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.

A Integração curricular da demonstração

Neste artigo, são discutidos os conceitos de demonstração e de esquema demonstrativo, bem como a relevância curricular da demonstração e os contextos favoráveis à sua aprendizagem. Alguns dos resultados do estudo, relativamente ao papel da demonstração no currículo, bem como ao modo como se desenvolveu o processo demonstrativo, são apresentados e discutidos. A metodologia adotada no estudo teve uma natureza interpretativa e os participantes no estudo foram uma turma de 9.º ano e a respetiva professora de Matemática. As conclusões do estudo apontam para o facto de os alunos tenderem a usar exemplos particulares para validar as suas afirmações matemáticas. Apontam ainda para as múltiplas funções da demonstração nas tarefas em que esta surgiu como um meio de descoberta da solução do problema. Sugerem também que a introdução e a negociação da importância da demonstração implicam uma intervenção curricular, na qual a professora detém um papel fundamental.

Modeling Allee Effect from Beta(p, 2) Densities

In this work we develop and investigate generalized populational growth models, adjusted from Beta(p, 2) densities, with Allee effect. The use of a positive parameter leads the presented generalization, which yields some more flexible models with variable extinction rates. An Allee limit is incorporated so that the models under study have strong Allee effect.

Superefficiency and Multiplier Adjustment in Data Envelopment Analysis

Copyright © 2013 Springer Netherlands.

Multiplier adjustment in data envelopment analysis

V Congreso de Eficiencia y Productividad EFIUCO, Córdoba, 19-20 Mayo 2011.

Quais os atributos que um auditor interno deve ter

Dissertação apresentada ao Instituto Superior de Contabilidade para a obtenção do Grau de Mestre em Auditoria

Educação para o Desenvolvimento Sustentável (EDS) no âmbito do Currículo Regional da Educação Básica da Região Autónoma dos Açores (CREB)

Mestrado, Educação Pré-Escolar e Ensino do 1.º Ciclo do Ensino Básico, 26 de Junho de 2013, Universidade dos Açores (Relatório de Estágio).

Scalable Unified Transform Architecture for Advanced Video Coding Embedded Systems

A novel high throughput and scalable unified architecture for the computation of the transform operations in video codecs for advanced standards is presented in this paper. This structure can be used as a hardware accelerator in modern embedded systems to efficiently compute all the two-dimensional 4 x 4 and 2 x 2 transforms of the H.264/AVC standard. Moreover, its highly flexible design and hardware efficiency allows it to be easily scaled in terms of performance and hardware cost to meet the specific requirements of any given video coding application. Experimental results obtained using a Xilinx Virtex-5 FPGA demonstrated the superior performance and hardware efficiency levels provided by the proposed structure, which presents a throughput per unit of area relatively higher than other similar recently published designs targeting the H.264/AVC standard. Such results also showed that, when integrated in a multi-core embedded system, this architecture provides speedup factors of about 120x concerning pure software implementations of the transform algorithms, therefore allowing the computation, in real-time, of all the above mentioned transforms for Ultra High Definition Video (UHDV) sequences (4,320 x 7,680 @ 30 fps).

Desenvolvimento de uma ferramenta de pré-selecção de recursos para empresas ágeis/virtuais

Mestrado em Engenharia Electrotécnica e de Computadores

O papel da angiogênese e da hemólise na úlcera de perna de pessoas com anemia falciforme

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Nuances in the embedment of ESDCG in the Azorean curriculum

Este capítulo tem origem na conferência «A Child's World - Working Together for a Better Future», que decorreu em Aberystwyth (Wales) entre 27 e 29 de Junho de 2012.

Android as a cloud ticket validator

Trabalho Final de Mestrado para a obtenção do grau de Mestre em Engenharia Informática e de Computadores

Grupos de simetria: identificação de padrões no património açoriano

Dissertação de Mestrado, Matemática para Professores, 3 de Abril de 2014, Universidade dos Açores.

A student personal system for Bologna process mobility

The Bologna Process aimed to build a European Higher Education Area with the objective of promoting students mobility. The adoption of Bologna Declaration directives requires a decentralized approach that accelerates student's mobility, based on frequently updated legislation. This paper proposes a student personal system to manage student's academic information. This system is supported by a flexible model that integrates, for instance, knowledge about the student attended courses or about a course that the student wishes to apply. Essentially, this model holds a (i) Student's Academic Record with skills acquired in academic course units, professional experience or training and an (ii) Individual Studies Plan, which places the student in a particular (iii) Course Plan setting the curricular structure that the student wishes to apply.

Intervenção pedagógica do futuro educador/professor e avaliação interativa nas práticas de estagiários e no discurso de docentes

Mestrado (PES II), Educação Pré-Escolar e Ensino do 1º Ciclo do Ensino Básico, 3 de Julho de 2014, Universidade dos Açores.