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Publicações

Publicações por LIAAD

2010

Evolutionary patterns at the RNase based gametophytic self-incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus)

Autores
Vieira, J; Ferreira, PG; Aguiar, B; Fonseca, NA; Vieira, CP;

Publicação
BMC EVOLUTIONARY BIOLOGY

Abstract
Background: Within Rosaceae, the RNase based gametophytic self-incompatibility (GSI) system has been studied at the molecular level in Maloideae and Prunus species that have been diverging for, at least, 32 million years. In order to understand RNase based GSI evolution within this family, comparative studies must be performed, using similar methodologies. Result: It is here shown that many features are shared between the two species groups such as levels of recombination at the S-RNase ( the S-pistil component) gene, and the rate at which new specificities arise. Nevertheless, important differences are found regarding the number of ancestral lineages and the degree of specificity sharing between closely related species. In Maloideae, about 17% of the amino acid positions at the S-RNase protein are found to be positively selected, and they occupy about 30% of the exposed protein surface. Positively selected amino acid sites are shown to be located on either side of the active site cleft, an observation that is compatible with current models of specificity determination. At positively selected amino acid sites, non-conservative changes are almost as frequent as conservative changes. There is no evidence that at these sites the most drastic amino acid changes may be more strongly selected. Conclusions: Many similarities are found between the GSI system of Prunus and Maloideae that are compatible with the single origin hypothesis for RNase based GSI. The presence of common features such as the location of positively selected amino acid sites and lysine residues that may be important for ubiquitylation, raise a number of issues that, in principle, can be experimentally addressed in Maloideae. Nevertheless, there are also many important differences between the two Rosaceae GSI systems. How such features changed during evolution remains a puzzling issue.

2010

Phylogeny of the Teashirt-related Zinc Finger (tshz) Gene Family and Analysis of the Developmental Expression of tshz2 and tshz3b in the Zebrafish

Autores
Santos, JS; Fonseca, NA; Vieira, CP; Vieira, J; Casares, F;

Publicação
DEVELOPMENTAL DYNAMICS

Abstract
The tshz genes comprise a family of evolutionarily conserved transcription factors. However, despite the major role played by Drosophila tsh during the development of the fruit fly, the expression and function of other tshz genes have been analyzed in a very limited set of organisms and, therefore, our current knowledge of these genes is still fragmentary. In this study, we perform detailed phylogenetic analyses of the tshz genes, identify the members of this gene family in zebrafish and describe the developmental expressions of two of them, tshz2 and tshz3b, and compare them with meis1, meis2.1, meis2.2, pax6a, and pax6b expression patterns. The expression patterns of these genes define a complex set of coexpression domains in the developing zebrafish brain where their gene products have the potential to interact. Developmental Dynamics 239:1010-1018, 2010. (C) 2010 Wiley-Liss, Inc.

2010

Predicting the Start of Protein alpha-Helices Using Machine Learning Algorithms

Autores
Camacho, R; Ferreira, R; Rosa, N; Guimaraes, V; Fonseca, NA; Costa, VS; de Sousa, M; Magalhaes, A;

Publicação
ADVANCES IN BIOINFORMATICS

Abstract

2010

A Review on Remote Monitoring Technology Applied to Implantable Electronic Cardiovascular Devices

Autores
Costa, PD; Rodrigues, PP; Reis, AH; Costa Pereira, A;

Publicação
TELEMEDICINE JOURNAL AND E-HEALTH

Abstract
Implantable electronic cardiovascular devices (IECD) include a broad spectrum of devices that have the ability to maintain rhythm, provide cardiac resynchronization therapy, and/or prevent sudden cardiac death. The incidence of bradyarrhythmias and other cardiac problems led to a broader use of IECD, which turned traditional follow-up into an extremely heavy burden for healthcare systems to support. Our aim was to assess the impact of remote monitoring on the follow-up of patients with IECD. We performed a review through PubMed using a specific query. The paper selection process included a three-step approach in which title, abstract, and cross-references were analyzed. Studies were then selected using previously defined inclusion criteria and analyzed according to the country of origin of the study, year, and journal of publication; type of study; and main issues covered. Twenty articles were included in this review. Eighty percent of the selected papers addressed clinical issues, from which 94% referred clinical events identification, clinical stability, time savings, or physician satisfaction as advantages, whereas 38% referred disadvantages that included both legal and technical issues. Forty-five percent of the papers referred patient issues, from which 89% presented advantages, focusing on patient acceptance/satisfaction, and patient time-savings. The main downsides were technical issues but patient privacy was also addressed. All the papers dealing with economic issues (20%) referred both advantages and disadvantages equally. Remote monitoring is presently a safe technology, widely accepted by patients and physicians, for its convenience, reassurance, and diagnostic potential. This review summarizes the principles of remote IECD monitoring presenting the current state-of-the-art. Patient safety and device interaction, applicability of current technology, and limitations of remote IECD monitoring are also addressed. The use of remote monitor should consider the selection of patients, the type of disease, and centers' availability to receive, interpret and respond to device alerts. Before remote IECD monitoring can be routinely used, technical, procedure, and ethical/legal issues should be addressed.

2010

Meta-Learning - Concepts and Techniques

Autores
Vilalta, R; Carrier, CGG; Brazdil, P;

Publicação
Data Mining and Knowledge Discovery Handbook, 2nd ed.

Abstract

2010

Determining the best classification algorithm with recourse to sampling and metalearning

Autores
Brazdil, P; Leite, R;

Publicação
Studies in Computational Intelligence

Abstract
Currently many classification algorithms exist and no algorithm exists that would outperform all the others. Therefore it is of interest to determine which classification algorithm is the best one for a given task. Although direct comparisons can be made for any given problem using a cross-validation evaluation, it is desirable to avoid this, as the computational costs are significant. We describe a method which relies on relatively fast pairwise comparisons involving two algorithms. This method is based on a previous work and exploits sampling landmarks, that is information about learning curves besides classical data characteristics. One key feature of this method is an iterative procedure for extending the series of experiments used to gather new information in the form of sampling landmarks. Metalearning plays also a vital role. The comparisons between various pairs of algorithm are repeated and the result is represented in the form of a partially ordered ranking. Evaluation is done by comparing the partial order of algorithm that has been predicted to the partial order representing the supposedly correct result. The results of our analysis show that the method has good performance and could be of help in practical applications. © 2010 Springer-Verlag Berlin Heidelberg.

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