Arrow Plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on samples subgroups

Background: A common task in analyzing microarray data is to determine which genes are differentially expressed across two (or more) kind of tissue samples or samples submitted under experimental conditions. Several statistical methods have been proposed to accomplish this goal, generally based on measures of distance between classes. It is well known that biological samples are heterogeneous because of factors such as molecular subtypes or genetic background that are often unknown to the experimenter. For instance, in experiments which involve molecular classification of tumors it is important to identify significant subtypes of cancer. Bimodal or multimodal distributions often reflect the presence of subsamples mixtures. Consequently, there can be genes differentially expressed on sample subgroups which are missed if usual statistical approaches are used. In this paper we propose a new graphical tool which not only identifies genes with up and down regulations, but also genes with differential expression in different subclasses, that are usually missed if current statistical methods are used. This tool is based on two measures of distance between samples, namely the overlapping coefficient (OVL) between two densities and the area under the receiver operating characteristic (ROC) curve. The methodology proposed here was implemented in the open-source R software. Results: This method was applied to a publicly available dataset, as well as to a simulated dataset. We compared our results with the ones obtained using some of the standard methods for detecting differentially expressed genes, namely Welch t-statistic, fold change (FC), rank products (RP), average difference (AD), weighted average difference (WAD), moderated t-statistic (modT), intensity-based moderated t-statistic (ibmT), significance analysis of microarrays (samT) and area under the ROC curve (AUC). On both datasets all differentially expressed genes with bimodal or multimodal distributions were not selected by all standard selection procedures. We also compared our results with (i) area between ROC curve and rising area (ABCR) and (ii) the test for not proper ROC curves (TNRC). We found our methodology more comprehensive, because it detects both bimodal and multimodal distributions and different variances can be considered on both samples. Another advantage of our method is that we can analyze graphically the behavior of different kinds of differentially expressed genes. Conclusion: Our results indicate that the arrow plot represents a new flexible and useful tool for the analysis of gene expression profiles from microarrays.

O papel da supervisão na avaliação de desempenho docente

Com as várias reformulações do processo de avaliação de desempenho docente (ADD), passou-se de um processo de avaliação dos professores assente na autoavaliação do docente, para um sistema de heteroavaliação que visa a prestação de contas e a seleção, mas também a melhoria de práticas e o desenvolvimento profissional, através do acompanhamento supervisivo. No entanto, a conciliação entre estas duas perspetivas não é fácil e tem gerado perplexidades e inquietações entre os avaliadores e entre os avaliados. Com este estudo, pretendemos conhecer a perspetiva de avaliadores e avaliados sobre o papel que a Supervisão detém no processo de avaliação de desempenho do professor e o seu contributo para o desenvolvimento profissional do professor e melhoria das práticas. Assim desenhou-se um plano de estudo qualitativo, exploratório e descritivo procurando captar o ponto de vista dos principais intervenientes no processo. O principal meio de recolha de dados foi a entrevista semiestruturada a 4 professores avaliadores e 4 professores avaliados do Departamento de Matemática e Ciências Experimentais de um Agrupamento de Escolas. Os resultados mostram que os docentes discordam do modelo de ADD, mas que o processo vivenciado teve caraterísticas positivas, dando os avaliadores especial relevância à oportunidade de conhecer outros processos de trabalho, a partir da observação de aulas. Avaliadores e avaliados referem ainda o bom relacionamento estabelecido entre ambos, contradizendo as preocupações expressas quando se pronunciaram sobre os problemas do modelo de avaliação. No entanto, ambos os subgrupos focam a falta de formação e qualificação profissional dos avaliadores. Em termos gerais, é possível concluir que a maior parte das dificuldades atribuídas pelos docentes ao modelo de ADD não foi depois sentida na implementação prática. Por outro lado, na opinião dos docentes, o processo experienciado não teve verdadeiro impacto na melhoria das práticas ou no desenvolvimento profissional dos docentes envolvidos. - Abstract The several reformulations of the process of the teacher performance evaluation made the process of evaluating teachers, which was first based on a self-evaluation change into a straight assessment system, which aims not only accountability and selection, but also the improvement of the practice and professional development through the supervision of the teaching practice. However, the conciliation between these perspectives has not been easy and has generated anxieties and perplexities among evaluators and evaluated. With this study we intend to know the perspective of the evaluators and of the evaluated concerning the role supervision has hold in the process of evaluating a teacher’s performance and its contribution to the professional development of the teacher and to the improvement of his practices. Thus, a qualitative, exploratory and descriptive study plan was drawn to get to know the viewpoint of the intervening ones in the process. The main means for data collection was based on a semi structured interview, targeting 4 teacher evaluators and 4 evaluated teachers of the Experimental Sciences and Mathematics Department of a group of Schools. The results show that teachers disagree with the teacher’s evaluation model, but the experienced process had positive characteristics. Besides, evaluators have given special relevance to the opportunity of getting to know other working methods thanks to the lessons’ observations. Evaluators and evaluated also refer the good relationship between both parts contradicting the fears they had when they first pronounced themselves about this evaluation model. However, both subgroups focus the lack of training and professional qualifications of the evaluators. So it’s possible to conclude that most worries mentioned by the teachers when referring to this model of teacher performance evaluation were not verified during its practical implementation. On the other hand, in the opinion of the involved teachers, the experienced process had no real impact on their practice improvement or on their professional development.

Psychosocial factors as predictors of quality of life in chronic portuguese patients

Background - Chronic illnesses are diseases of long duration and generally of slow progression. They cause significant quality of life impairment. The aim of this study was to analyse psychosocial predictors of quality of life and of subjective well-being in chronic Portuguese patients. Methods - Chronic disease patients (n = 774) were recruited from central Portuguese Hospitals. Participants completed self-reported questionnaires assessing socio-demographic, clinical, psychosocial and outcome variables: quality of life (HRQL) and subjective well-being (SWB). MANCOVA analyses were used to test psychosocial factors as determinants of HRQL and SWB. Results - After controlling for socio-demographic and clinical variables, results showed that dispositional optimism, positive affect, spirituality, social support and treatment adherence are significant predictors of HRQL and SWB. Similar predictors of quality of life, such as positive affect, treatment adherence and spirituality, were found for subgroups of disease classified by medical condition. Conclusions - The work identifies psychosocial factors associated with quality of life. The predictors for the entire group of different chronic diseases are similar to the ones found in different chronic disease subgroups: positive affect, social support, treatment adherence and spirituality. Patients with more positive affect, additional social support, an adequate treatment adherence and a feel-good spirituality, felt better with the disease conditions and consequently had a better quality of life. This study contributes to understanding and improving the processes associated with quality of life, which is relevant for health care providers and chronic diseases support.

Avaliação de desempenho docente: efeitos no desenvolvimento profissional.

Dissertação apresentada à Escola Superior de Educação de Lisboa para obtenção de grau de mestre em Ciências da Educação - Especialização Supervisão em Educação

Avaliação de desempenho docente e seus atores

Dissertação apresentada à Escola Superior de Educação de Lisboa para obtenção de grau de mestre em Supervisão em Educação

Constraining multi-Higgs flavour models

To study a flavour model with a non-minimal Higgs sector one must first define the symmetries of the fields; then identify what types of vacua exist and how they may break the symmetries; and finally determine whether the remnant symmetries are compatible with the experimental data. Here we address all these issues in the context of flavour models with any number of Higgs doublets. We stress the importance of analysing the Higgs vacuum expectation values that are pseudo-invariant under the generators of all subgroups. It is shown that the only way of obtaining a physical CKM mixing matrix and, simultaneously, non-degenerate and non-zero quark masses is requiring the vacuum expectation values of the Higgs fields to break completely the full flavour group, except possibly for some symmetry belonging to baryon number. The application of this technique to some illustrative examples, such as the flavour groups Delta (27), A(4) and S-3, is also presented.