Statistics and kinetics of single-molecule electron transfer dynamics in complex environments: A simulation model study

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

Variation in mandible shape in Thrichomys apereoides (Mammalia: Rodentia): Geometric analysis of a complex morphological structure

The model of development and evolution of complex morphological structures conceived by Atchley and Hall in 1991 (Biol. Rev. 66:101-157), which establishes that changes at the macroscopic, morphogenetic level can be statistically detected as variation in skeletal units at distinct scales, was applied in combination with the formalism of geometric morphometrics to study variation in mandible shape among populations of the rodent species Thrichomys apereoides. The thin-plate spline technique produced geometric descriptors of shape derived from anatomical landmarks in the mandible, which we used with graphical and inferential approaches to partition the contribution of global and localized components to the observed differentiation in mandible shape. A major pattern of morphological differentiation in T. apereoides is attributable to localized components of shape at smaller geometric scales associated with specific morphogenetic units of the mandible. On the other hand, a clinal trend of variation is associated primarily with localized components of shape at larger geometric scales. Morphogenetic mechanisms assumed to be operating to produce the observed differentiation in the specific units of the mandible include mesenchymal condensation differentiation, muscle hypertrophy, and tooth growth. Perspectives for the application of models of morphological evolution and geometric morphometrics to morphologically based systematic biology are considered.

Assessing the above-ground biomass of a complex tropical rainforest using a canopy crane

Current estimates of the total biomass in tropical rainforests vary considerably; this is due in large part to the different approaches that are used to calculate biomass. In this study we have used a canopy crane to measure the tree architectures in a 1 ha plot of complex mesophyll vine forest at Cape Tribulation, Australia. Methods were developed to measure and calculate the crown and stem biomass of six major species of tree and palm (Alstonia scholaris (Apocynaceae), Cleistanthus myrianthus (Euphorbiaceae), Endiandra microneura (Lauraceae), Myristica insipida (Myristicaceae), Acmena graveolens (Myrtaceae), Normanbya normanbyi (Arecaceae)) using the unique access provided by the crane. This has allowed the first non-destructive biomass estimate to be carried out for a forest of this type. Allometric equations which relate tree biomass to the measured variable 'diameter at breast height' were developed for the six species, and a general equation was also developed for trees on the plot. The general equation was similar in form to equations developed for tropical rainforests in Brazil and New Guinea. The species equations were applied at the level of families, the generalized equation was applied to the remaining species which allowed the biomass of a total of 680 trees to be calculated. This has provided a current estimate of 270 t ha-1 above-ground biomass at the Australian Canopy Crane site; a value comparable to lowland rainforests in Panama and French Guiana. Using the same tree database seven alternative allometric equations (literature equations for tropical rainforests) were used to calculate the site biomass, the range was large (252-446 t ha-1) with only three equations providing estimates within 34 t ha-1 (12.5%) of the site value. Our use of multiple species-specific allometric equations has provided a site estimate only slightly larger (1%) than that obtained using allometric equations developed specifically for tropical wet rainforests. We have demonstrated that it is possible to non-destructively measure the biomass in a complex forest using an on-site canopy crane. In conjunction the development of crown maps and a detailed tree architecture database allows changes in forest structure to be followed quantitatively. © 2007 Ecological Society of Australia.

Diversity of social wasps on semideciduous seasonal forest fragments with different surrounding matrix in Brazil

We surveyed social wasps (Polistinae) present in forest fragments of northwest of So Paulo state with different surroundings composed of a matrix of citrus crops and sugarcane in the expectation that the former matrix would be more diverse than the latter. We collected specimens actively using attractive liquids. We obtained 20 species in Magda, 13 in Bebedouro, 13 in Mato, and 19 in Barretos. The most common genus was Agelaia in all of the areas. The greatest Shannon-Wiener index of diversity was obtained in Magda (H' = 2.12). Species such as Brachygastra moebiana, Metapolybia docilis, Mischocyttarus ignotus, M. paulistanus and M. consimilis had not been recorded on recent surveys in the state. Furthermore M. consimilis is a new record for the state. We concluded that, with our data, a relation between the occurrence of social wasps and the surrounding matrix was not detected. © 2011 Getulio Minoru Tanaka Junior and Fernando Barbosa Noll.

The evolution of behavioural systems: a study of grooming in rodents

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Markovian versus non-Markovian stochastic quantization of a complex-action model

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Complex modal analysis of a slender vertical rotor by finite elements method

In this paper, natural frequencies were analyzed (axial, torsional and flexural) and frequency response of a vertical rotor with a hard disk at the edge through the classical modal and complex analysis. The equation that rules the movement was obtained through the Lagrangian formulation. The model considered the effects of bending, torsion and axial deformation of the shaft, besides the gravitational and gyroscopic effects. The finite element method was used to discretize the structure into hollow cylindrical elements with 12 degrees of freedom. Mass, stiffness and gyroscopic matrices were explained consistently. The classical modal analysis, usually applied to stationary structures, does not consider an important characteristic of rotating machinery which are the methods of forward and backward whirl. Initially, through the traditional modal analysis, axial and torsional natural frequencies were obtained in a static shaft, since they do not suffer the influence of gyroscopic effects. Later research was performed by complex modal analysis. This type of tool, based on the use of complex coordinates to describe the dynamic behavior of rotating shaft, allows the decomposition of the system in two submodes, backward and forward. Thus, it is possible to clearly visualize that the orbit and direction of the precessional motion around the line of the rotating shaft is not deformed. A finite element program was developed using MATLAB (TM) and numerical simulations were performed to validate this model. Natural frequencies and directional frequency forced response (dFRF) were obtained using the complex modal analysis for a simple vertical rotor and also for a typical drill string used in the construction of oil wells.

Changes in cells's secretory organelles and extracellular matrix during endochondral ossification in the mandibular condyle of the growing rat

The mandibular condyle from 20-day-old rats was examined in the electron microscope with particular attention to intracellular secretory granules and extracellular matrix. Moreover, type II collagen was localized by an immunoperoxidase method. The condyle has been divided into five layers: (1) the most superficial, articular layer, (2) polymorphic cell layer, (3) flattened cell layer, (4) upper hypertrophic, and (5) lower hypertrophic cell layers. In the articular layer, the cells seldom divide, but in the polymorphic layer and upper part of the flattened cell layer, mitosis gives rise to new cells. In these layers, cells produce two types of secretory granules, usually in distinct stacks of the Golgi apparatus; type a, cylindrical granules, in which 300-nm-long threads are packed in bundles which appear lucent after formaldehyde fixation; and type b, spherical granules loaded with short, dotted filaments. The matrix is composed of thick banded lucent fibrils in a loose feltwork of short, dotted filaments. The cells arising from mitosis undergo endochondral differentiation, which begins in the lower part of the flattened cell layer and is completed in the upper hypertrophic cell layer; it is followed by gradual cell degeneration in the lower hypertrophic cell layer. The cells produce two main types of secretory granules: type b as above; and type c, ovoid granules containing 300-nm-long threads associated with short, dotted filaments. A possibly different secretory granule, type d, dense and cigar-shaped, is also produced. The matrix is composed of thin banded fibrils in a dense feltwork. In the matrix of the superficial layers, the lucency of the fibrils indicated that they were composed of collagen I, whereas the lucency of the cylindrical secretory granules suggested that they transported collagen I precursors to the matrix. Moreover, the use of ruthenium red indicated that the feltwork was composed of proteoglycan; the dotted filaments packed in spherical granules were similar to, and presumably the source of, the matrix feltwork. The superficial layers did not contain collagen II and were collectively referred to as perichondrium. In the deep layers, the ovoid secretory granules displayed collagen II antigenicity and were likely to transport precursors of this collagen to the matrix, where it appeared in the thin banded fibrils. That these granules also carried proteoglycan to the matrix was suggested by their content of short dotted filaments. Thus the deep layers contained collagen II and proteoglycan as in cartilage; they were collectively referred to as the hyaline cartilage region.

Complex modal analysis of a vertical rotor through finite element method

Natural frequencies were analyzed (axial, torsional and flexural) and frequency response of a vertical rotor with a hard disk at the edge through the classical and complex modal analysis. The mathematical modeling was based on the theory of Euler-Bernoulli beam. The equation that rules the movement was obtained through the Lagrangian formulation. The model considered the effects of bending, torsion and axial deformation of the shaft, besides the gravitational and gyroscopic effects. The finite element method was used to discretize the structure into hollow cylindrical elements with 12 degrees of freedom. Mass, stiffness and gyroscopic matrices were explained consistently. This type of tool, based on the use of complex coordinates to describe the dynamic behavior of rotating shaft, allows the decomposition of the system in two submodes, backward and forward. Thus, it is possible to clearly visualize that the orbit and direction of the precessional motion around the line of the rotating shaft is not deformed. A finite element program was developed using Matlab ®, and numerical simulations were performed to validate this model.

Complex networks analysis of language complexity

Methods from statistical physics, such as those involving complex networks, have been increasingly used in the quantitative analysis of linguistic phenomena. In this paper, we represented pieces of text with different levels of simplification in co-occurrence networks and found that topological regularity correlated negatively with textual complexity. Furthermore, in less complex texts the distance between concepts, represented as nodes, tended to decrease. The complex networks metrics were treated with multivariate pattern recognition techniques, which allowed us to distinguish between original texts and their simplified versions. For each original text, two simplified versions were generated manually with increasing number of simplification operations. As expected, distinction was easier for the strongly simplified versions, where the most relevant metrics were node strength, shortest paths and diversity. Also, the discrimination of complex texts was improved with higher hierarchical network metrics, thus pointing to the usefulness of considering wider contexts around the concepts. Though the accuracy rate in the distinction was not as high as in methods using deep linguistic knowledge, the complex network approach is still useful for a rapid screening of texts whenever assessing complexity is essential to guarantee accessibility to readers with limited reading ability. Copyright (c) EPLA, 2012

Word sense disambiguation via high order of learning in complex networks

Complex networks have been employed to model many real systems and as a modeling tool in a myriad of applications. In this paper, we use the framework of complex networks to the problem of supervised classification in the word disambiguation task, which consists in deriving a function from the supervised (or labeled) training data of ambiguous words. Traditional supervised data classification takes into account only topological or physical features of the input data. On the other hand, the human (animal) brain performs both low- and high-level orders of learning and it has facility to identify patterns according to the semantic meaning of the input data. In this paper, we apply a hybrid technique which encompasses both types of learning in the field of word sense disambiguation and show that the high-level order of learning can really improve the accuracy rate of the model. This evidence serves to demonstrate that the internal structures formed by the words do present patterns that, generally, cannot be correctly unveiled by only traditional techniques. Finally, we exhibit the behavior of the model for different weights of the low- and high-level classifiers by plotting decision boundaries. This study helps one to better understand the effectiveness of the model. Copyright (C) EPLA, 2012

Discriminating Different Classes of Biological Networks by Analyzing the Graphs Spectra Distribution

The brain's structural and functional systems, protein-protein interaction, and gene networks are examples of biological systems that share some features of complex networks, such as highly connected nodes, modularity, and small-world topology. Recent studies indicate that some pathologies present topological network alterations relative to norms seen in the general population. Therefore, methods to discriminate the processes that generate the different classes of networks (e. g., normal and disease) might be crucial for the diagnosis, prognosis, and treatment of the disease. It is known that several topological properties of a network (graph) can be described by the distribution of the spectrum of its adjacency matrix. Moreover, large networks generated by the same random process have the same spectrum distribution, allowing us to use it as a "fingerprint". Based on this relationship, we introduce and propose the entropy of a graph spectrum to measure the "uncertainty" of a random graph and the Kullback-Leibler and Jensen-Shannon divergences between graph spectra to compare networks. We also introduce general methods for model selection and network model parameter estimation, as well as a statistical procedure to test the nullity of divergence between two classes of complex networks. Finally, we demonstrate the usefulness of the proposed methods by applying them to (1) protein-protein interaction networks of different species and (2) on networks derived from children diagnosed with Attention Deficit Hyperactivity Disorder (ADHD) and typically developing children. We conclude that scale-free networks best describe all the protein-protein interactions. Also, we show that our proposed measures succeeded in the identification of topological changes in the network while other commonly used measures (number of edges, clustering coefficient, average path length) failed.

Structure-semantics interplay in complex networks and its effects on the predictability of similarity in texts

The classification of texts has become a major endeavor with so much electronic material available, for it is an essential task in several applications, including search engines and information retrieval. There are different ways to define similarity for grouping similar texts into clusters, as the concept of similarity may depend on the purpose of the task. For instance, in topic extraction similar texts mean those within the same semantic field, whereas in author recognition stylistic features should be considered. In this study, we introduce ways to classify texts employing concepts of complex networks, which may be able to capture syntactic, semantic and even pragmatic features. The interplay between various metrics of the complex networks is analyzed with three applications, namely identification of machine translation (MT) systems, evaluation of quality of machine translated texts and authorship recognition. We shall show that topological features of the networks representing texts can enhance the ability to identify MT systems in particular cases. For evaluating the quality of MT texts, on the other hand, high correlation was obtained with methods capable of capturing the semantics. This was expected because the golden standards used are themselves based on word co-occurrence. Notwithstanding, the Katz similarity, which involves semantic and structure in the comparison of texts, achieved the highest correlation with the NIST measurement, indicating that in some cases the combination of both approaches can improve the ability to quantify quality in MT. In authorship recognition, again the topological features were relevant in some contexts, though for the books and authors analyzed good results were obtained with semantic features as well. Because hybrid approaches encompassing semantic and topological features have not been extensively used, we believe that the methodology proposed here may be useful to enhance text classification considerably, as it combines well-established strategies. (c) 2012 Elsevier B.V. All rights reserved.

Growth kinetics of CdS in germanium oxide glassy matrix

In the present work we revisit the size data of CdS microcrystals previously collected in the glassy matrix of Germanium oxide. The CdS clusters analyzed using electron microscopy images have shown a wurtzite structure. The mean average radius, dispersion and volume evaluated from the histograms showed good agreement for t(1/3), t(2/3) and t laws, respectively. We observed that the amount of microcrystals remains constant throughout the heat treatment process, as well as that the radii distribution has a lower limit and increases with heat treatment. The distribution of radii follows a distribution similar to the Lifshitz-Slyozov-Wagner distribution limited in the origin. Discussions led to the conclusion that the growth of CdS is a process that occurs after the fluctuating nucleation and coalescence phases. We then analyze the growth process, assuming that the evaporation is overcome by the precipitation rate, stabilizing all clusters with respect to dissolution back into the matrix. The problem was simplified neglecting anisotropy and the assuming a spherical shape for clusters and particles. The low interface tension was described in terms of an empirical potential barrier in the surface of the cluster. The growth dynamics developed considering that the number of clusters remains constant, and that the minimum size of these clusters grow with time, as the first order approximation showed a good agreement with the flaw. (C) 2012 Elsevier B.V. All rights reserved.

WEAR OF MATRIX OVERDENTURE ATTACHMENTS AFTER ONE TO EIGHT YEARS OF CLINICAL USE

Statement of problem. Matrices of unsplinted attachment systems are generally reported to be the weak component of implant overdentures, often requiring frequent maintenance. Clinical wear results in reduced retention of the prosthesis, requiring activation or renewal of the matrix to restore the initial level of retention. Purpose. The purpose of this retrospective study was to measure the wear of the matrix of a ball attachment after various periods of clinical wear. Material and methods. Seventy specimens of 3 groups of matrices of ball attachments that had been in use for mean periods of 12.3 months (1Y group, n=26), 39.0 months (3Y group, n=28) and 95.6 months (8Y group, n=16) were retrieved from 35 patients (2 specimens per patient) and measured on a coordinate measuring machine equipped with a touch trigger probe. Ten unused matrices were used as controls (CTRL group). The external and internal matrix diameters and deviations from circularity were measured. For the various time periods, the decreases in matrix thickness were calculated and compared with controls. Kruskal-Wallis 1-way ANOVA by ranks, followed by the Mann-Whitney post hoc tests, were conducted to test for differences in median values among groups (alpha=.05). Results. For the internal upper diameter of the matrices tested, the Kruskal-Wallis and Mann-Whitney tests revealed significant differences for the 3 groups compared to the controls. For group 1Y, a significant difference (P<.001) of the internal upper diameter was found compared to the CTRL group. Compared to the controls, the nonparametric analyses for groups 3Y and 8Y showed significant differences for the internal upper diameter (P<.001) and deviations from circularity (P<.001). For groups 1Y, 3Y and 8Y, matrix thickness losses were 07, 47 and 70 pm, respectively. Conclusions. Within the limitations of this study, it was observed that one year of clinical wear had limited effect on the ball attachment matrices. Three to 8 years of clinical use resulted in a significant decrease of matrix thickness, especially at the tip of the retentive lamellae. (J Prosthet Dent 2012;107:191-198)