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.

Português L2: ensino da escrita e input linguístico

Esta dissertação de mestrado é baseada numa investigação – ação, realizada numa turma de 3º e 4º anos do 1º ciclo. Partindo da análise de uma situação problemática de ensino a crianças oriundas de meios de imigração foi realizada uma investigação que visava intervir na aprendizagem da escrita. Foi aplicado um pré-teste, escrita de uma narrativa tendo como estímulo um conjunto de imagens. Após a sua análise, delineámos uma intervenção de modo a melhorar os aspetos em que as crianças apresentavam dificuldades. A intervenção pedagógica focalizou o ensino da escrita enquanto processo e, dado do que o português não é a língua materna das crianças, demos uma atenção especial ao input textual, recorrendo à leitura obras literárias para crianças. Após a intervenção, foi realizado o pós-teste, sob as mesmas condições que o pré-teste, e observaram-se melhorias acentuadas na competência de escrita das crianças.

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.

SiC pinpin photonic for linking the visible spectrum to the telecom gap

Expanding far beyond traditional applications at telecommunications wavelengths, the SiC photonic devices has recently proven its merits for working with visible range optical signals. Reconfigurable wavelength selectors are essential sub-systems for implementing reconfigurable WDM networks and optical signal processing. Visible range to telecom band spectral translation in SiC/Si can be accomplished using wavelength selector under appropriated optical bias, acting as reconfigurable active filters. In this paper we present a monolithically integrated wavelength selector based on a multilayer SiC/Si integrated optical filters that requires optical switches to select wavelengths. The selector filter is realized by using double pin/pin a-SiC:H photodetector with front and back biased optical gating elements. Red, green, blue and violet communication channels are transmitted together, each one with a specific bit sequence. The combined optical signal is analyzed by reading out the generated photocurrent, under different background wavelengths applied either from the front or the back side. The backgrounds acts as channel selectors that selects one or more channels by splitting portions of the input multi-channel optical signals across the front and back photodiodes. The transfer characteristics effects due to changes in steady state light, irradiation side and frequency are presented. The relationship between the optical inputs and the digital output levels is established. (C) 2014 Elsevier B.V. All rights reserved.

Optical nonlinearity in Tandem SI-C photodetectors

The behavior of tandem pin heterojunctions based on a-SiC: H alloys is investigated under different optical and electrical bias conditions. The devices are optimized to act as optically selective wavelength filters. Depending on the device configuration (optical gaps, thickness, sequence of cells in the stack structure) and on the applied voltage (positive or negative) and optical bias (wavelength, intensity, frequency) it is possible to combine the wavelength discrimination function with the self amplification of the signal. This wavelength nonlinearity allows the amplification or the rejection of a weak signal-impulse. The device works as an active tunable optical filter for wavelength selection and can be used as an add/drop multiplexer (ADM) which enables data to enter and leave an optical network bit stream without having to demultiplex the stream. Results show that, even under weak transient input signals, the background wavelength controls the output signal. This nonlinearity, due to the transient asymmetrical light penetration of the input channels across the device together with the modification on the electrical field profile due to the optical bias, allows tuning an input channel without demultiplexing the stream. This high optical nonlinearity makes the optimized devices attractive for the amplification of all optical signals. Transfer characteristics effects due to changes in steady state light, control d.c. voltage and applied light pulses are presented. Based on the experimental results and device configuration an optoelectronic model is developed. The transfer characteristics effects due to changes in steady state light, dc control voltage or applied light pulses are simulated and compared with the experimental data. A good agreement was achieved.

Estudo comparativo de linguagem e dos comportamentos interativos pais- filhos aos 15 meses de vida

Dissertação apresentada à Escola Superior de Educação de Lisboa para a obtenção do grau de Mestre em Intervenção Precoce

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.