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.

The complete sequence of a 9000 bp fragment of the right arm of Saccharomyces cerevisiae chromosome VII contains four previously unknown open reading frames

We report the sequence of a 9000 bp fragment from the right arm of Saccharomyces cerevisiae chromosome VII. Analysis of the sequence revealed four complete previously unknown open reading frames, which were named G7587, G7589, G7591 and G7594 following standard rules for provisional nomenclature. Outstanding features of some of these proteins were the homology of the putative protein coded by G7589 with proteins involved in transcription regulation and the transmembrane domains predicted in the putative protein coded by G7591.

Market power analysis in the Iberian electricity market using a conjectural variations model

In the last years the electricity industry has faced a restructuring process. Among the aims of this process was the increase in competition, especially in the generation activity where firms would have an incentive to become more efficient. However, the competitive behavior of generating firms might jeopardize the expected benefits of the electricity industry liberalization. The present paper proposes a conjectural variations model to study the competitive behavior of generating firms acting in liberalized electricity markets. The model computes a parameter that represents the degree of competition of each generating firm in each trading period. In this regard, the proposed model provides a powerful methodology for regulatory and competition authorities to monitor the competitive behavior of generating firms. As an application of the model, a study of the day-ahead Iberian electricity market (MIBEL) was conducted to analyze the impact of the integration of the Portuguese and Spanish electricity markets on the behavior of generating firms taking into account the hourly results of the months of June and July of 2007. The advantages of the proposed methodology over other methodologies used to address market power, namely Residual Supply index and Lerner index are highlighted. (C) 2014 Elsevier Ltd. All rights reserved.

Price forecasting in the day-ahead Iberian electricity market using a conjectural variations Arima model

Price forecast is a matter of concern for all participants in electricity markets, from suppliers to consumers through policy makers, which are interested in the accurate forecast of day-ahead electricity prices either for better decisions making or for an improved evaluation of the effectiveness of market rules and structure. This paper describes a methodology to forecast market prices in an electricity market using an ARIMA model applied to the conjectural variations of the firms acting in an electricity market. This methodology is applied to the Iberian electricity market to forecast market prices in the 24 hours of a working day. The methodology was then compared with two other methodologies, one called naive and the other a direct forecast of market prices using also an ARIMA model. Results show that the conjectural variations price forecast performs better than the naive and that it performs slightly better than the direct price forecast.

A teaching-learning sequence of colour informed by history and philosophy of science

In this work, we present a teaching-learning sequence on colour intended to a pre-service elementary teacher programme informed by History and Philosophy of Science. Working in a socio-constructivist framework, we made an excursion on the history of colour. Our excursion through history of colour, as well as the reported misconception on colour helps us to inform the constructions of the teaching-learning sequence. We apply a questionnaire both before and after each of the two cycles of action-research in order to assess students’ knowledge evolution on colour and to evaluate our teaching-learning sequence. Finally, we present a discussion on the persistence of deep-rooted alternative conceptions.

A didactic sequence of elementary geometric optics Informed by history and philosophy of science

The concepts and instruments required for the teaching and learning of geometric optics are introduced in the didactic processwithout a proper didactic transposition. This claim is secured by the ample evidence of both wide- and deep-rooted alternative concepts on the topic. Didactic transposition is a theory that comes from a reflection on the teaching and learning process in mathematics but has been used in other disciplinary fields. It will be used in this work in order to clear up the main obstacles in the teachinglearning process of geometric optics. We proceed to argue that since Newton’s approach to optics, in his Book I of Opticks, is independent of the corpuscular or undulatory nature of light, it is the most suitable for a constructivist learning environment. However, Newton’s theory must be subject to a proper didactic transposition to help overcome the referred alternative concepts. Then is described our didactic transposition in order to create knowledge to be taught using a dialogical process between students’ previous knowledge, history of optics and the desired outcomes on geometrical optics in an elementary pre-service teacher training course. Finally, we use the scheme-facet structure of knowledge both to analyse and discuss our results as well as to illuminate shortcomings that must be addressed in our next stage of the inquiry.