PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

Background: With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results: PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions: PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net.

O natural e o farmacológico: padrões de consumo terapêutico na população portuguesa

Neste artigo identificam-se os padrões de consumo terapêutico na população portuguesa, visando dar conta de um novo padrão emergente nas sociedades modernas, aqui designado de Pluralismo Terapêutico, noção com a qual se categoriza o uso conjugado ou alternado de recursos farmacológicos e naturais nas trajetórias terapêuticas dos indivíduos. O respetivo suporte empírico decorre de uma investigação, já concluída, que teve por base uma amostra nacional representativa. Os resultados mostram uma dualização dos consumos terapêuticos que é constituída por um padrão dominante de Farmacologismo – i.e., uso exclusivo de fármacos – coexistente com uma tendência crescente de pluralismo terapêutico. O efeito das fontes de informação terapêutica e dos seus usos leigos, bem como das perceções sociais de risco sobre o natural e o farmacológico, constitui neste estudo uma referência analítica central para a interpretação dos padrões encontrados. - ABSTRACT: In this article we identify patterns of therapeutic consumption, with the purpose of assessing an emerging pattern in modern societies, here designated as Therapeutic Pluralism, referring to the conjugated or alternated use of pharmacological and natural resources in the therapeutic trajectories of individuals. The empirical basis for this analysis stems from a concluded research on the topic, and is focused on a questionnaire administered to a representative sample of the Portuguese population. The results show a duality in therapeutic consumptions, expressed in the coexistence of a dominant pattern of Pharmacologism – that is, the exclusive therapeutic consumption of pharmaceuticals – and a growing trend towards therapeutic pluralism. The effects of information sources on health and its lay uses, as well as of the social perceptions of risk concerning the natural and the pharmacological, constitute key analytical references for this study’s interpretation of the identified patterns.

ECG Analysis Using Consensus Clustering

Biosignals analysis has become widespread, upstaging their typical use in clinical settings. Electrocardiography (ECG) plays a central role in patient monitoring as a diagnosis tool in today's medicine and as an emerging biometric trait. In this paper we adopt a consensus clustering approach for the unsupervised analysis of an ECG-based biometric records. This type of analysis highlights natural groups within the population under investigation, which can be correlated with ground truth information in order to gain more insights about the data. Preliminary results are promising, for meaningful clusters are extracted from the population under analysis. © 2014 EURASIP.

Dynamical analysis in growth models: Blumberg’s equation

We present a new dynamical approach to the Blumberg's equation, a family of unimodal maps. These maps are proportional to Beta(p, q) probability densities functions. Using the symmetry of the Beta(p, q) distribution and symbolic dynamics techniques, a new concept of mirror symmetry is defined for this family of maps. The kneading theory is used to analyze the effect of such symmetry in the presented models. The main result proves that two mirror symmetric unimodal maps have the same topological entropy. Different population dynamics regimes are identified, when the intrinsic growth rate is modified: extinctions, stabilities, bifurcations, chaos and Allee effect. To illustrate our results, we present a numerical analysis, where are demonstrated: monotonicity of the topological entropy with the variation of the intrinsic growth rate, existence of isentropic sets in the parameters space and mirror symmetry.

Dimensionless analysis of constrained damping treatments

One of the most effective ways of controlling vibrations in plate or beam structures is by means of constrained viscoelastic damping treatments. Contrary to the unconstrained configuration, the design of constrained and integrated layer damping treatments is multifaceted because the thickness of the viscoelastic layer acts distinctly on the two main counterparts of the strain energy the volume of viscoelastic material and the shear strain field. In this work, a parametric study is performed exploring the effect that the design parameters, namely the thickness/length ratio, constraining layer thickness, material modulus, natural mode and boundary conditions have on these two counterparts and subsequently, on the treatment efficiency. This paper presents five parametric studies, namely, the thickness/length ratio, the constraining layer thickness, material properties, natural mode and boundary conditions. The results obtained evidence an interesting effect when dealing with very thin viscoelastic layers that contradicts the standard treatment efficiency vs. layer thickness relation; hence, the potential optimisation of constrained and integrated viscoelastic treatments through the use of properly designed thin multilayer configurations is justified. This work presents a dimensionless analysis and provides useful general guidelines for the efficient design of constrained and integrated damping treatments based on single or multi-layer configurations. (C) 2012 Elsevier Ltd. All rights reserved.

Mutation accumulation in Tetrahymena

Background - The rate and fitness effects of mutations are key in understanding the evolution of every species. Traditionally, these parameters are estimated in mutation accumulation experiments where replicate lines are propagated in conditions that allow mutations to randomly accumulate without the purging effect of natural selection. These experiments have been performed with many model organisms but we still lack empirical estimates of the rate and effects of mutation in the protists. Results - We performed a mutation accumulation (MA) experiment in Tetrahymena thermophila, a species that can reproduce sexually and asexually in nature, and measured both the mean decline and variance increase in fitness of 20 lines. The results obtained with T. thermophila were compared with T. pyriformis that is an obligate asexual species. We show that MA lines of T. thermophila go to extinction at a rate of 1.25 clonal extinctions per bottleneck. In contrast, populations of T. pyriformis show a much higher resistance to extinction. Variation in gene copy number is likely to be a key factor in explaining these results, and indeed we show that T. pyriformis has a higher mean copy number per cell than T. thermophila. From fitness measurements during the MA experiment, we infer a rate of mutation to copy number variation of 0.0333 per haploid MAC genome of T. thermophila and a mean effect against copy number variation of 0.16. A strong effect of population size in the rate of fitness decline was also found, consistent with the increased power of natural selection. Conclusions - The rate of clonal extinction measured for T. thermophila is characteristic of a mutational degradation and suggests that this species must undergo sexual reproduction to avoid the deleterious effects detected in the laboratory experiments. We also suggest that an increase in chromosomal copy number associated with the phenotypic assortment of amitotic divisions can provide an alternative mechanism to escape the deleterious effect of random chromosomal copy number variation in species like T. pyriformis that lack the resetting mechanism of sexual reproduction. Our results are relevant to the understanding of cell line longevity and senescence in ciliates.

Water quality issues in rivers, lakes and reservoirs in Asian countries: an approach to the problems and the methodologies

Water covers over 70% of the Earth's surface, and is vital for all known forms of life. But only 3% of the Earth's water is fresh water, and less than 0.3% of all freshwater is in rivers, lakes, reservoirs and the atmosphere. However, rivers and lakes are an important part of fresh surface water, amounting to about 89%. In this Master Thesis dissertation, the focus is on three types of water bodies – rivers, lakes and reservoirs, and their water quality issues in Asian countries. The surface water quality in a region is largely determined both by the natural processes such as climate or geographic conditions, and the anthropogenic influences such as industrial and agricultural activities or land use conversion. The quality of the water can be affected by pollutants discharge from a specific point through a sewer pipe and also by extensive drainage from agriculture/urban areas and within basin. Hence, water pollutant sources can be divided into two categories: Point source pollution and Non-point source (NPS) pollution. Seasonal variations in precipitation and surface run-off have a strong effect on river discharge and the concentration of pollutants in water bodies. For example, in the rainy season, heavy and persistent rain wash off the ground, the runoff flow increases and may contain various kinds of pollutants and, eventually, enters the water bodies. In some cases, especially in confined water bodies, the quality may be positive related with rainfall in the wet season, because this confined type of fresh water systems allows high dilution of pollutants, decreasing their possible impacts. During the dry season, the quality of water is largely related to industrialization and urbanization pollution. The aim of this study is to identify the most common water quality problems in Asian countries and to enumerate and analyze the methodologies used for assessment of water quality conditions of both rivers and confined water bodies (lakes and reservoirs). Based on the evaluation of a sample of 57 papers, dated between 2000 and 2012, it was found that over the past decade, the water quality of rivers, lakes, and reservoirs in developing countries is being degraded. Water pollution and destruction of aquatic ecosystems have caused massive damage to the functions and integrity of water resources. The most widespread NPS in Asian countries and those which have the greatest spatial impacts are urban runoff and agriculture. Locally, mine waste runoff and rice paddy are serious NPS problems. The most relevant point pollution sources are the effluents from factories, sewage treatment plant, and public or household facilities. It was found that the most used methodology was unquestionably the monitoring activity, used in 49 of analyzed studies, accounting for 86%. Sometimes, data from historical databases were used as well. It can be seen that taking samples from the water body and then carry on laboratory work (chemical analyses) is important because it can give an understanding of the water quality. 6 papers (11%) used a method that combined monitoring data and modeling. 6 papers (11%) just applied a model to estimate the quality of water. Modeling is a useful resource when there is limited budget since some models are of free download and use. In particular, several of used models come from the U.S.A, but they have their own purposes and features, meaning that a careful application of the models to other countries and a critical discussion of the results are crucial. 5 papers (9%) focus on a method combining monitoring data and statistical analysis. When there is a huge data matrix, the researchers need an efficient way of interpretation of the information which is provided by statistics. 3 papers (5%) used a method combining monitoring data, statistical analysis and modeling. These different methods are all valuable to evaluate the water quality. It was also found that the evaluation of water quality was made as well by using other types of sampling different than water itself, and they also provide useful information to understand the condition of the water body. These additional monitoring activities are: Air sampling, sediment sampling, phytoplankton sampling and aquatic animal tissues sampling. Despite considerable progress in developing and applying control regulations to point and NPS pollution, the pollution status of rivers, lakes, and reservoirs in Asian countries is not improving. In fact, this reflects the slow pace of investment in new infrastructure for pollution control and growing population pressures. Water laws or regulations and public involvement in enforcement can play a constructive and indispensable role in environmental protection. In the near future, in order to protect water from further contamination, rapid action is highly needed to control the various kinds of effluents in one region. Environmental remediation and treatment of industrial effluent and municipal wastewaters is essential. It is also important to prevent the direct input of agricultural and mine site runoff. Finally, stricter environmental regulation for water quality is required to support protection and management strategies. It would have been possible to get further information based in the 57 sample of papers. For instance, it would have been interesting to compare the level of concentrations of some pollutants in the diferente Asian countries. However the limit of three months duration for this study prevented further work to take place. In spite of this, the study objectives were achieved: the work provided an overview of the most relevant water quality problems in rivers, lakes and reservoirs in Asian countries, and also listed and analyzed the most common methodologies.

Comunicação do risco natural em Portugal

Na presente dissertação pretende-se compreender como é que a comunicação do risco é considerada pelos profissionais ligados à gestão do risco no domínio das calamidades naturais em Portugal. Para tal, além da fundamentação teórica acerca do objeto de estudo deste trabalho, ou seja, da comunicação do risco, pretende-se reunir algumas pistas que permitam compreender a visão que os profissionais ligados à gestão do risco, nomeadamente no âmbito das calamidades naturais têm desta disciplina de comunicação. É igualmente propósito desta dissertação aferir se a sociedade civil tem acesso a informação no que concerne a comportamentos redutores do risco no domínio da ocorrência de uma catástrofe natural, tais como um sismo ou um tornado. Neste sentido, pretende-se, portanto clarificar, em primeiro lugar, se existem, de facto, esforços de comunicação no que diz respeito à divulgação de informação sobre os riscos inerentes a um determinado fenómeno natural. E, segundo compreender o motivo pelo qual a sociedade civil portuguesa não tem um papel ativo no processo de gestão do risco: será que esta inércia se deve à falta de interesse (aliada à ignorância) da população no que concerne a temática do risco, em particular, no domínio da ocorrência de catástrofes naturais. Por fim, na presente dissertação é apresentado um guia de boas práticas para porta-vozes no domínio da comunicação do risco.

Water quality in lakes and reservoirs in China

Dissertation elaborated for the partial fulfilment of the requirements of the Master Degree in Civil Engineering in the Speciality Area of Hydarulics