available. For some parameters the attribute tables provide the link between the HSU data set and e.g. the soil map(s) rather than the data itself. The HSU data set is closely linked the USCIE data set.