A fractional calculus perspective in the evolutionary design of combinational circuits

This paper analyses the performance of a genetic algorithm (GA) in the synthesis of digital circuits using two novel approaches. The first concept consists in improving the static fitness function by including a discontinuity evaluation. The measure of variability in the error of the Boolean table has similarities with the function continuity issue in classical calculus. The second concept extends the static fitness by introducing a fractional-order dynamical evaluation.

Controling delayed transitions with applications to prevent single species extinctions

A new method is proposed to control delayed transitions towards extinction in single population theoretical models with discrete time undergoing saddle-node bifurcations. The control method takes advantage of the delaying properties of the saddle remnant arising after the bifurcation, and allows to sustain populations indefinitely. Our method, which is shown to work for deterministic and stochastic systems, could generally be applied to avoid transitions tied to one-dimensional maps after saddle-node bifurcations.

Low temperature structural transitions in dipolar hard spheres: the influence on magnetic properties

We investigate the structural chain-to-ring transition at low temperature in a gas of dipolar hard spheres (DRS). Due to the weakening of entropic contribution, ring formation becomes noticeable when the effective dipole-dipole magnetic interaction increases, It results in the redistribution of particles from usually observed flexible chains into flexible rings. The concentration (rho) of DI-IS plays a crucial part in this transition: at a very low rho only chains and rings are observed, whereas even a slight increase of the volume fraction leads to the formation of branched or defect structures. As a result, the fraction of DHS aggregated in defect-free rings turns out to be a non-monotonic function of rho. The average ring size is found to be a slower increasing function of rho when compared Lo that of chains. Both theory and computer simulations confirm the dramatic influence of the ring formation on the rho-dependence of the initial magnetic susceptibility (chi) when the temperature decreases. The rings clue to their zero total dipole moment are irresponsive to a weak magnetic field and drive to the strong decrease of the initial magnetic susceptibility. (C) 2014 Elsevier B.V. All rights reserved.

Temperature-induced structural transitions in self-assembling magnetic nanocolloids

With the help of a unique combination of density functional theory and computer simulations, we discover two possible scenarios, depending on concentration, for the hierarchical self-assembly of magnetic nanoparticles on cooling. We show that typically considered low temperature clusters, i.e. defect-free chains and rings, merge into more complex branched structures through only three types of defects: four-way X junctions, three-way Y junctions and two-way Z junctions. Our accurate calculations reveal the predominance of weakly magnetically responsive rings cross-linked by X defects at the lowest temperatures. We thus provide a strategy to fine-tune magnetic and thermodynamic responses of magnetic nanocolloids to be used in medical and microfluidics applications.

An agent-based evolutionary approach for manufacturing system layout design

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Electrotécnica e de Computadores

Study of forbidden transitions in atomic systems

A Thesis submitted for the co-tutelle degree of Doctor in Physics at Universidade Nova de Lisboa and Université Pierre et Marie Curie

A Fractional Calculus Perspective in the Evolutionary Design of Combinational Circuits

This paper analyses the performance of a genetic algorithm (GA) in the synthesis of digital circuits using two novel approaches. The first concept consists in improving the static fitness function by including a discontinuity evaluation. The measure of variability in the error of the Boolean table has similarities with the function continuity issue in classical calculus. The second concept extends the static fitness by introducing a fractional-order dynamical evaluation.

Neolithic transitions: can genetic data help us understand a major demographic event in human prehistory?

Dissertation presented to obtain the Ph.D degree in Biology

Long-term behaviour of railway transitions under dynamic loading application to soft soil sites

Dissertação para obtenção do Grau de Doutor em Engenharia Civil

The origin and diversification of an evolutionary novelty: lessons from Drosophila oogenesis

In any area of study, it is necessary to define the subject of investigation. In the case of evolutionary novelty this is a particularly difficult task, as a clear definition of the concept that is suitable across di↵erent levels of biological organization has yet to emerge. We proceed with a definition for morphological novelty proposed by M¨uller and Wagner (1991), and introduce the dorsal appendages on eggs of Drosophilidae as such a novelty. These structures are part of the eggshell, and help supply oxygen to the embryo. A wide variety of phenotypes can be found, which is thought to have a single origin in the common ancestor of Drosophilidae.(...)

Clinical and evolutionary characteristics of four patients with pulmonary histoplasmosis reported in the Paraíba Paulista Valley region

The type of pulmonary histoplasmosis presents limited lesions to the lungs, with symptoms that are clinically and radiological similar to chronic pulmonary tuberculosis. This paper describes the clinical features of four cases of pulmonary histoplasmosis. Aspects of diagnostic and clinical, epidemiological, laboratorial and imaging exams are discussed, in addition to the clinical status of the individuals five years after disease onset. The treatment of choice was oral medication, following which all the patients improved. It is important to understand the clinical status and the difficulties concerning the differential diagnosis of histoplasmosis, to assist the proper indication of cases, thus reducing potential confusion with other diseases.

An integrated approach to Physcomitrella patens transcriptomics reveals importantclues of the evolutionary development of plant organs and sexual reproduction

Land plant evolution required the generation of a new body plan that could resist the harsher and fluctuating environmental conditions found outside of aquatic environments. Unraveling the genetic basis of plant developmental innovations is not only revealing in terms of an evolutionary point of view, but it is also important for understanding the emergence of agronomically important traits. Comparative genetic studies between basal and modern land plants, both at the genome and trancriptome levels, can help in the generation of hypotheses related to the genetic basis of plant evolutionary development.(...)

The Impact of income support programs on transitions to employment

The income support programs are created with the purpose of fighting both, the poverty trap and the inactivity trap. The balance between both is fragile and hard to find. Thus, the goal of this work is to contribute to solve this issue by finding how income support programs, particularly the Portuguese RSI, affect transitions to employment. This is made through duration analysis, namely using Cox and Competing Risks models. A particular feature is introduced in this work as it incorporates the possibility of Defective Risks. The estimated hazard elasticity with respect to the amount of RSI received for individuals who move to employment is -0,41. More than a half of RSI receivers stays for more than a year and the probability of never leaving to employment is 44%. The results appear to indicate that RSI has affected negatively transitions to employment.

Evolutionary dynamics of Chlamydia trachomatis genome and identification of molecular patterns of hypothetical protein coding genes

The obligate intracellular bacterium Chlamydia trachomatis is a human pathogen of major public health significance. Strains can be classified into 15 main serovars (A to L3) that preferentially cause ocular infections (A-C), genital infections (D-K) or lymphogranuloma venereum (LGV) (L1-L3), but the molecular basis behind their distinct tropism, ecological success and pathogenicity is not welldefined. Most chlamydial research demands culture in eukaryotic cell lines, but it is not known if stains become laboratory adapted. By essentially using genomics and transcriptomics, we aimed to investigate the evolutionary patterns underlying the adaptation of C. trachomatis to the different human tissues, given emphasis to the identification of molecular patterns of genes encoding hypothetical proteins, and to understand the adaptive process behind the C. trachomatis in vivo to in vitro transition. Our results highlight a positive selection-driven evolution of C. trachomatis towards nichespecific adaptation, essentially targeting host-interacting proteins, namely effectors and inclusion membrane proteins, where some of them also displayed niche-specific expression patterns. We also identified potential "ocular-specific" pseudogenes, and pointed out the major gene targets of adaptive mutations associated with LGV infections. We further observed that the in vivo-derived genetic makeup of C. trachomatis is not significantly compromised by its long-term laboratory propagation. In opposition, its introduction in vitro has the potential to affect the phenotype, likely yielding virulence attenuation. In fact, we observed a "genital-specific" rampant inactivation of the virulence gene CT135, which may impact the interpretation of data derived from studies requiring culture. Globally, the findings presented in this Ph.D. thesis contribute for the understanding of C.trachomatis adaptive evolution and provides new insights into the biological role of C. trachomatishypothetical proteins. They also launch research questions for future functional studies aiming toclarify the determinants of tissue tropism, virulence or pathogenic dissimilarities among C. trachomatisstrains.

Nutritional plasticity and evolutionary divergence in the Drosophila ovary

The environment can modify developmental trajectories and generate a range of distinct phenotypes without altering an organism’s genome, a widespread phenomenon called developmental plasticity. The past decades have seen a resurgent interest in understanding how developmental plasticity contributes to evolutionary processes, as it can produce phenotypic variation among individuals and facilitate diversification among populations that inhabit distinct ecological niches. To better understand the importance of plastic responses for evolutionary change, we need to explore how the environment alters development to produce phenotypic variation and then compare this to how genetic variation influences these same developmental processes.(...)