Application of computer-aided tomography techniques to visualize kelp holdfast structure reveals the importance of habitat complexity for supporting marine biodiversity

Ecosystem engineers that increase habitat complexity are keystone species in marine systems, increasing shelter and niche availability, and therefore biodiversity. For example, kelp holdfasts form intricate structures and host the largest number of organisms in kelp ecosystems. However, methods that quantify 3D habitat complexity have only seldom been used in marine habitats, and never in kelp holdfast communities. This study investigated the role of kelp holdfasts (Laminaria hyperborea) in supporting benthic faunal biodiversity. Computer-aided tomography (CT-) scanning was used to quantify the three-dimensional geometrical complexity of holdfasts, including volume, surface area and surface fractal dimension (FD). Additionally, the number of haptera, number of haptera per unit of volume, and age of kelps were estimated. These measurements were compared to faunal biodiversity and community structure, using partial least-squares regression and multivariate ordination. Holdfast volume explained most of the variance observed in biodiversity indices, however all other complexity measures also strongly contributed to the variance observed. Multivariate ordinations further revealed that surface area and haptera per unit of volume accounted for the patterns observed in faunal community structure. Using 3D image analysis, this study makes a strong contribution to elucidate quantitative mechanisms underlying the observed relationship between biodiversity and habitat complexity. Furthermore, the potential of CT-scanning as an ecological tool is demonstrated, and a methodology for its use in future similar studies is established. Such spatially resolved imager analysis could help identify structurally complex areas as biodiversity hotspots, and may support the prioritization of areas for conservation.

Application of computer-aided tomography techniques to visualize kelp holdfast structure reveals the importance of habitat complexity for supporting marine biodiversity

Ecosystem engineers that increase habitat complexity are keystone species in marine systems, increasing shelter and niche availability, and therefore biodiversity. For example, kelp holdfasts form intricate structures and host the largest number of organisms in kelp ecosystems. However, methods that quantify 3D habitat complexity have only seldom been used in marine habitats, and never in kelp holdfast communities. This study investigated the role of kelp holdfasts (Laminaria hyperborea) in supporting benthic faunal biodiversity. Computer-aided tomography (CT-) scanning was used to quantify the three-dimensional geometrical complexity of holdfasts, including volume, surface area and surface fractal dimension (FD). Additionally, the number of haptera, number of haptera per unit of volume, and age of kelps were estimated. These measurements were compared to faunal biodiversity and community structure, using partial least-squares regression and multivariate ordination. Holdfast volume explained most of the variance observed in biodiversity indices, however all other complexity measures also strongly contributed to the variance observed. Multivariate ordinations further revealed that surface area and haptera per unit of volume accounted for the patterns observed in faunal community structure. Using 3D image analysis, this study makes a strong contribution to elucidate quantitative mechanisms underlying the observed relationship between biodiversity and habitat complexity. Furthermore, the potential of CT-scanning as an ecological tool is demonstrated, and a methodology for its use in future similar studies is established. Such spatially resolved imager analysis could help identify structurally complex areas as biodiversity hotspots, and may support the prioritization of areas for conservation.

Padrões de organização das assembleias de aves florestais em uma paisagem fragmentada de Floresta Atlântica

Brazil is home to one of the richest avifaunas the world, which is subject to high levels of environmental degradation, in particular forest fragmentation. The Atlantic Forest biome depicts this history of devastation and today remains as small isolated fragments on highly degraded landscapes. This project aimed to evaluate the effects of forest fragmentation in an area with Atlantic Forest remnants in northern Paraná (Brazil) on the distribution and the organization of assemblage of forest birds and tested the hypothesis that the structure of the assembly in the fragments is different than expected by chance. We did four qualitative samplings of birds in three sets of forest fragments in the landscape, each with three fragments: large, medium and small. The method applied in the sampling was point counts along transects, traveled randomly for four hours in each fragment. Samples were taken in two periods: from September to November / 2013, and between March and May / 2014. The structure of the meeting was assessed by rates of co-occurring species (Checkerboard and CScore) and α diversity patterns (wealth) and β (turnover of species), while the landscape structure was analyzed from the parameters: area, distance between fragments, fractal dimension, edge density, fragment shape index and nuclear area index. The null hypothesis of no structure in the assembly of birds in the landscape was tested with null models from the co-occurrence indexes. The effects of landscape structure on the assembly of the structure were analyzed by the Mantel test and principal component analysis (PCA). The assembly of the structure in the landscape showed a pattern of spatiotemporal organization significantly different from that expected by chance, revealing a structure most influenced by segregation of the species. The fragments showed significant differences in richness, unlike sets of fragments, indicating relative homogeneity in the landscape structure. The differences between the size and the distance between the fragments significantly influenced the patterns of organization of the meeting of forest birds in the landscape and patterns of α and β diversity, indicating that the higher the fragment and smaller distances between them, more the standard of species cooccurrence is different than expected by chance. Thus, the fragmented landscape of remnants of the northern Paraná Atlantic Forest still has availability of environmental resources and physical characteristics that allow a persistent organizational structure of the assembly of forest birds in space over time.

Biomonitoramento da comunidade de macroinvertebrados de um reservatório de abastecimento público no sul do Brasil

The faunal inventory of the macroinvertebrate community is important to the environmental assessment, since this biota is sensitive to human disturbance. The reservoir of Rio Verde, located on the first plateau of Paraná, is inserted into an agricultural region with several forest fragments Araucaria. The aim of this study was to evaluate the environmental integrity of the reservoir through ecological indexes of macroinvertebrate community benthic and associated with macrophytes. Five sampling points were defined in the study area, which comprise distinct microhabitats in the basin. There were four sampling campaigns, each by weather station: Spring (2014); Summer (2015); Autumn (2015) and Winter (2015). In each sample were measured abiotic various parameters in the field and be collected water samples for nutrient analysis in the laboratory. The macroinvertebrates were collected in triplicate at adapted Macan method using mesh sieve 1 mm and CPUE (catch per unit effort) for 20 minutes. In order to pellet sample was used a dredger model Petersen 2L. Still in the field, by season, samples were collected from macrophytes Myriophyllum aquaticum (Vell) Verdc. and Potamogeton montevidensis A. Benn. in triplicates in the fluvial region of the reservoir, to analyze the associated fractal dimension and macrofauna. For this we used a PVC sampler specific volume 0.025 m3. the following ecological descriptors were calculated in each case: abundance, wealth tax, wealth Margalef, Shannon-Wiener diversity, evenness evenness through the Past software. The index Biological Monitoring Working Party (BMWP) for monitoring sampling points was also calculated. Regarding the statistical analysis, we used the analysis of PERMANOVA to compare points and seasons and canonical correspondence analysis (CCoA) for variables. Regarding M. aquaticum and P. montevidensis it was not verified difference to the average associated macroinvertebrates. However there was a difference for abundance of organisms in the fractal dimension and biomass of specimens. M. aquaticum is more complex and took more macrofauna in relation to P. montevidensis. Regarding the monitoring of the reservoir, it showed up mesotrophic with moderate nutrient concentrations and within the regulatory limits. Benthic macrofauna showed statistical differences in relation to the reservoir region, sample point and temporal variation. The BMWP index showed that the river region has the highest biotic integrity (in all samples above 70 points), and the ecological descriptors of wealth and Margalef diversity of Shannon- Wiener higher. In point 4 (dam downstream) were recorded evidence of possible impacts due to lower wealth and BMWP index which resulted in a questionable quality water. New approaches are needed to focus on the aquatic community in the best understanding of this ecosystem and also with a view to environmental preservation of the Green River Basin.

Morphological traits of surveillant/activated microglia during an experimentally induced acute neuroinflammatory process

Several studies show that morphological changes of microglia over the course of inflammation are tightly coupled to function. However the progressive transformation into activated microglia is poorly characterized. AIMS: This study aimed to establish a spatiotemporal correlation between quantifiable morphological parameters of microglia and the spread of an acute ventricular inflammatory process. METHODS: Inflammation was induced by a single injection of the enzyme neuraminidase within the lateral ventricle of rats. Animals were sacrificed 2, 4 and 12 hours after injection. Coronal slices were immunostained with Iba1 to label microglia and with IL1β to delimit the spread of inflammation. Digital images were obtained by scanning the labelled sections. Single microglia images were randomly selected from periventricular areas of caudate putamen, hippocampus and hypothalamus. FracLac for ImageJ software was used to measure the following morphological parameters: fractal dimension, lacunarity, area, perimeter and density. RESULTS: Significant differences were found in fractal dimension, lacunarity, perimeter and density of microglia cells of neuraminidase injected rats compared to sham animals. However no differences were found in the parameter “area”. In hipoccampus there was a delay in the significant change of the measured parameters. These morphological changes correlated with IL1β-expression in the same areas. CONCLUSIONS: Ventricular inflammation induced by neuraminidase provokes quantifiable morphological changes in microglia restricted to areas labelled with IL1β. Morphological parameters of microglia such as fractal dimension, lacunarity, perimeter and density are sensitive and valuable tools to quantify activation. However, the extensively used parameter “area” did not change upon microglia activation.

Os fractais no urbanismo

Dissertação para obtenção do grau de Mestre em Arquitectura com Especialização em Urbanismo, apresentada na Universidade de Lisboa - Faculdade de Arquitectura.

Simulação de fluxo de fluidos em meios porosos desordenados uma análise de efeito de escala na estimativa da permeabilidade e do coeficiente de arrasto

The present study provides a methodology that gives a predictive character the computer simulations based on detailed models of the geometry of a porous medium. We using the software FLUENT to investigate the flow of a viscous Newtonian fluid through a random fractal medium which simplifies a two-dimensional disordered porous medium representing a petroleum reservoir. This fractal model is formed by obstacles of various sizes, whose size distribution function follows a power law where exponent is defined as the fractal dimension of fractionation Dff of the model characterizing the process of fragmentation these obstacles. They are randomly disposed in a rectangular channel. The modeling process incorporates modern concepts, scaling laws, to analyze the influence of heterogeneity found in the fields of the porosity and of the permeability in such a way as to characterize the medium in terms of their fractal properties. This procedure allows numerically analyze the measurements of permeability k and the drag coefficient Cd proposed relationships, like power law, for these properties on various modeling schemes. The purpose of this research is to study the variability provided by these heterogeneities where the velocity field and other details of viscous fluid dynamics are obtained by solving numerically the continuity and Navier-Stokes equations at pore level and observe how the fractal dimension of fractionation of the model can affect their hydrodynamic properties. This study were considered two classes of models, models with constant porosity, MPC, and models with varying porosity, MPV. The results have allowed us to find numerical relationship between the permeability, drag coefficient and the fractal dimension of fractionation of the medium. Based on these numerical results we have proposed scaling relations and algebraic expressions involving the relevant parameters of the phenomenon. In this study analytical equations were determined for Dff depending on the geometrical parameters of the models. We also found a relation between the permeability and the drag coefficient which is inversely proportional to one another. As for the difference in behavior it is most striking in the classes of models MPV. That is, the fact that the porosity vary in these models is an additional factor that plays a significant role in flow analysis. Finally, the results proved satisfactory and consistent, which demonstrates the effectiveness of the referred methodology for all applications analyzed in this study.

Análise não linear de séries temporais e aplicações à Psicologia

Nesta dissertação estudámos as séries temporais que representam a complexa dinâmica do comportamento. Demos especial atenção às técnicas de dinâmica não linear. As técnicas fornecem-nos uma quantidade de índices quantitativos que servem para descrever as propriedades dinâmicas do sistema. Estes índices têm sido intensivamente usados nos últimos anos em aplicações práticas em Psicologia. Estudámos alguns conceitos básicos de dinâmica não linear, as características dos sistemas caóticos e algumas grandezas que caracterizam os sistemas dinâmicos, que incluem a dimensão fractal, que indica a complexidade de informação contida na série temporal, os expoentes de Lyapunov, que indicam a taxa com que pontos arbitrariamente próximos no espaço de fases da representação do espaço dinâmico, divergem ao longo do tempo, ou a entropia aproximada, que mede o grau de imprevisibilidade de uma série temporal. Esta informação pode então ser usada para compreender, e possivelmente prever, o comportamento. ABSTRACT: ln this thesis we studied the time series that represent the complex dynamic behavior. We focused on techniques of nonlinear dynamics. The techniques provide us a number of quantitative indices used to describe the dynamic properties of the system. These indices have been extensively used in recent years in practical applications in psychology. We studied some basic concepts of nonlinear dynamics, the characteristics of chaotic systems and some quantities that characterize the dynamic systems, including fractal dimension, indicating the complexity of information in the series, the Lyapunov exponents, which indicate the rate at that arbitrarily dose points in phase space representation of a dynamic, vary over time, or the approximate entropy, which measures the degree of unpredictability of a series. This information can then be used to understand and possibly predict the behavior.

Improving multivariate data streams clustering.

Clustering data streams is an important task in data mining research. Recently, some algorithms have been proposed to cluster data streams as a whole, but just few of them deal with multivariate data streams. Even so, these algorithms merely aggregate the attributes without touching upon the correlation among them. In order to overcome this issue, we propose a new framework to cluster multivariate data streams based on their evolving behavior over time, exploring the correlations among their attributes by computing the fractal dimension. Experimental results with climate data streams show that the clusters' quality and compactness can be improved compared to the competing method, leading to the thoughtfulness that attributes correlations cannot be put aside. In fact, the clusters' compactness are 7 to 25 times better using our method. Our framework also proves to be an useful tool to assist meteorologists in understanding the climate behavior along a period of time.

The Meaningful Fractal Fuzzy Dimension Applied to the Design of Self Organizing Maps

This paper presents the principal results of a detailed study about the use of the Meaningful Fractal Fuzzy Dimension measure in the problem in determining adequately the topological dimension of output space of a Self-Organizing Map. This fractal measure is conceived by combining the Fractals Theory and Fuzzy Approximate Reasoning. In this work this measure was applied on the dataset in order to obtain a priori knowledge, which is used to support the decision making about the SOM output space design. Several maps were designed with this approach and their evaluations are discussed here.

Construction of fractal interpolation surfaces on rectangular grids

We present a general method of generating continuous fractal interpolation surfaces by iterated function systems on an arbitrary data set over rectangular grids and estimate their Box-counting dimension.

Construction of recurrent fractal interpolation surfaces(RFISs) on rectangular grids

A recurrent iterated function system (RIFS) is a genaralization of an IFS and provides nonself-affine fractal sets which are closer to natural objects. In general, it's attractor is not a continuous surface in R3. A recurrent fractal interpolation surface (RFIS) is an attractor of RIFS which is a graph of bivariate continuous interpolation function. We introduce a general method of generating recurrent interpolation surface which are at- tractors of RIFSs about any data set on a grid.

Análise fractal da vasculatura arteriolar e venular da retina em pessoas sem doença ocular

Although it has been suggested that retinal vasculature is a diffusion-limited aggregation (DLA) fractal, no study has been dedicated to standardizing its fractal analysis . The aims of this project was to standardize a method to estimate the fractal dimensions of retinal vasculature and to characterize their normal values; to determine if this estimation is dependent on skeletization and on segmentation and calculation methods; to assess the suitability of the DLA model and to determine the usefulness of log-log graphs in characterizing vasculature fractality . To achieve these aims, the information, mass-radius and box counting dimensions of 20 eyes vasculatures were compared when the vessels were manually or computationally segmented; the fractal dimensions of the vasculatures of 60 eyes of healthy volunteers were compared with those of 40 DLA models and the log-log graphs obtained were compared with those of known fractals and those of non-fractals. The main results were: the fractal dimensions of vascular trees were dependent on segmentation methods and dimension calculation methods, but there was no difference between manual segmentation and scale-space, multithreshold and wavelet computational methods; the means of the information and box dimensions for arteriolar trees were 1.29. against 1.34 and 1.35 for the venular trees; the dimension for the DLA models were higher than that for vessels; the log-log graphs were straight, but with varying local slopes, both for vascular trees and for fractals and non-fractals. This results leads to the following conclusions: the estimation of the fractal dimensions for retinal vasculature is dependent on its skeletization and on the segmentation and calculation methods; log-log graphs are not suitable as a fractality test; the means of the information and box counting dimensions for the normal eyes were 1.47 and 1.43, respectively, and the DLA model with optic disc seeding is not sufficient for retinal vascularization modeling

Fractal character of the SAXS correlation volume in poly(ethylene glycol)/silica hybrid wet gels

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)