Structural analysis of SNARE motifs from sea perch, Lateolabrax japonicus by computerized approaches

Three cDNA sequences encoding four SNARE (N-ethylmaleimide-sensitive fusion protein attachment protein receptors) motifs were cloned from sea perch, and the deduced peptide sequences were analyzed for structural prediction by using 14 different web servers and softwares. The "ionic layer" structure, the three dimensional extension and conformational characters of the SNARE 7S core complex by using bioinformatics approaches were compared respectively with those from mammalian X-ray crystallographic investigations. The result suggested that the formation and stabilization of fish SNARE core complex might be driven by hydrophobic association, hydrogen bond among R group of core amino acids and electrostatic attraction at molecular level. This revealed that the SNARE proteins interaction of the fish may share the same molecular mechanism with that of mammal, indicating the universality and solidity of SNARE core complex theory. This work is also an attempt to get the protein 3D structural information which appears to be similar to that obtained through X-ray crystallography, only by using computerized approaches. (C) 2007 Elsevier Ltd. All rights reserved.

Impact of difference accuracy on computational properties of vertical grids for a nonhydrostatic model

Starting from nonhydrostatic Boussinesq approximation equations, a general method is introduced to deduce the dispersion relationships. A comparative investigation is performed on inertia-gravity wave with horizontal lengths of 100, 10 and 1 km. These are examined using the second-order central difference scheme and the fourth-order compact difference scheme on vertical grids that are currently available from the perspectives of frequency, horizontal and vertical component of group velocity. These findings are compared to analytical solutions. The obtained results suggest that whether for the second-order central difference scheme or for the fourth-order compact difference scheme, Charny-Phillips and Lorenz ( L) grids are suitable for studying waves at the above-mentioned horizontal scales; the Lorenz time-staggered and Charny-Phillips time staggered (CPTS) grids are applicable only to the horizontal scales of less than 10 km, and N grid ( unstaggered grid) is unsuitable for simulating waves at any horizontal scale. Furthermore, by using fourth-order compact difference scheme with higher difference precision, the errors of frequency and group velocity in horizontal and vertical directions produced on all vertical grids in describing the waves with horizontal lengths of 1, 10 and 100 km cannot inevitably be decreased. So in developing a numerical model, the higher-order finite difference scheme, like fourth-order compact difference scheme, should be avoided as much as possible, typically on L and CPTS grids, since it will not only take many efforts to design program but also make the calculated group velocity in horizontal and vertical directions even worse in accuracy.

Networked tourism: from world destinations to inter-organizations

Na última década, a referência ao conceito de redes cresceu rapidamente entre a literatura sobre turismo, geralmente aplicado a tópicos como as interorganizações, estrutura de multi-destinos, espaços de Turismo online, entre outros. O conceito de rede difundiu-se na natureza e na sociedade, em áreas que vão desde a Biologia à Medicina, ou da Economia à Gestão, e o conhecimento sobre redes tem vindo a impulsionar uma teoria comum para facilitar a compreensão de diferentes sistemas complexos e a representação das ligações entre organizações, acções, bens, proteínas ou pessoas. A tese teve como propósito o encontro de um eixo comum entre dois campos férteis de investigação através de uma revisão teórica sistemática. A investigação sobre redes complexas é um campo recente na Física que tem vindo a desenvolver-se bastante na última década com fortes aplicações interdisciplinares. Por outro lado, a análise de redes sociais é uma área de investigação activa em Sociologia e Economia há bastante tempo. O estudo das implicações das redes complexas para a ciência das redes de turismo é uma área promissora já com resultados fascinantes. A tese tem três resultados principais. Primeiro, traz conhecimento das ricas áreas de conhecimento sobre redes complexas e redes sociais. Em segundo lugar, apresenta modelos evolutivos que melhor se adaptam às chegadas turísticas internacionais. Como se organizam as redes sociais? Como é que os indivíduos escolhem os seus destinos de viagem? Estes são exemplos de questões que serão abordadas na tese. Em terceiro lugar, discute resultados que fazem notar comportamentos comuns entre redes em turismo e outras redes reais. O que é comum a todas as redes na natureza? Adicionalmente, os padrões encontrados entre os destinos turísticos mostram um comportamento não social, com destinos mais característicos de redes económicas e sistemas tecnológicos que questionam a faceta social do sector do turismo. Por acréscimo, a rede de transportes aéreos e a rede de turismo mostram diferenças consideráveis que se podem dever a razões políticas ou outras que provavelmente explicam o aumento da utilização de voos charters.

The oscillatory bioelectrical signal from plants explained by a simulated electrical model and tested using Lempel-Ziv complexity

This paper demonstrates the oscillatory characteristics of electrical signals acquired from two ornamental plant types (Epipremnum pinnatum and Philodendron scandens - Family Araceae), using a noninvasive acquisition system. The electrical signal was recorded using Ag/AgCl superficial electrodes inside a Faraday cage. The presence of the oscillatory electric generator was shown using a classical power spectral density. The Lempel and Ziv complexity measurement showed that the plant signal was not noise despite its nonlinear behavior. The oscillatory characteristics of the signal were explained using a simulated electrical model that establishes that for a frequency range from 5 to 15 Hz, the oscillatory characteristic is higher than for other frequency ranges. All results show that non-invasive electrical plant signals can be acquired with improvement of signal-to-noise ratio using a Faraday cage, and a simple electrical model is able to explain the electrical signal being generated. (C) 2010 Elsevier B.V. All rights reserved.

Tidal friction in close-in satellites and exoplanets: The Darwin theory re-visited

This report is a review of Darwin`s classical theory of bodily tides in which we present the analytical expressions for the orbital and rotational evolution of the bodies and for the energy dissipation rates due to their tidal interaction. General formulas are given which do not depend on any assumption linking the tidal lags to the frequencies of the corresponding tidal waves (except that equal frequency harmonics are assumed to span equal lags). Emphasis is given to the cases of companions having reached one of the two possible final states: (1) the super-synchronous stationary rotation resulting from the vanishing of the average tidal torque; (2) capture into the 1:1 spin-orbit resonance (true synchronization). In these cases, the energy dissipation is controlled by the tidal harmonic with period equal to the orbital period (instead of the semi-diurnal tide) and the singularity due to the vanishing of the geometric phase lag does not exist. It is also shown that the true synchronization with non-zero eccentricity is only possible if an extra torque exists opposite to the tidal torque. The theory is developed assuming that this additional torque is produced by an equatorial permanent asymmetry in the companion. The results are model-dependent and the theory is developed only to the second degree in eccentricity and inclination (obliquity). It can easily be extended to higher orders, but formal accuracy will not be a real improvement as long as the physics of the processes leading to tidal lags is not better known.

Chirikov diffusion in the asteroidal three-body resonance (5,-2,-2)

The theory of diffusion in many-dimensional Hamiltonian system is applied to asteroidal dynamics. The general formulation developed by Chirikov is applied to the NesvornA1/2-Morbidelli analytic model of three-body (three-orbit) mean-motion resonances (Jupiter-Saturn-asteroid). In particular, we investigate the diffusion along and across the separatrices of the (5, -2, -2) resonance of the (490) Veritas asteroidal family and their relationship to diffusion in semi-major axis and eccentricity. The estimations of diffusion were obtained using the Melnikov integral, a Hadjidemetriou-type sympletic map and numerical integrations for times up to 10(8) years.

Genetic algorithm inversion of the average 1D crustal structure using local and regional earthquakes

Knowing the best 1D model of the crustal and upper mantle structure is useful not only for routine hypocenter determination, but also for linearized joint inversions of hypocenters and 3D crustal structure, where a good choice of the initial model can be very important. Here, we tested the combination of a simple GA inversion with the widely used HYPO71 program to find the best three-layer model (upper crust, lower crust, and upper mantle) by minimizing the overall P- and S-arrival residuals, using local and regional earthquakes in two areas of the Brazilian shield. Results from the Tocantins Province (Central Brazil) and the southern border of the Sao Francisco craton (SE Brazil) indicated an average crustal thickness of 38 and 43 km, respectively, consistent with previous estimates from receiver functions and seismic refraction lines. The GA + HYPO71 inversion produced correct Vp/Vs ratios (1.73 and 1.71, respectively), as expected from Wadati diagrams. Tests with synthetic data showed that the method is robust for the crustal thickness, Pn velocity, and Vp/Vs ratio when using events with distance up to about 400 km, despite the small number of events available (7 and 22, respectively). The velocities of the upper and lower crusts, however, are less well constrained. Interestingly, in the Tocantins Province, the GA + HYPO71 inversion showed a secondary solution (local minimum) for the average crustal thickness, besides the global minimum solution, which was caused by the existence of two distinct domains in the Central Brazil with very different crustal thicknesses. (C) 2010 Elsevier Ltd. All rights reserved.

Programs to compute magnetization to density ratio and the magnetization inclination from 3-D gravity and magnetic anomalies

Vector field formulation based on the Poisson theorem allows an automatic determination of rock physical properties (magnetization to density ratio-MDR-and the magnetization inclination-MI) from combined processing of gravity and magnetic geophysical data. The basic assumptions (i.e., Poisson conditions) are: that gravity and magnetic fields share common sources, and that these sources have a uniform magnetization direction and MDR. In addition, the previously existing formulation was restricted to profile data, and assumed sufficiently elongated (2-D) sources. For sources that violate Poisson conditions or have a 3-D geometry, the apparent values of MDR and MI that are generated in this way have an unclear relationship to the actual properties in the subsurface. We present Fortran programs that estimate MDR and MI values for 3-D sources through processing of gridded gravity and magnetic data. Tests with simple geophysical models indicate that magnetization polarity can be successfully recovered by MDR-MI processing, even in cases where juxtaposed bodies cannot be clearly distinguished on the basis of anomaly data. These results may be useful in crustal studies, especially in mapping magnetization polarity from marine-based gravity and magnetic data. (c) 2007 Elsevier Ltd. All rights reserved.

Consistency in approximate entropy given by a volumetric estimate

Non-linear methods for estimating variability in time-series are currently of widespread use. Among such methods are approximate entropy (ApEn) and sample approximate entropy (SampEn). The applicability of ApEn and SampEn in analyzing data is evident and their use is increasing. However, consistency is a point of concern in these tools, i.e., the classification of the temporal organization of a data set might indicate a relative less ordered series in relation to another when the opposite is true. As highlighted by their proponents themselves, ApEn and SampEn might present incorrect results due to this lack of consistency. In this study, we present a method which gains consistency by using ApEn repeatedly in a wide range of combinations of window lengths and matching error tolerance. The tool is called volumetric approximate entropy, vApEn. We analyze nine artificially generated prototypical time-series with different degrees of temporal order (combinations of sine waves, logistic maps with different control parameter values, random noises). While ApEn/SampEn clearly fail to consistently identify the temporal order of the sequences, vApEn correctly do. In order to validate the tool we performed shuffled and surrogate data analysis. Statistical analysis confirmed the consistency of the method. (C) 2008 Elsevier Ltd. All rights reserved.

Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

Efficiency issues of evolutionary k-means

One of the top ten most influential data mining algorithms, k-means, is known for being simple and scalable. However, it is sensitive to initialization of prototypes and requires that the number of clusters be specified in advance. This paper shows that evolutionary techniques conceived to guide the application of k-means can be more computationally efficient than systematic (i.e., repetitive) approaches that try to get around the above-mentioned drawbacks by repeatedly running the algorithm from different configurations for the number of clusters and initial positions of prototypes. To do so, a modified version of a (k-means based) fast evolutionary algorithm for clustering is employed. Theoretical complexity analyses for the systematic and evolutionary algorithms under interest are provided. Computational experiments and statistical analyses of the results are presented for artificial and text mining data sets. (C) 2010 Elsevier B.V. All rights reserved.

Using non-homogeneous Poisson models with multiple change-points to estimate the number of ozone exceedances in Mexico City

In this paper, we consider some non-homogeneous Poisson models to estimate the probability that an air quality standard is exceeded a given number of times in a time interval of interest. We assume that the number of exceedances occurs according to a non-homogeneous Poisson process (NHPP). This Poisson process has rate function lambda(t), t >= 0, which depends on some parameters that must be estimated. We take into account two cases of rate functions: the Weibull and the Goel-Okumoto. We consider models with and without change-points. When the presence of change-points is assumed, we may have the presence of either one, two or three change-points, depending of the data set. The parameters of the rate functions are estimated using a Gibbs sampling algorithm. Results are applied to ozone data provided by the Mexico City monitoring network. In a first instance, we assume that there are no change-points present. Depending on the adjustment of the model, we assume the presence of either one, two or three change-points. Copyright (C) 2009 John Wiley & Sons, Ltd.

Investigation of a new GRASP-based clustering algorithm applied to biological data

A large amount of biological data has been produced in the last years. Important knowledge can be extracted from these data by the use of data analysis techniques. Clustering plays an important role in data analysis, by organizing similar objects from a dataset into meaningful groups. Several clustering algorithms have been proposed in the literature. However, each algorithm has its bias, being more adequate for particular datasets. This paper presents a mathematical formulation to support the creation of consistent clusters for biological data. Moreover. it shows a clustering algorithm to solve this formulation that uses GRASP (Greedy Randomized Adaptive Search Procedure). We compared the proposed algorithm with three known other algorithms. The proposed algorithm presented the best clustering results confirmed statistically. (C) 2009 Elsevier Ltd. All rights reserved.

Revealing the whiteboard to blind students: An inclusive approach to provide mediation in synchronous e-learning activities

Promoting the inclusion of students with disabilities in e-learning systems has brought many challenges for researchers and educators. The use of synchronous communication tools such as interactive whiteboards has been regarded as an obstacle for inclusive education. In this paper, we present the proposal of an inclusive approach to provide blind students with the possibility to participate in live learning sessions with whiteboard software. The approach is based on the provision of accessible textual descriptions by a live mediator. With the accessible descriptions, students are able to navigate through the elements and explore the content of the class using screen readers. The method used for this study consisted of the implementation of a software prototype within a virtual learning environment and a case study with the participation of a blind student in a live distance class. The results from the case study have shown that this approach can be very effective, and may be a starting point to provide blind students with resources they had previously been deprived from. The proof of concept implemented has shown that many further possibilities may be explored to enhance the interaction of blind users with educational content in whiteboards, and further pedagogical approaches can be investigated from this proposal. (C) 2009 Elsevier Ltd. All rights reserved.

Alignment-based extraction of multiword expressions

Due to idiosyncrasies in their syntax, semantics or frequency, Multiword Expressions (MWEs) have received special attention from the NLP community, as the methods and techniques developed for the treatment of simplex words are not necessarily suitable for them. This is certainly the case for the automatic acquisition of MWEs from corpora. A lot of effort has been directed to the task of automatically identifying them, with considerable success. In this paper, we propose an approach for the identification of MWEs in a multilingual context, as a by-product of a word alignment process, that not only deals with the identification of possible MWE candidates, but also associates some multiword expressions with semantics. The results obtained indicate the feasibility and low costs in terms of tools and resources demanded by this approach, which could, for example, facilitate and speed up lexicographic work.