New insights into host-parasite ubiquitin proteome dynamics in P. falciparum infected red blood cells using a TUBEs-MS approach

Malaria, caused by Plasmodium falciparum (P. falciparum), ranks as one of the most baleful infectious diseases worldwide. New antimalarial treatments are needed to face existing or emerging drug resistant strains. Protein degradation appears to play a significant role during the asexual intraerythrocytic developmental cycle (IDC) of P. falciparum. Inhibition of the ubiquitin proteasome system (UPS), a major intracellular proteolytic pathway, effectively reduces infection and parasite replication. P. falciparum and erythrocyte UPS coexist during IDC but the nature of their relationship is largely unknown. We used an approach based on Tandem Ubiquitin-Binding Entities (TUBEs) and 1D gel electrophoresis followed by mass spectrometry to identify major components of the TUBEs-associated ubiquitin proteome of both host and parasite during ring, trophozoite and schizont stages. Ring-exported protein (REX1), a P. falciparum protein located in Maurer's clefts and important for parasite nutrient import, was found to reach a maximum level of ubiquitylation in trophozoites stage. The Homo sapiens (H. sapiens) TUBEs associated ubiquitin proteome decreased during the infection, whereas the equivalent P. falciparum TUBEs-associated ubiquitin proteome counterpart increased. Major cellular processes such as DNA repair, replication, stress response, vesicular transport and catabolic events appear to be regulated by ubiquitylation along the IDC P. falciparum infection.

Toplological Entropy in the Syncronization of Piecewise Linear and Monotone Maps. Coupled Duffing Oscillators

In this paper is presented a relationship between the synchronization and the topological entropy. We obtain the values for the coupling parameter, in terms of the topological entropy, to achieve synchronization of two unidirectional and bidirectional coupled piecewise linear maps. In addition, we prove a result that relates the synchronizability of two m-modal maps with the synchronizability of two conjugated piecewise linear maps. An application to the unidirectional and bidirectional coupled identical chaotic Duffing equations is given. We discuss the complete synchronization of two identical double-well Duffing oscillators, from the point of view of symbolic dynamics. Working with Poincare cross-sections and the return maps associated, the synchronization of the two oscillators, in terms of the coupling strength, is characterized.

Dynamical behaviour on the parameter space: new populational growth models proportional to beta densities

We present new populational growth models, generalized logistic models which are proportional to beta densities with shape parameters p and 2, where p > 1, with Malthusian parameter r. The complex dynamical behaviour of these models is investigated in the parameter space (r, p), in terms of topological entropy, using explicit methods, when the Malthusian parameter r increases. This parameter space is split into different regions, according to the chaotic behaviour of the models.

Pricing intraday dynamics across EUAS and CERS markets

The relative contribution of European Union Allowances (EUAs) and Certified Emission Reductions (CERs) to the price discovery of their common true value has been empirically studied using daily data with inconclusive results. In this paper, we study the short-run and long-run price dynamics between EUAs and CERs future contracts using intraday data. We report a bidirectional feedback causality relationship both in the short-run and in the long-run, with the EUA's market being the leader.

Entropy analysis of DNA code dynamics in human chromosomes

Deoxyribonucleic acid, or DNA, is the most fundamental aspect of life but present day scientific knowledge has merely scratched the surface of the problem posed by its decoding. While experimental methods provide insightful clues, the adoption of analysis tools supported by the formalism of mathematics will lead to a systematic and solid build-up of knowledge. This paper studies human DNA from the perspective of system dynamics. By associating entropy and the Fourier transform, several global properties of the code are revealed. The fractional order characteristics emerge as a natural consequence of the information content. These properties constitute a small piece of scientific knowledge that will support further efforts towards the final aim of establishing a comprehensive theory of the phenomena involved in life.

Fractional dynamics in DNA

This paper addresses the DNA code analysis in the perspective of dynamics and fractional calculus. Several mathematical tools are selected to establish a quantitative method without distorting the alphabet represented by the sequence of DNA bases. The association of Gray code, Fourier transform and fractional calculus leads to a categorical representation of species and chromosomes.

Autoinhibition of TBCB regulates EB1-mediated microtubule dynamics

Tubulin cofactors (TBCs) participate in the folding, dimerization, and dissociation pathways of the tubulin dimer. Among them, TBCB and TBCE are two CAP-Gly domain-containing proteins that together efficiently interact with and dissociate the tubulin dimer. In the study reported here we showed that TBCB localizes at spindle and midzone microtubules during mitosis. Furthermore, the motif DEI/M-COO− present in TBCB, which is similar to the EEY/F-COO− element characteristic of EB proteins, CLIP-170, and α-tubulin, is required for TBCE–TBCB heterodimer formation and thus for tubulin dimer dissociation. This motif is responsible for TBCB autoinhibition, and our analysis suggests that TBCB is a monomer in solution. Mutants of TBCB lacking this motif are derepressed and induce microtubule depolymerization through an interaction with EB1 associated with microtubule tips. TBCB is also able to bind to the chaperonin complex CCT containing α-tubulin, suggesting that it could escort tubulin to facilitate its folding and dimerization, recycling or degradation.

Symbolic dynamics and renormalization of non-autonomous k periodic dynamical systems

The purpose of this paper was to introduce the symbolic formalism based on kneading theory, which allows us to study the renormalization of non-autonomous periodic dynamical systems.

An Extension of Gompertzian Growth Dynamics Weibull and Frechet Models

In this work a new probabilistic and dynamical approach to an extension of the Gompertz law is proposed. A generalized family of probability density functions, designated by Beta* (p, q), which is proportional to the right hand side of the Tsoularis-Wallace model, is studied. In particular, for p = 2, the investigation is extended to the extreme value models of Weibull and Frechet type. These models, described by differential equations, are proportional to the hyper-Gompertz growth model. It is proved that the Beta* (2, q) densities are a power of betas mixture, and that its dynamics are determined by a non-linear coupling of probabilities. The dynamical analysis is performed using techniques of symbolic dynamics and the system complexity is measured using topological entropy. Generally, the natural history of a malignant tumour is reflected through bifurcation diagrams, in which are identified regions of regression, stability, bifurcation, chaos and terminus.

Reproductive dynamics of Sterna hirundinacea Lesson, 1831 in Ilha dos Cardos, Santa Catarina, Brazil

In this work, we intend to describe the reproductive dynamics of Sterna hirundinacea in an island fromSouth Brazil.We studied the reproductive biology of this species in its natural environment and provide data on their growth, survival, and reproductive success in Ilha dosCardos, SantaCatarina, South Brazil. Samplingswere carried out daily on the island throughout the reproductive seasons of 2003, 2005, and 2006 and the different stages of development of the chicks were characterized according to age, length of the beak, and plumage characteristics.We provide a basic equation Lm = 167.91 (1 – e −0.062t−(−0.23)) to determine the approximate age of individuals using their body mass. The main cause of chick mortality on the island was natural (63.17% in 2003, 81.41% in 2005, and 79.96% in 2006), whereas predation contributed to mortality in a proportion of 38.83% in 2003, 18.59% in 2005, and 20.04% in 2006.The absence in the area of the chicks’ main predator, Kelp gull (Larus dominicanus), the large number of chicks that reached the final stages of development, and their reproductive success demonstrate that Ilha dos Cardos is an important breeding site for the species in southern Brazil.

Imported and autochthonous cases in the dynamics of dengue epidemics in Brazil

OBJECTIVE: To estimate the basic reproduction number (R0) of dengue fever including both imported and autochthonous cases. METHODS: The study was conducted based on epidemiological data of the 2003 dengue epidemic in Brasília, Brazil. The basic reproduction number is estimated from the epidemic curve, fitting linearly the increase of initial cases. Aiming at simulating an epidemic with both autochthonous and imported cases, a "susceptible-infectious-resistant" compartmental model was designed, in which the imported cases were considered as an external forcing. The ratio between R0 of imported versus autochthonous cases was used as an estimator of real R0. RESULTS: The comparison of both reproduction numbers (only autochthonous versus all cases) showed that considering all cases as autochthonous yielded a R0 above one, although the real R0 was below one. The same results were seen when the method was applied on simulated epidemics with fixed R0. This method was also compared to some previous proposed methods by other authors and showed that the latter underestimated R0 values. CONCLUSIONS: It was shown that the inclusion of both imported and autochthonous cases is crucial for the modeling of the epidemic dynamics, and thus provides critical information for decision makers in charge of prevention and control of this disease.

Dynamics and orchestral effects in late Eighteenth-Century portuguese organ music: the works of José Marques e Silva (1782-1837) and the organs of António Xavier Machado e Cerveira (1756-1828)

A maioria dos órgãos históricos portugueses data dos finais do século XVIII ou do princípio do século XIX. Durante este período foi construído um invulgar número de instrumentos em Lisboa e nas áreas circundantes por António Xavier Machado e Cerveira (1756-1828) e outros organeiros menos prolíficos. O estudo desses órgãos, muitos dos quais (restaurados ou não) se encontram próximos das condições originais, permite a identificação de um tipo de instrumento com uma morfologia específica, claramente emancipada do chamado «órgão ibérico». No entanto, até muito recentemente, não era conhecida música que se adaptasse às idiossincrasisas daqueles instrumentos. O recente estudo das obras para órgão de José Marques e Silva (1782-1837) permitiu clarificar esta situação. Bem conhecido durante a sua vida como organista e compositor, José Marques e Silva foi um dos ultimos mestres do Seminário Patriarcal. A importância da sua produção musical reside não só num substancial número de obras com autoria firmemente estabelecida – escritas, na maior parte, para coro misto com acompanhamento de órgão obbligato – mas também na íntima relação entre a sua escrita e a morfologia dos órgãos construídos em Portugal durante a sua vida. Este artigo enfatiza a importância de José Marques e Silva (indubitavelmente, o mais significativo compositor português para órgão do seu tempo) sublinhando a relevância das suas obras para órgão solo, cujo uso extensivo de escrita idiomática e indicações de registação fazem delas um dos mais importantes documentos só início do século XIX sobre a prática organística em Portugal.

Fractional dynamics and MDS visualization of earthquake phenomena

This paper analyses earthquake data in the perspective of dynamical systems and fractional calculus (FC). This new standpoint uses Multidimensional Scaling (MDS) as a powerful clustering and visualization tool. FC extends the concepts of integrals and derivatives to non-integer and complex orders. MDS is a technique that produces spatial or geometric representations of complex objects, such that those objects that are perceived to be similar in some sense are placed on the MDS maps forming clusters. In this study, over three million seismic occurrences, covering the period from January 1, 1904 up to March 14, 2012 are analysed. The events are characterized by their magnitude and spatiotemporal distributions and are divided into fifty groups, according to the Flinn–Engdahl (F–E) seismic regions of Earth. Several correlation indices are proposed to quantify the similarities among regions. MDS maps are proven as an intuitive and useful visual representation of the complex relationships that are present among seismic events, which may not be perceived on traditional geographic maps. Therefore, MDS constitutes a valid alternative to classic visualization tools for understanding the global behaviour of earthquakes.

Multidimensional scaling analysis of the dynamics of a country economy

This paper analyzes the Portuguese short-run business cycles over the last 150 years and presents the multidimensional scaling (MDS) for visualizing the results. The analytical and numerical assessment of this long-run perspective reveals periods with close connections between the macroeconomic variables related to government accounts equilibrium, balance of payments equilibrium, and economic growth. The MDS method is adopted for a quantitative statistical analysis. In this way, similarity clusters of several historical periods emerge in the MDS maps, namely, in identifying similarities and dissimilarities that identify periods of prosperity and crises, growth, and stagnation. Such features are major aspects of collective national achievement, to which can be associated the impact of international problems such as the World Wars, the Great Depression, or the current global financial crisis, as well as national events in the context of broad political blueprints for the Portuguese society in the rising globalization process.

Fractional dynamics of genetic algorithms using hexagonal space tessellation

The paper formulates a genetic algorithm that evolves two types of objects in a plane. The fitness function promotes a relationship between the objects that is optimal when some kind of interface between them occurs. Furthermore, the algorithm adopts an hexagonal tessellation of the two-dimensional space for promoting an efficient method of the neighbour modelling. The genetic algorithm produces special patterns with resemblances to those revealed in percolation phenomena or in the symbiosis found in lichens. Besides the analysis of the spacial layout, a modelling of the time evolution is performed by adopting a distance measure and the modelling in the Fourier domain in the perspective of fractional calculus. The results reveal a consistent, and easy to interpret, set of model parameters for distinct operating conditions.