Shape analysis using fractal dimension: A curvature based approach

The present work shows a novel fractal dimension method for shape analysis. The proposed technique extracts descriptors from a shape by applying a multi-scale approach to the calculus of the fractal dimension. The fractal dimension is estimated by applying the curvature scale-space technique to the original shape. By applying a multi-scale transform to the calculus, we obtain a set of descriptors which is capable of describing the shape under investigation with high precision. We validate the computed descriptors in a classification process. The results demonstrate that the novel technique provides highly reliable descriptors, confirming the efficiency of the proposed method. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4757226]

Integrated biomarker responses as environmental status descriptors of a coastal zone (Sao Paulo, Brazil)

Sao Paulo state (Brazil) has one of the most overpopulated coastal zones in South America, where previous studies have already detected sediment and water contamination. However, biological-based monitoring considering signals of xenobiotic exposure and effects are scarce. The present study employed a battery of biomarkers under field conditions to assess the environmental quality of this coastal zone. For this purpose, the activity of CYP 450, antioxidant enzymes, DNA damage, lipid peroxidation and lysosomal membrane were analysed in caged mussels and integrated using Factorial Analysis. A representation of estimated factor scores was performed in order to confirm the factor descriptions characterizing the studied areas. Biomarker responses indicated signals of mussels` impaired health during the monitoring, which pointed to the impact of different sources of contaminants in the water quality and identified critical areas. This integrated approach produced a rapid, sensitive and cost-effective assessment, which could be incorporated as a descriptor of environmental status in future coastal zones biomonitoring. (C) 2011 Elsevier Inc. All rights reserved.

A new species of the neotropical catfish genus Trichomycterus (Siluriformes : Trichomycteridae) representing a new body shape for the family

Trichomycterus crassicaudatus is described as a new species from the Rio Iguacu basin in southern Brazil. The new species has an exceptionally deep posterior region of the body (caudal peduncle depth 22.8-25.4% SL), resulting in an overall shape which distinguishes it at once from all other members of the Trichomycteridae. The caudal fin of the species is broad-based and forked, a shape also distinguishing it from all other species in the family. A number of autapomorphic modifications of T. crassicaudatus are associated with the deepening of the caudal region, including an elongation of the hemal and neural spines of the vertebrae at the middle of the caudal peduncle. Phylogenetic relationships of the new species are yet unresolved, but it shares a similar color pattern and a thickening of caudal-fin procurrent rays with T. stawiarski, a poorly-known species also from the Rio Iguacu basin. Coloration and body shape also include similarities with T. lewi from Venezuela.

Investigating South American biogeographic history using patterns of skull shape variation on Cerdocyon thous (Mammalia: Canidae)

Patterns of geographic variation of the canid Cerdocyon thous have historically been obscured by its remarkable intraspecific morphological variability. The observed distribution is highly associated with phytophysiognomy, a feature considered highly dynamic along geological time. In the present study, we tested whether vegetation distribution during the Holocene Glacial Maximum of South America (HGM) explains the patterns of morphological variation within Cerdocyon thous. The species was divided in groups according to paleohabitats that could support their presence during the HGM, and then tested for differences in skull morphometrics. The results obtained demonstrate that the climatic changes during the HGM influenced the population structure of this species, resulting in the establishment of geographical groups with different degrees of morphological cohesion. Higher morphological cohesion found in the Northern group might be explained by the marked discontinuity between its geographical range and the rest of the species`distribution. The Eastern and Southern morphological divergence is less striking and, although this could be related to past vegetation distribution, the disappearance of those barriers leads to a population structure that could be slowly breaking down. (C) 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 77-84.

Color texture analysis based on fractal descriptors

Color texture classification is an important step in image segmentation and recognition. The color information is especially important in textures of natural scenes, such as leaves surfaces, terrains models, etc. In this paper, we propose a novel approach based on the fractal dimension for color texture analysis. The proposed approach investigates the complexity in R, G and B color channels to characterize a texture sample. We also propose to study all channels in combination, taking into consideration the correlations between them. Both these approaches use the volumetric version of the Bouligand-Minkowski Fractal Dimension method. The results show a advantage of the proposed method over other color texture analysis methods. (C) 2011 Elsevier Ltd. All rights reserved.

Abiotic factors shape temporal variation in the structure of an ant-plant network

Despite recognition of key biotic processes in shaping the structure of biological communities, few empirical studies have explored the influences of abiotic factors on the structural properties of mutualistic networks. We tested whether temperature and precipitation contribute to temporal variation in the nestedness of mutualistic ant-plant networks. While maintaining their nested structure, nestedness increased with mean monthly precipitation and, particularly, with monthly temperature. Moreover, some species changed their role in network structure, shifting from peripheral to core species within the nested network. We could summarize that abiotic factors affect plant species in the vegetation (e.g., phenology), meaning presence/absence of food sources, consequently an increase/decrease of associations with ants, and finally, these variations to fluctuations in nestedness. While biotic factors are certainly important, greater attention needs to be given to abiotic factors as underlying determinants of the structures of ecological networks.

Self-Organizing Maps of Molecular Descriptors for Sesquiterpene Lactones and Their Application to the Chemotaxonomy of the Asteraceae Family

The Asteraceae, one of the largest families among angiosperms, is chemically characterised by the production of sesquiterpene lactones (SLs). A total of 1,111 SLs, which were extracted from 658 species, 161 genera, 63 subtribes and 15 tribes of Asteraceae, were represented and registered in two dimensions in the SISTEMATX, an in-house software system, and were associated with their botanical sources. The respective 11 block of descriptors: Constitutional, Functional groups, BCUT, Atom-centred, 2D autocorrelations, Topological, Geometrical, RDF, 3D-MoRSE, GETAWAY and WHIM were used as input data to separate the botanical occurrences through self-organising maps. Maps that were generated with each descriptor divided the Asteraceae tribes, with total index values between 66.7% and 83.6%. The analysis of the results shows evident similarities among the Heliantheae, Helenieae and Eupatorieae tribes as well as between the Anthemideae and Inuleae tribes. Those observations are in agreement with systematic classifications that were proposed by Bremer, which use mainly morphological and molecular data, therefore chemical markers partially corroborate with these classifications. The results demonstrate that the atom-centred and RDF descriptors can be used as a tool for taxonomic classification in low hierarchical levels, such as tribes. Descriptors obtained through fragments or by the two-dimensional representation of the SL structures were sufficient to obtain significant results, and better results were not achieved by using descriptors derived from three-dimensional representations of SLs. Such models based on physico-chemical properties can project new design SLs, similar structures from literature or even unreported structures in two-dimensional chemical space. Therefore, the generated SOMs can predict the most probable tribe where a biologically active molecule can be found according Bremer classification.

Shape Changes of Pt Nanoparticles Induced by Deposition on Mesoporous Silica

Polyvinylpyrollidone (PVP)-capped platinum nanoparticles (NPs) are found to change shape from spherical to flat when deposited on mesoporous silica substrates (SBA-15). Transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS), and extended X-ray absorption fine structure (EXAFS) analyses are used in these studies. The SAXS results indicate that, after deposition, the 2 nm NPs have an average gyration radius 22% larger than in solution, while the EXAFS measurements indicate a decrease in first neighbor co-ordination number from 9.3 to 7.4. The deformation of these small capped NPs is attributed to interactions with the surface of the SBA-15 support, as evidenced by X-ray absorption near-edge structure (XANES).

Shape isomerism and shape coexistence effects on the Coulomb energy differences in the N = Z nucleus As-66 and neighboring T=1 multiplets

Excited states of the N = Z = 33 nucleus As-66 have been populated in a fusion-evaporation reaction and studied using gamma-ray spectroscopic techniques. Special emphasis was put into the search for candidates for the T = 1 states. A new 3(+) isomer has been observed with a lifetime of 1.1(3) ns. This is believed to be the predicted oblate shape isomer. The excited levels are discussed in terms of the shell model and of the complex excited Vampir approaches. Coulomb energy differences are determined from the comparison of the T = 1 states with their analog partners. The unusual behavior of the Coulomb energy differences in the A = 70 mass region is explained through different shape components (oblate and prolate) within the members of the same isospin multiplets. This breaking of the isospin symmetry is attributed to the correlations induced by the Coulomb interaction.

Relationship between Crystal Shape, Photoluminescence, and Local Structure in SrTiO3 Synthesized by Microwave-Assisted Hydrothermal Method

This paper describes the effect of using different titanium precursors on the synthesis and physical properties of SrTiO3 powders obtained by microwave-assisted hydrothermal method. X-ray diffraction measurements, X-ray absorption near-edge structure (XANES) spectroscopy, field emission scanning electron microscopy (FE-SEM), and high-resolution transmission electron microscopy (HRTEM) were carried out to investigate the structural and optical properties of the SrTiO3 spherical and cubelike-shaped particles. The appropriate choice of the titanium precursor allowed the control of morphological and photoluminescence (PL) properties of SrTiO3 compound. The PL emission was more intense in SrTiO3 samples composed of spherelike particles. This behavior was attributed to the existence of a lower amount of defects due to the uniformity of the spherical particles.

Fractal descriptors based on Fourier spectrum applied to texture analysis

This work proposes the development and study of a novel technique lot the generation of fractal descriptors used in texture analysis. The novel descriptors are obtained from a multiscale transform applied to the Fourier technique of fractal dimension calculus. The power spectrum of the Fourier transform of the image is plotted against the frequency in a log-log scale and a multiscale transform is applied to this curve. The obtained values are taken as the fractal descriptors of the image. The validation of the proposal is performed by the use of the descriptors for the classification of a dataset of texture images whose real classes are previously known. The classification precision is compared to other fractal descriptors known in the literature. The results confirm the efficiency of the proposed method. (C) 2012 Elsevier B.V. All rights reserved.

Climatic oscillations shape the phylogeographical structure of Atlantic Forest fire-eye antbirds (Aves: Thamnophilidae)

In the present study, mitochondrial (mt)DNA sequence data were used to examine the genetic structure of fire-eye antbirds (genus Pyriglena) along the Atlantic Forest and the predictions derived from the river hypothesis and from a Last Glacial Maximum Pleistocene refuge paleomodel were compared to explain the patterns of genetic variation observed in these populations. A total of 266 individuals from 45 populations were sampled over a latitudinal transect and a number of phylogeographical and population genetics analytical approaches were employed to address these questions. The pattern of mtDNA variation observed in fire-eye antbirds provides little support for the view that populations were isolated by the modern course of major Atlantic Forest rivers. Instead, the data provide stronger support for the predictions of the refuge model. These results add to the mounting evidence that climatic oscillations appear to have played a substantial role in shaping the phylogeographical structure and possibly the diversification of many taxa in this region. However, the results also illustrate the potential for more complex climatic history and historical changes in the geographical distribution of Atlantic Forest than envisioned by the refuge model. (c) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 900824.

Shape and function of the perineal muscles of viscacha (Lagostomus maximus)

Pieri N.C.G., Alicia M. Flamini A.M., Barbeito C.G., Casals J.B., Roque K.B., Favaron P.O., Miglino M.A. & Martins D.S. 2012. [Shape and function of the perineal muscles of viscacha (Lagostomus maximus).] Forma e funcao dos musculos perineais da viscacha (Lagostomus maximus). Pesquisa Veterinaria Brasileira 32(2):183-187. Departamento de Zootecnia, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de Sao Paulo, Av. Duque de Caxias Norte 225, Pirassununga, SP 13635-900, Brazil. E-mail: daniele@usp.br. Among the rodent species studied we can highlight the wide variation in the morphology of the male reproductive system. Thus, considering the ecological importance of rodents, and the large number and geographical representation of this animal, as well as shortages regarding the reproductive anatomy, we developed this study with viscacha, a South American histricomorph rodent. As this species has some very peculiar reproductive features, we described the gross anatomy of the perineal muscles and the role of copulatory behavior. The perineal region of viscacha is composed of five muscles, three of which are arranged in the superficial genitourinary diaphragm, as Musculus ischiocavernosus, M. bulbocavernosus and M. bulbospongiosus, and the muscles that lie at the pelvic diaphragm, M. levator ani and M. retractor penis. Therefore, we emphasize that the study of the pelvic floor in wild animals is of great value, then contribute to a better understanding of the mechanisms related to erection and ejaculation or collaborate with studies on the reproduction of animals.

Sesquiterpene Lactones with Anti-Hepatitis C Virus Activity Using Molecular Descriptors

Hepatitis C is a worldwide public health problem. The available therapies are limited by their partial effectiveness and with meaningful side-effects. Sesquiterpene lactones (SLs) are a group of natural products with a wide variety of chemical structures and biological activities associated. There are few studies about the influence of the molecular structure of SLs for the anti-hepatitis C virus activity. In the present work, SLs are investigated in a subgenomic RNA replicon assay system and were analyzed using multiple linear regression along with self-organizing maps with DRAGON descriptors in order to identify the structural requirements for their biological activity and to predict the inhibitory potency of SLs. Characteristics such as stereochemistry and electronic effects demonstrated to be important for their anti-HCV activity, and the SOM produced a clear separation betwenn active and inactive compounds. Therefore, it is possible to use this map as a filter for virtual screening to predict the anti-HCV activity of SLs.

Brazilian sardine (Sardinella brasiliensis Steindachner, 1879) spawning and nursery habitats: spatial-scale partitioning and multiscale relationships with thermohaline descriptors

We provide a detailed account of the spatial structure of the Brazilian sardine (Sardinella brasiliensis) spawning and nursery habitats, using ichthyoplankton data from nine surveys (1976-1993) covering the Southeastern Brazilian Bight (SBB). The spatial variability of sardine eggs and larvae was partitioned into predefined spatial-scale classes (broad scale, 200-500 km; medium scale, 50-100 km; and local scale, <50 km). The relationship between density distributions at both developmental stages and environmental descriptors (temperature and salinity) was also explored within these spatial scales. Spatial distributions of sardine eggs were mostly structured on medium and local scales, while larvae were characterized by broad-and medium-scale distributions. Broad-and medium-scale surface temperatures were positively correlated with sardine densities, for both developmental stages. Correlations with salinity were predominantly negative and concentrated on a medium scale. Broad-scale structuring might be explained by mesoscale processes, such as pulsing upwelling events and Brazil Current meandering at the northern portion of the SBB, while medium-scale relationships may be associated with local estuarine outflows. The results indicate that processes favouring vertical stability might regulate the spatial extensions of suitable spawning and nursery habitats for the Brazilian sardine.