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.

Factors influencing innovation decision making in Portuguese firms

There is an undeniable positive effect of innovation for both firms and the economy, with particular regards to the financial performance of firms. However, there is an important role of the decision making process for the allocation of resources to finance the innovation process. The aim of this paper is to understand what factors explain the decision making process in innovation activities of Portuguese firms. This is an empirical study, based on the modern theoretical approaches, which has relied on five key aspects for innovation: barriers, sources, cooperation, funding; and the decision making process. Primary data was collected through surveys to firms that have applied for innovation programmes within the Portuguese innovation agency. Univariate and multivariate statistical techniques were used. Our results suggest that the factors that mostly influence the Portuguese firms’ innovation decision-making processes are economical and financial (namely those related to profit increase and labour costs reduction).

Spatial analysis of urban violence based on emergency room data

OBJECTIVE: To estimate the spatial intensity of urban violence events using wavelet-based methods and emergency room data. METHODS: Information on victims attended at the emergency room of a public hospital in the city of São Paulo, Southeastern Brazil, from January 1, 2002 to January 11, 2003 were obtained from hospital records. The spatial distribution of 3,540 events was recorded and a uniform random procedure was used to allocate records with incomplete addresses. Point processes and wavelet analysis technique were used to estimate the spatial intensity, defined as the expected number of events by unit area. RESULTS: Of all georeferenced points, 59% were accidents and 40% were assaults. There is a non-homogeneous spatial distribution of the events with high concentration in two districts and three large avenues in the southern area of the city of São Paulo. CONCLUSIONS: Hospital records combined with methodological tools to estimate intensity of events are useful to study urban violence. The wavelet analysis is useful in the computation of the expected number of events and their respective confidence bands for any sub-region and, consequently, in the specification of risk estimates that could be used in decision-making processes for public policies.

Potencialidades e utilização do espaço recreio: um estudo desenvolvido em escolas do 1.º ciclo do ensino básico

Dissertação apresentada para a obtenção do grau de Mestre em Educação - Área de Especialização em Didática das Ciências

Difficulties in the Learning of Statistics by the Students of the Primary Education

The present study, covering students from public schools and a private school on the island of São Miguel (Azores, Portugal), aims to meet the difficulties of the students of the 3rd and 4th years of the primary education in solving tasks involving construction, reading and interpreting tables and statistical graphs, in the context of Organization and Data Handling (ODH). We present the main results obtained from statistical methods, among which we highlight some non-parametric hypothesis tests and the Categorical Principal Component Analysis (CatPCA), given the nature of the variables included in the questionnaire (mostly nominal and ordinal variables).

A influência da cultura e do julgamento profissional sobre a contabilidade : uma análise sob o ponto de vista dos preparadores da informação em Portugal

Mestrado em Auditoria

PAH air pollution at a Portuguese urban area: carcinogenic risks and sources identification

This study aimed to characterize air pollution and the associated carcinogenic risks of polycyclic aromatic hydrocarbon (PAHs) at an urban site, to identify possible emission sources of PAHs using several statistical methodologies, and to analyze the influence of other air pollutants and meteorological variables on PAH concentrations.The air quality and meteorological data were collected in Oporto, the second largest city of Portugal. Eighteen PAHs (the 16 PAHs considered by United States Environment Protection Agency (USEPA) as priority pollutants, dibenzo[a,l]pyrene, and benzo[j]fluoranthene) were collected daily for 24 h in air (gas phase and in particles) during 40 consecutive days in November and December 2008 by constant low-flow samplers and using polytetrafluoroethylene (PTFE) membrane filters for particulate (PM10 and PM2.5 bound) PAHs and pre-cleaned polyurethane foam plugs for gaseous compounds. The other monitored air pollutants were SO2, PM10, NO2, CO, and O3; the meteorological variables were temperature, relative humidity, wind speed, total precipitation, and solar radiation. Benzo[a]pyrene reached a mean concentration of 2.02 ngm−3, surpassing the EU annual limit value. The target carcinogenic risks were equal than the health-based guideline level set by USEPA (10−6) at the studied site, with the cancer risks of eight PAHs reaching senior levels of 9.98×10−7 in PM10 and 1.06×10−6 in air. The applied statistical methods, correlation matrix, cluster analysis, and principal component analysis, were in agreement in the grouping of the PAHs. The groups were formed according to their chemical structure (number of rings), phase distribution, and emission sources. PAH diagnostic ratios were also calculated to evaluate the main emission sources. Diesel vehicular emissions were the major source of PAHs at the studied site. Besides that source, emissions from residential heating and oil refinery were identified to contribute to PAH levels at the respective area. Additionally, principal component regression indicated that SO2, NO2, PM10, CO, and solar radiation had positive correlation with PAHs concentrations, while O3, temperature, relative humidity, and wind speed were negatively correlated.

On sampling collection procedure effectiveness for forest soil characterization

One of the most important measures to prevent wild forest fires is the use of prescribed and controlled burning actions as it reduce the fuel mass availability. The impact of these management activities on soil physical and chemical properties varies according to the type of both soil and vegetation. Decisions in forest management plans are often based on the results obtained from soil-monitoring campaigns. Those campaigns are often man-labor intensive and expensive. In this paper we have successfully used the multivariate statistical technique Robust Principal Analysis Compounds (ROBPCA) to investigate on the sampling procedure effectiveness for two different methodologies, in order to reflect on the possibility of simplifying and reduce the sampling collection process and its auxiliary laboratory analysis work towards a cost-effective and competent forest soil characterization.

Forest soil short term response to prescribed fire: an approach by Principal Components Analysis

In the current context of serious climate changes, where the increase of the frequency of some extreme events occurrence can enhance the rate of periods prone to high intensity forest fires, the National Forest Authority often implements, in several Portuguese forest areas, a regular set of measures in order to control the amount of fuel mass availability (PNDFCI, 2008). In the present work we’ll present a preliminary analysis concerning the assessment of the consequences given by the implementation of prescribed fire measures to control the amount of fuel mass in soil recovery, in particular in terms of its water retention capacity, its organic matter content, pH and content of iron. This work is included in a larger study (Meira-Castro, 2009(a); Meira-Castro, 2009(b)). According to the established praxis on the data collection, embodied in multidimensional matrices of n columns (variables in analysis) by p lines (sampled areas at different depths), and also considering the quantitative data nature present in this study, we’ve chosen a methodological approach that considers the multivariate statistical analysis, in particular, the Principal Component Analysis (PCA ) (Góis, 2004). The experiments were carried out in a soil cover over a natural site of Andaluzitic schist, in Gramelas, Caminha, NW Portugal, who was able to maintain itself intact from prescribed burnings from four years and was submit to prescribed fire in March 2008. The soils samples were collected from five different plots at six different time periods. The methodological option that was adopted have allowed us to identify the most relevant relational structures inside the n variables, the p samples and in two sets at the same time (Garcia-Pereira, 1990). Consequently, and in addition to the traditional outputs produced from the PCA, we have analyzed the influence of both sampling depths and geomorphological environments in the behavior of all variables involved.

Energy-dispersive x-ray fluorescence analysis of modern coloured glasses from Marinha Grande (Portugal)

X-Ray Spectrom. 2003; 32: 396–401

Multiple sequence alignment correction using constraints

Trabalho apresentado no âmbito do European Master in Computational Logics, como requisito parcial para obtenção do grau de Mestre em Computational Logics

Comparing wind generation profiles: A circular data approach

The importance of wind power energy for energy and environmental policies has been growing in past recent years. However, because of its random nature over time, the wind generation cannot be reliable dispatched and perfectly forecasted, becoming a challenge when integrating this production in power systems. In addition the wind energy has to cope with the diversity of production resulting from alternative wind power profiles located in different regions. In 2012, Portugal presented a cumulative installed capacity distributed over 223 wind farms [1]. In this work the circular data statistical methods are used to analyze and compare alternative spatial wind generation profiles. Variables indicating extreme situations are analyzed. The hour (s) of the day where the farm production attains its maximum daily production is considered. This variable was converted into circular variable, and the use of circular statistics enables to identify the daily hour distribution for different wind production profiles. This methodology was applied to a real case, considering data from the Portuguese power system regarding the year 2012 with a 15-minutes interval. Six geographical locations were considered, representing different wind generation profiles in the Portuguese system.In this work the circular data statistical methods are used to analyze and compare alternative spatial wind generation profiles. Variables indicating extreme situations are analyzed. The hour (s) of the day where the farm production attains its maximum daily production is considered. This variable was converted into circular variable, and the use of circular statistics enables to identify the daily hour distribution for different wind production profiles. This methodology was applied to a real case, considering data from the Portuguese power system regarding the year 2012 with a 15-minutes interval. Six geographical locations were considered, representing different wind generation profiles in the Portuguese system.

Modelos de previsão de produção para centrais mini-hídricas

O constante crescimento dos produtores em regime especial aliado à descentralização dos pontos injetores na rede, tem permitido uma redução da importação de energia mas também tem acarretado maiores problemas para a gestão da rede. Estes problemas estão relacionados com o facto da produção estar dependente das condições climatéricas, como é o caso dos produtores eólicos, hídricos e solares. A previsão da energia produzida em função da previsão das condições climatéricas tem sido alvo de atenção por parte da comunidade empresarial do setor, pelo facto de existir modelos razoáveis para a previsão das condições climatéricas a curto prazo, e até a longo prazo. Este trabalho trata, em concreto, do problema da previsão de produção em centrais mini-hídricas, apresentando duas propostas para essa previsão. Em ambas as propostas efetua-se inicialmente a previsão do caudal que chega à central, sendo esta depois convertida em potência que é injetada na rede. Para a previsão do caudal utilizaram-se dois métodos estatísticos: o método Holt-Winters e os modelos ARMAX. Os dois modelos de previsão propostos consideram um horizonte temporal de uma semana, com discretização horária, para uma central no norte de Portugal, designadamente a central de Penide. O trabalho também contempla um pequeno estudo da bibliografia existente tanto para a previsão da produção como de afluências de centrais hidroelétricas. Aborda, ainda, conceitos relacionados com as mini-hídricas e apresenta uma caraterização do parque de centrais mini-hídricas em Portugal.

Teorias e modelos organizacionais

Este trabalho propõe-se a investigar as teorias e modelos organizacionais e a respetiva aplicabilidade nas organizações portuguesas. Após a revisão da literatura sobre modelos organizacionais, foi efetuada uma investigação quantitativa através de um questionário online com a finalidade de avaliar quais os modelos organizacionais predominantemente utilizados e quais as características organizacionais que levam à utilização de determinado modelo. Através de métodos estatísticos analisaram-se os resultados do inquérito com o objetivo de verificar a existência de possíveis relações entre diversas características das organizações e o modelo organizacional usado. Foi possível concluir que o modelo organizacional Burocrático é o modelo predominantemente utilizado pelos respondentes e que as organizações que adotam o modelo burocrático parecem conseguir implementar processos sistemáticos de inovação compatibilizando as regras e procedimentos com a capacidade para aprender e se adaptar. O setor de atividade e a dimensão das organizações são as variáveis que mais influenciam a adoção do modelo organizacional. A investigação contribui para o conhecimento teórico e pratico sobre modelos organizacionais e sobre a sua aplicação em diferentes tipos de organizações portuguesas e para a compreensão e capacitação dos engenheiros do tema da cultura organizacional, de modo a poderem trabalhar de forma efetiva em grupos multidisciplinares que criem valor para as respetivas organizações, inovando e aplicando a engenharia e tecnologia para lidar com as questões e desafios atuais referidos pelo relatório da UNESCO (1).

Modelling and optimization of the ion exchange membrane bioreactor for removal of anionic pollutants from drinking water streams

Dissertação para obtenção do Grau de Doutor em Engenharia Química, especialidade de Engenharia Bioquímica