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.

The effect of music marketing: A consumer perspective

The purpose of this thesis is to get a consumer perspective regarding event marketing in music festivals. Event marketing is a tool used by marketers that evolved out of philanthropy and commercial sponsorship. Brands are more and more using music or other entertainment moments to create a strong relationship with their clients, and the target group at these events, the millennial generation. Brands use sponsoring and therefore event marketing for several reasons as: increase brand awareness; create brand image; re-position the brand/product in the minds of consumers; increase profit over a short period; and, achieve larger market share. Nonetheless, we wonder how is this tool seen by consumers? To understand this, a preliminary research with nine interviews was conducted to obtain basic ideas about event marketing. Afterwards the main research was developed, also using interviews, to get deeper insights. With this thesis, it is possible to conclude that some brands are able to create brand awareness on attendees through brand sponsorship. Moreover, entertainment activities in festivals are well seen by consumers, they like it and are able to describe it well, even though it is more about the activity itself than the brand promoting it. Furthermore, it was possible to understand that experiential marketing in a festival might have a positive effect on consumers as it might create a link between the event and the brand. Finally, we recommend some actions, for brands to develop in future music festivals.

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.(...)

An evolutionary multi-objective optimization system for earthworks

Earthworks involve the levelling or shaping of a target area through the moving or processing of the ground surface. Most construction projects require earthworks, which are heavily dependent on mechanical equipment (e.g., excavators, trucks and compactors). Often, earthworks are the most costly and time-consuming component of infrastructure constructions (e.g., road, railway and airports) and current pressure for higher productivity and safety highlights the need to optimize earthworks, which is a nontrivial task. Most previous attempts at tackling this problem focus on single-objective optimization of partial processes or aspects of earthworks, overlooking the advantages of a multi-objective and global optimization. This work describes a novel optimization system based on an evolutionary multi-objective approach, capable of globally optimizing several objectives simultaneously and dynamically. The proposed system views an earthwork construction as a production line, where the goal is to optimize resources under two crucial criteria (costs and duration) and focus the evolutionary search (non-dominated sorting genetic algorithm-II) on compaction allocation, using linear programming to distribute the remaining equipment (e.g., excavators). Several experiments were held using real-world data from a Portuguese construction site, showing that the proposed system is quite competitive when compared with current manual earthwork equipment allocation.

Comparison of single and multi-objective evolutionary algorithms for robust link-state routing

Traffic Engineering (TE) approaches are increasingly impor- tant in network management to allow an optimized configuration and resource allocation. In link-state routing, the task of setting appropriate weights to the links is both an important and a challenging optimization task. A number of different approaches has been put forward towards this aim, including the successful use of Evolutionary Algorithms (EAs). In this context, this work addresses the evaluation of three distinct EAs, a single and two multi-objective EAs, in two tasks related to weight setting optimization towards optimal intra-domain routing, knowing the network topology and aggregated traffic demands and seeking to mini- mize network congestion. In both tasks, the optimization considers sce- narios where there is a dynamic alteration in the state of the system, in the first considering changes in the traffic demand matrices and in the latter considering the possibility of link failures. The methods will, thus, need to simultaneously optimize for both conditions, the normal and the altered one, following a preventive TE approach towards robust configurations. Since this can be formulated as a bi-objective function, the use of multi-objective EAs, such as SPEA2 and NSGA-II, came nat- urally, being those compared to a single-objective EA. The results show a remarkable behavior of NSGA-II in all proposed tasks scaling well for harder instances, and thus presenting itself as the most promising option for TE in these scenarios.

Combining data mining and evolutionary computation for multi-criteria optimization of earthworks

Earthworks tasks aim at levelling the ground surface at a target construction area and precede any kind of structural construction (e.g., road and railway construction). It is comprised of sequential tasks, such as excavation, transportation, spreading and compaction, and it is strongly based on heavy mechanical equipment and repetitive processes. Under this context, it is essential to optimize the usage of all available resources under two key criteria: the costs and duration of earthwork projects. In this paper, we present an integrated system that uses two artificial intelligence based techniques: data mining and evolutionary multi-objective optimization. The former is used to build data-driven models capable of providing realistic estimates of resource productivity, while the latter is used to optimize resource allocation considering the two main earthwork objectives (duration and cost). Experiments held using real-world data, from a construction site, have shown that the proposed system is competitive when compared with current manual earthwork design.

MOEA/VAN: Multiobjective Evolutionary Algorithm based on Vector Angle Neighborhood

Natural selection favors the survival and reproduction of organisms that are best adapted to their environment. Selection mechanism in evolutionary algorithms mimics this process, aiming to create environmental conditions in which artificial organisms could evolve solving the problem at hand. This paper proposes a new selection scheme for evolutionary multiobjective optimization. The similarity measure that defines the concept of the neighborhood is a key feature of the proposed selection. Contrary to commonly used approaches, usually defined on the basis of distances between either individuals or weight vectors, it is suggested to consider the similarity and neighborhood based on the angle between individuals in the objective space. The smaller the angle, the more similar individuals. This notion is exploited during the mating and environmental selections. The convergence is ensured by minimizing distances from individuals to a reference point, whereas the diversity is preserved by maximizing angles between neighboring individuals. Experimental results reveal a highly competitive performance and useful characteristics of the proposed selection. Its strong diversity preserving ability allows to produce a significantly better performance on some problems when compared with stat-of-the-art algorithms.

Form tutors in the joint teaching of music: perspectives and experiences

In the Portuguese school system, form tutors (FTs) are an intermediate education management structure. The form tutor is responsible for a position of coordination and orientation with a «threefold function»: a relationship with students, relationship with the student’s family and relationship with other class teachers. The joint teaching of music is a part of the educational system in basic education. It is optional and provides musical and instrumental training to students who are interested in taking it. In order to achieve this, there is a system, subject to protocols, between general education schools and schools specializing in teaching music. There is also the position of FT in specialized schools and it also includes a «threefold function». However, these FTs have the additional role of representing music teachers at the class council, which is held at the general education school. Thus, in these cases, both FTs have a fourth joint area, between the music school and the general education school, which makes the relationship between them even more complex. This paper is based on the analysis of empirical data obtained from the testimonies of FTs regarding their representations and experiences in leadership and the coordination of teachers among schools in which there is a joint teaching system. The aim of collecting narratives is to look into some of the main challenges and confrontations related to leadership issues, which we assume to be the focus of those who have the role of form tutor in that specific context.

The music of language: an ERP investigation of the effects of musical training on emotional prosody processing

Recent studies have demonstrated the positive effects of musical training on the perception of vocally expressed emotion. This study investigated the effects of musical training on event-related potential (ERP) correlates of emotional prosody processing. Fourteen musicians and fourteen control subjects listened to 228 sentences with neutral semantic content, differing in prosody (one third with neutral, one third with happy and one third with angry intonation), with intelligible semantic content (semantic content condition--SCC) and unintelligible semantic content (pure prosody condition--PPC). Reduced P50 amplitude was found in musicians. A difference between SCC and PPC conditions was found in P50 and N100 amplitude in non-musicians only, and in P200 amplitude in musicians only. Furthermore, musicians were more accurate in recognizing angry prosody in PPC sentences. These findings suggest that auditory expertise characterizing extensive musical training may impact different stages of vocal emotional processing.

An evolutionary approach to the use of Petri net based models: from parallel controllers to HW/SW co-design

"A workshop within the 19th International Conference on Applications and Theory of Petri Nets - ICATPN’1998"

Application of receptive music therapy in internal medicine and cardiology

OBJECTIVE: To investigate the effects of receptive music therapy in clinical practice. METHODS: Receptive music therapy was individually applied via musical auditions, including five stages: musical stimulation, sensation, situation, reflection, and behavioral alteration. Following anamnesis and obtainment of consent, patients answered a first questionnaire on health risk evaluation (Q1), and after participating in 16 weekly music therapy sessions, answered a second one (Q2). RESULTS: Two men and 8 women, aged above 18 years, referred to us due to symptoms of stress, emotional suffering, and the need to change lifestyles (health risk behavior) were studied between August 1998 and December 1999. Comparison between answers to Q1 and Q2, showed a trend (P=0.059) for reduction of ingestion of cholesterol-rich foods and for increased prospects in life with a tendency towards improvement, and also of increased intake of fiber-rich food (55.6%), increased levels of personal satisfaction (44.5%), and decreased levels of stress (66.7%). CONCLUSION: The study demonstrated decreased stress levels and increased personal satisfaction, higher consumption of fiber-rich food, lower cholesterol intake, and a better perspective on life, suggesting that receptive music therapy may be applied in clinical practice as an auxiliary therapeutic intervention for the treatment of behavioral health risks.

Data-driven system identification via evolutionary retrieval of Takagi-Sugeno fuzzy models

Systemidentification, evolutionary automatic, data-driven model, fuzzy Takagi-Sugeno grammar, genotype interpretability, toxicity-prediction

Adaptive methods for user-centered organization of music collections

Zugl.: Magdeburg, Univ., Fak. für Informatik, Diss., 2011