Phylogenetic relationship of dengue virus type 3 isolated in Brazil and Paraguay and global evolutionary divergence dynamics

Background: Dengue is the most important mosquito-borne viral disease worldwide. Dengue virus comprises four antigenically related viruses named dengue virus type 1 to 4 (DENV1-4). DENV-3 was re-introduced into the Americas in 1994 causing outbreaks in Nicaragua and Panama. DENV-3 was introduced in Brazil in 2000 and then spread to most of the Brazilian States, reaching the neighboring country, Paraguay in 2002. In this study, we have analyzed the phylogenetic relationship of DENV-3 isolated in Brazil and Paraguay with viruses isolated worldwide. We have also analyzed the evolutionary divergence dynamics of DENV-3 viruses. Results: The entire open reading frame (ORF) of thirteen DENV-3 isolated in Brazil (n = 9) and Paraguay (n = 4) were sequenced for phylogenetic analysis. DENV-3 grouped into three main genotypes (I, II and III). Several internal clades were found within each genotype that we called lineage and sub-lineage. Viruses included in this study belong to genotype III and grouped together with viruses isolated in the Americas within the lineage III. The Brazilian viruses were further segregated into two different sub-lineage, A and B, and the Paraguayan into the sub-lineage B. All three genotypes showed internal grouping. The nucleotide divergence was in average 6.7% for genotypes, 2.7% for lineages and 1.5% for sub-lineages. Phylogenetic trees constructed with any of the protein gene sequences showed the same segregation of the DENV-3 in three genotypes. Conclusion: Our results showed that two groups of DENV-3 genotypes III circulated in Brazil during 2002-2009, suggesting different events of introduction of the virus through different regions of the country. In Paraguay, only one group DENV-3 genotype III is circulating that is very closely related to the Brazilian viruses of sub-lineage B. Different degree of grouping can be observed for DENV-3 and each group showed a characteristic evolutionary divergence. Finally, we have observed that any protein gene sequence can be used to identify the virus genotype.

New Insights on Nontechnical Losses Characterization Through Evolutionary-Based Feature Selection

Although nontechnical losses automatic identification has been massively studied, the problem of selecting the most representative features in order to boost the identification accuracy and to characterize possible illegal consumers has not attracted much attention in this context. In this paper, we focus on this problem by reviewing three evolutionary-based techniques for feature selection, and we also introduce one of them in this context. The results demonstrated that selecting the most representative features can improve a lot of the classification accuracy of possible frauds in datasets composed by industrial and commercial profiles.

Modularity and evolutionary constraints in a baculovirus gene regulatory network

Abstract Background The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape and behave. The Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is a large double-stranded DNA virus, whose genome may encode for 152 open reading frames (ORFs). Here we present the analysis of the ordered cascade of the AgMNPV gene expression. Results We observed an earlier onset of the expression than previously reported for other baculoviruses, especially for genes involved in DNA replication. Most ORFs were expressed at higher levels in a more permissive host cell line. Genes with more than one copy in the genome had distinct expression profiles, which could indicate the acquisition of new functionalities. The transcription gene regulatory network (GRN) for 149 ORFs had a modular topology comprising five communities of highly interconnected nodes that separated key genes that are functionally related on different communities, possibly maximizing redundancy and GRN robustness by compartmentalization of important functions. Core conserved functions showed expression synchronicity, distinct GRN features and significantly less genetic diversity, consistent with evolutionary constraints imposed in key elements of biological systems. This reduced genetic diversity also had a positive correlation with the importance of the gene in our estimated GRN, supporting a relationship between phylogenetic data of baculovirus genes and network features inferred from expression data. We also observed that gene arrangement in overlapping transcripts was conserved among related baculoviruses, suggesting a principle of genome organization. Conclusions Albeit with a reduced number of nodes (149), the AgMNPV GRN had a topology and key characteristics similar to those observed in complex cellular organisms, which indicates that modularity may be a general feature of biological gene regulatory networks.

Does Evolution matter?: a case study in Brazil of the effects of an evolutionary-thinking academic atmosphere in postgraduate students' belief in God/religious belief

Although the theory of evolution is more than 150 years old, a substantial proportion of the world population does not mention it when explaining the origin of human beings. The usual alternative conception is offered by creationism, one of the main obstacles to full acceptance of evolution in many countries. National polls have demonstrated that schooling and religiosity are negatively correlated, with scientists being one of the least religious professionals. Herein we analyzed both (1) the profile of 1st semester undergraduate students and (2), thesis and dissertations, concerning religious and evolutionary thoughts from Biology and Veterinary Schools at the largest university of South America. We have shown that students of Biology are biased towards evolution before they enter university and also that the presence of an evolutionary-thinking academic atmosphere influences the deism/religiosity beliefs of postgraduate students.

Spinal cord injury as a trigger to develop periodic leg movements during sleep: an evolutionary perspective

The primary trigger to periodic limb movement (PLM) during sleep is still unknown. Its association with the restless legs syndrome (RLS) is established in humans and was reported in spinal cord injury (SCI) patients classified by the American Spinal Injury Association (ASIA) as A. Its pathogenesis has not been completely unraveled, though recent advances might enhance our knowledge about those malfunctions. PLM association with central pattern generator (CPG) is one of the possible pathologic mechanisms involved. This article reviewed the advances in PLM and RLS genetics, the evolution of CPG functioning, and the neurotransmitters involved in CPG, PLM and RLS. We have proposed that SCI might be a trigger to develop PLM.

The evolutionary implications of hemipenial morphology of rattlesnake Crotalus durissus terrificus (Laurent, 1768) (Serpentes: Viperidae: Crotalinae)

Most amniotes vertebrates have an intromittent organ to deliver semen. The reptile Sphenodon and most birds lost the ancestral penis and developed a cloaca-cloaca mating. Known as hemipenises, the copulatory organ of Squamata shows unique features between the amniotes intromittent organ. They are the only paired intromittent organs across amniotes and are fully inverted and encapsulated in the tail when not in use. The histology and ultrastructure of the hemipenes of Crotalus durissus rattlesnake is described as the evolutionary implications of the main features discussed. The organization of hemipenis of Crotalus durissus terrificus in two concentric corpora cavernosa is similar to other Squamata but differ markedly from the organization of the penis found in crocodilians, testudinata, birds and mammals. Based on the available data, the penis of the ancestral amniotes was made of connective tissue and the incorporation of smooth muscle in the framework of the sinusoids occurred independently in mammals and Crotalus durissus. The propulsor action of the muscle retractor penis basalis was confirmed and therefore the named should be changed to musculus hemipenis propulsor.The retractor penis magnus found in Squamata has no homology to the retractor penis of mammals, although both are responsible for the retraction of the copulatory organ

Size-dependent phase transitions in nanostructured zirconia-scandia solid solutions.

Size effects on phase stability and phase transitions in technologically relevant materials have received growing attention. Several works reported that metastable phases can be retained at room temperature in nanomaterials, these phases generally corresponding to the high-temperature polymorph of the same material in bulk state. Additionally, size-dependent shifts in solubility limits and/or in the transition temperatures for on heating or on cooling cycles have been observed. ZrO2-Sc2O3 (zirconia-scandia) solid solutions are known to exhibit very high oxygen ion conductivity provided their structure is composed of cubic and/or pseudocubic tetragonal phases. Unfortunately, for solid zirconia-scandia polycrystalline samples with typical micrometrical average crystal sizes, the high-conductivity cubic phase is only stable above 600°C. Depending on composition, three low-conductivity rhombo-hedral phases (β, γ and δ) are stable below 600°C down to room temperature, within the compositional range of interest for SOFCs. In previous investigations, we showed that the rhombohedral phases can be avoided in nanopowders with average crystallite size lower than 35 nm.

Multi-objective evolutionary algorithm for single and multiple fault service restoration in large-scale distribution systems

Network reconfiguration for service restoration (SR) in distribution systems is a complex optimization problem. For large-scale distribution systems, it is computationally hard to find adequate SR plans in real time since the problem is combinatorial and non-linear, involving several constraints and objectives. Two Multi-Objective Evolutionary Algorithms that use Node-Depth Encoding (NDE) have proved able to efficiently generate adequate SR plans for large distribution systems: (i) one of them is the hybridization of the Non-Dominated Sorting Genetic Algorithm-II (NSGA-II) with NDE, named NSGA-N; (ii) the other is a Multi-Objective Evolutionary Algorithm based on subpopulation tables that uses NDE, named MEAN. Further challenges are faced now, i.e. the design of SR plans for larger systems as good as those for relatively smaller ones and for multiple faults as good as those for one fault (single fault). In order to tackle both challenges, this paper proposes a method that results from the combination of NSGA-N, MEAN and a new heuristic. Such a heuristic focuses on the application of NDE operators to alarming network zones according to technical constraints. The method generates similar quality SR plans in distribution systems of significantly different sizes (from 3860 to 30,880 buses). Moreover, the number of switching operations required to implement the SR plans generated by the proposed method increases in a moderate way with the number of faults.

Human Abuses of Coral Reefs- Adaptive Responses and Regime Transitions

During the last few decades, coral reefs have become a disappearing feature of tropical marine environments, and those reefs that do remain are severely threatened. It is understood that humans have greately altered the environment under which these ecosystems previously have thrived and evoloved. Overharvesting of fish stocks, global warming and pollution are some of the most prominent threats, acting on coral reefs at several spatial and temporal scales. Presently, it is common that coral reefs have been degraded into alternative ecosystem regimes, such as macroalgae-dominated or sea urchin-barren. Although these ecosystems could potentially return to coral dominance in a long-term perspective, when considdering current conditions, it seems likely that they will persist in their degraded states. Thus, recovery of coral reefs cannot be taken for granted on a human timescale. Multiple stressors and disturbances, which are increasingly characteristic of coral reef environments today, are believed to act synergistically and produce ecological surprises. However, current knowledge of effects of compounded disturbances and stress is limited. Based on five papers, this thesis investigates the sublethal response of multiple stressors on coral physiology, as well as the effects of compounded stress and disturbance on coral reef structure and function. Adaptive responses to stress and disturbance in relation to prior experience are highlighted. The thesis further explores how inherent characteristics (traits) of corals and macroalgae may influence regime expression when faced with altered disturbance regimes, in particular overfishing, eutrophication, elevated temperature, and enhanced substrate availability. Finally, possibilities of affecting the resilience of macroalgae-dominaed reefs and shifting the community composition towards a coral-dominated regime are explored.

On uncertainty and robustness in evolutionary optimization-based multicriterio decision-making

Programa de Doctorado: Sistemas Inteligentes y Aplicaciones Numéricas en Ingeniería

Evolutionary methods for self-organizing cooperation in peer-to-peer networks

The Peer-to-Peer network paradigm is drawing the attention of both final users and researchers for its features. P2P networks shift from the classic client-server approach to a high level of decentralization where there is no central control and all the nodes should be able not only to require services, but to provide them to other peers as well. While on one hand such high level of decentralization might lead to interesting properties like scalability and fault tolerance, on the other hand it implies many new problems to deal with. A key feature of many P2P systems is openness, meaning that everybody is potentially able to join a network with no need for subscription or payment systems. The combination of openness and lack of central control makes it feasible for a user to free-ride, that is to increase its own benefit by using services without allocating resources to satisfy other peers’ requests. One of the main goals when designing a P2P system is therefore to achieve cooperation between users. Given the nature of P2P systems based on simple local interactions of many peers having partial knowledge of the whole system, an interesting way to achieve desired properties on a system scale might consist in obtaining them as emergent properties of the many interactions occurring at local node level. Two methods are typically used to face the problem of cooperation in P2P networks: 1) engineering emergent properties when designing the protocol; 2) study the system as a game and apply Game Theory techniques, especially to find Nash Equilibria in the game and to reach them making the system stable against possible deviant behaviors. In this work we present an evolutionary framework to enforce cooperative behaviour in P2P networks that is alternative to both the methods mentioned above. Our approach is based on an evolutionary algorithm inspired by computational sociology and evolutionary game theory, consisting in having each peer periodically trying to copy another peer which is performing better. The proposed algorithms, called SLAC and SLACER, draw inspiration from tag systems originated in computational sociology, the main idea behind the algorithm consists in having low performance nodes copying high performance ones. The algorithm is run locally by every node and leads to an evolution of the network both from the topology and from the nodes’ strategy point of view. Initial tests with a simple Prisoners’ Dilemma application show how SLAC is able to bring the network to a state of high cooperation independently from the initial network conditions. Interesting results are obtained when studying the effect of cheating nodes on SLAC algorithm. In fact in some cases selfish nodes rationally exploiting the system for their own benefit can actually improve system performance from the cooperation formation point of view. The final step is to apply our results to more realistic scenarios. We put our efforts in studying and improving the BitTorrent protocol. BitTorrent was chosen not only for its popularity but because it has many points in common with SLAC and SLACER algorithms, ranging from the game theoretical inspiration (tit-for-tat-like mechanism) to the swarms topology. We discovered fairness, meant as ratio between uploaded and downloaded data, to be a weakness of the original BitTorrent protocol and we drew inspiration from the knowledge of cooperation formation and maintenance mechanism derived from the development and analysis of SLAC and SLACER, to improve fairness and tackle freeriding and cheating in BitTorrent. We produced an extension of BitTorrent called BitFair that has been evaluated through simulation and has shown the abilities of enforcing fairness and tackling free-riding and cheating nodes.

Optimization of thin noise barrier designs using Evolutionary Algorithms and a Dual BEM Formulation

[EN]This works aims at assessing the acoustic efficiency of differente this noise barrier models. These designs frequently feature complex profiles and their implementarion in shape optimization processes may not always be easy in terms of determining their topological feasibility. A methodology to conduct both overall shape and top edge optimisations of thin cross section acoustic barriers by idealizing them as profiles with null boundary thickness is proposed.

Application of evolutionary algorithms and the boundary element method in the optimization of noise barrier profiles

[EN]This Ph.D. thesis presents a general, robust methodology that may cover any type of 2D acoustic optimization problem. A procedure involving the coupling of Boundary Elements (BE) and Evolutionary Algorithms is proposed for systematic geometric modifications of road barriers that lead to designs with ever-increasing screening performance. Numerical simulations involving single- and multi-objective optimizations of noise barriers of varied nature are included in this document. results disclosed justify the implementation of this methodology by leading to optimal solutions of previously defined topologies that, in general, greatly outperform the acoustic efficiency of classical, widely used barrier designs normally erected near roads.

TNFRSF13B Genetic variability an anthropological - evolutionary approach to Biomedical Research

In the recent years TNFRSF13B coding variants have been implicated by clinical genetics studies in Common Variable Immunodeficiency (CVID), the most common clinically relevant primary immunodeficiency in individuals of European ancestry, but their functional effects in relation to the development of the disease have not been entirely established. To examine the potential contribution of such variants to CVID, the more comprehensive perspective of an evolutionary approach was applied in this study, underling the belief that evolutionary genetics methods can play a role in dissecting the origin, causes and diffusion of human diseases, representing a powerful tool also in human health research. For this purpose, TNFRSF13B coding region was sequenced in 451 healthy individuals belonging to 26 worldwide populations, in addition to 96 control, 77 CVID and 38 Selective IgA Deficiency (IgAD) individuals from Italy, leading to the first achievement of a global picture of TNFRSF13B nucleotide diversity and haplotype structure and making suggestion of its evolutionary history possible. A slow rate of evolution, within our species and when compared to the chimpanzee, low levels of genetic diversity geographical structure and the absence of recent population specific selective pressures were observed for the examined genomic region, suggesting that geographical distribution of its variability is more plausibly related to its involvement also in innate immunity rather than in adaptive immunity only. This, together with the extremely subtle disease/healthy samples differences observed, suggests that CVID might be more likely related to still unknown environmental and genetic factors, rather than to the nature of TNFRSF13B variants only.