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.

Quality of life of the caregivers of people with aphasia. A systematic review.

Purpose: Systematic review to identify the factors associated to the quality of life (QOL) of the caregivers of people with aphasia (PWA). Methods: Studies were searched using Medline, Pubmed, Cochrane Library, CINAHL, PsycINFO and Web of Science databases. Peer-reviewed papers that studied the QOL of PWA’s caregivers or the consequences of aphasia in caregivers’ life were included. Findings were extracted from the studies that met the inclusion criteria. Results: No data is available reporting particularly the QOL of PWA caregivers’ or their QOL predictors. Nevertheless, it was possible to extract aspects related to QOL from the studies that report the consequences of aphasia, and life changes in PWA’s caregivers. Nine (9) studies including PWA’s caregivers were found, but only 5 reported data separately on them. Methodological heterogeneity impedes cross-study comparisons, although some considerations can be made. PWA’s caregivers reported life changes such as: loss of freedom; social isolation; new responsibilities; anxiety; emotional loneliness; need for support and respite. Conclusions: Changes in social relationships, in emotional status, increased burden and need for support and respite were experienced by PWA’s caregivers. Stroke QOL studies need to include PWA caregivers’ and report separately on them. Further research is needed in this area in order to determine their QOL predictors and identify what interventions and referrals better suit their needs.

ß-lactamases in the biochemistry and molecular biology laboratory

β-lactamases are hydrolytic enzymes that inactivate the β-lactam ring of antibiotics such as penicillins and cephalosporins. The major diversity of studies carried out until now have mainly focused on the characterization of β-lactamases recovered among clinical isolates of Gram-positive staphylococci and Gram-negative enterobacteria, amongst others. However, only some studies refer to the detection and development of β-lactamases carriers in healthy humans, sick animals, or even in strains isolated from environmental stocks such as food, water, or soils. Considering this, we proposed a 10-week laboratory programme for the Biochemistry and Molecular Biology laboratory for majors in the health, environmental, and agronomical sciences. During those weeks, students would be dealing with some basic techniques such as DNA extraction, bacterial transformation, polymerase chain reaction (PCR), gel electrophoresis, and the use of several bioinformatics tools. These laboratory exercises would be conducted as a mini research project in which all the classes would be connected with the previous ones. This curriculum was compared in an experiment involving two groups of students from two different majors. The new curriculum, with classes linked together as a mini research project, was taught to a major in Pharmacy and an old curriculum was taught to students from environmental health. The results showed that students who were enrolled in the new curriculum obtained better results in the final exam than the students who were enrolled in the former curriculum. Likewise, these students were found to be more enthusiastic during the laboratory classes than those from the former curriculum.

Divulgação online da religião católica - estudo de caso: análise do website da Diocese do Porto

Dissertação de Mestrado apresentada ao Instituto Superior de Contabilidade e Administração do Porto para a obtenção do grau de Mestre em Marketing Digital, sob orientação de Mestre António da Silva Vieira

Motivations in volunteer work

The objective of this paper is to review and discuss the literature about volunteers’ motivations to donate their time to NGOs (Non Governmental Organisations). According to Parboteeah, Cullenb & Lim (2004) management research has not paid much attention to voluntarism, however, voluntarism is a substantial part of productive work for many societies. Wilson & Pimm (1996) show that in Great Britain about 39% of the adult population has been involved in some volunteer activity for some period of time. In the U.S.A. these values reach 50% (Wilson & Pimm, 1996). Considering the benefits that voluntarism can bring to an organisation, we understand that more attention must be devoted to this phenomenon. The more an organisation knows volunteers, the better this organisation will be able to meet the needs and expectations of these individuals. We present a literature review that illustrates and compares the different motivations associated with volunteer work. The paper includes a bibliographical databases search in specialised journals. The search used the key words “motivations” and “voluntarism” (in the heading and text body) and covered all numbers between 2000 and 2007. We identify the existence of repeated motivations (Holmberg & Söderlung, 2005; Prouteau & Wolff, 2008; Soupourmas & Ironmonger, 2001; Yavas & Riecken, 1997), which allow the establishment of a typology of volunteers’ motivations, based on four categories: altruism, social needs, self-esteem, learning and self-development. Finally we identify three main gaps in the literature that justify further research. First, research focusing on the differences between motivations related to volunteers’ "Attraction" versus "Retention" in NGO’s is nil. Second, the great majority of the studies rely on north American (USA and Canada) and Australian context, which demands for further research in European countries. Third, the majority of NGOs researched are related to sport, art or the environment, and it would be interesting to explore the relationship between motivation and NGO type. These questions may obtain interesting answers for NGO management, in particular with regard to volunteer attraction and retention.

As motivações no trabalho voluntário

Este trabalho revê e discute a literatura sobre as motivações dos voluntários para doarem o seu tempo às ONG’s. Quanto melhor uma organização conhecer os voluntários, mais essa organização poderá ir de encontro às necessidades e expectativas desses mesmos indivíduos. Por isso, compreender as motivações que podem levar um indivíduo a doar o seu tempo a uma determinada organização é relevante na gestão das ONG’s. Primeiro, o artigo discute o estado da arte do voluntariado formal e as motivações dos indivíduos voluntários não dirigentes. Apresenta-se uma pesquisa a bases de dados bibliográficas, que inclui revistas especializadas na investigação de voluntariado. Depois, o artigo mostra e compara os diferentes tipos de motivações associadas ao trabalho voluntário e propõe uma tipologia que agrupa as motivações dos voluntários em quatro tipos: altruísmo, pertença, ego e reconhecimento social e aprendizagem e desenvolvimento. Por fim, efectua-se uma análise que indica três lacunas na literatura das motivações dos voluntários que justificam investigação adicional: (i) a omissão de diferenças entre as motivações relacionadas com a “Atracção” versus a “Retenção” dos voluntários; (ii) a focalização das investigações no contexto norte-americano e australiano; e (iii) a ausência de análises comparativas que relacionem as motivações por tipos de ONG’s.

Processing XML with Java – a performance benchmark

Over time, XML markup language has acquired a considerable importance in applications development, standards definition and in the representation of large volumes of data, such as databases. Today, processing XML documents in a short period of time is a critical activity in a large range of applications, which imposes choosing the most appropriate mechanism to parse XML documents quickly and efficiently. When using a programming language for XML processing, such as Java, it becomes necessary to use effective mechanisms, e.g. APIs, which allow reading and processing of large documents in appropriated manners. This paper presents a performance study of the main existing Java APIs that deal with XML documents, in order to identify the most suitable one for processing large XML files

Performance analysis of Java APIS for XML processing

Over time, XML markup language has acquired a considerable importance in applications development, standards definition and in the representation of large volumes of data, such as databases. Today, processing XML documents in a short period of time is a critical activity in a large range of applications, which imposes choosing the most appropriate mechanism to parse XML documents quickly and efficiently. When using a programming language for XML processing, such as Java, it becomes necessary to use effective mechanisms, e.g. APIs, which allow reading and processing of large documents in appropriated manners. This paper presents a performance study of the main existing Java APIs that deal with XML documents, in order to identify the most suitable one for processing large XML files.

Relação existente entre as exportações e as restrições financeiras das empresas industriais do setor têxtil

Dissertação de Mestrado em Finanças Empresariais

Mental health and psychiatry research in Brazil: scientific production from 1999 to 2003

OBJECTIVE: To assess the extent of mental health scientific production in Brazil from 1999 to 2003, and to identify the nature of the publications generated, their sources of finance and the ways of publicly disseminating the research findings. METHODS: Searches for publications were conducted in the Medline and PsychInfo databases for the period 1999-2003. A semi-structured questionnaire developed by an international team was applied to 626 mental health researchers, covering each interviewee's educational background, research experience, access to funding sources, public impact and research priorities. The sample was composed by 626 mental health researchers identified from 792 publications indexed on Medline and PsychInfo databases for the period above, and from a list of reviewers of Revista Brasileira de Psiquiatria. RESULTS: In Brazil, 792 publications were produced by 525 authors between 1999 and 2003 (441 indexed in Medline and 398 in the ISI database). The main topics were: depression (29.1%), substance misuse (14.6%), psychoses (10%), childhood disorders (7%) and dementia (6.7%). Among the 626 Brazilian mental health researchers, 329 answered the questionnaire. CONCLUSIONS: There were steadily increasing numbers of Brazilian articles on mental health published in foreign journals from 1999 to 2003: the number of articles in Medline tripled and it doubled in the ISI database. The content of these articles corresponded to the priorities within mental health, but there is a need for better interlinking between researchers and mental health policymakers.

Insuficiência cardíaca: a utilidade da Ecocardiografia

Objetivos Os principais objetivos deste trabalho foram: 1) Rever as características da IC: epidemiologia, conceito, classificação, etiologia, fisiopatologia, diagnóstico e tratamento; 2) Demonstrar a importância da Ecocardiografia na IC: (a) no diagnóstico, (b) no acompanhamento e (c) na seleção da opção terapêutica. Como objetivo secundário: Reunir toda a informação com vista à produção de um manual de apoio às aulas. Metodologia Os estudos que serviram de base a este trabalho foram pesquisados a partir das palavras-chave “echocardiography”, “heart failure”, “diagnosis”, “treatment” utilizando as bases de dados PubMed, Scopus e ISI Web of Science. A pesquisa foi limitada a artigos publicados em português, inglês e espanhol, sem restrição por tipo de artigo ou ano de publicação. Ao longo da realização deste trabalho, foram sendo recolhidas referências de outros artigos citados nos estudos inicialmente selecionados, expandindo assim a bibliografia. Para conhecer a situação particular de Portugal, foram pesquisados estudos realizados com a população portuguesa. Foi dada particular atenção às várias recomendações existentes quer para a “Insuficiência Cardíaca” quer para a “Utilidade da Ecocardiografia”, disponíveis gratuitamente online, pois estas desempenham um papel fundamental quer na prática clínica, quer na investigação (estudos epidemiológicos, estudos obrigacionais e ensaios clínicos).

CCTα

In the cell, the correct folding of many proteins depends on the function of preexisting ones known as Molecular Chaperones (for a review see Hartl and Hayer-Hartl 2009). These, were defined as proteins that bind to and stabilize an otherwise unstable conformation of another protein, and by controlling binding and release, facilitate its correct fate in vivo, be it folding, oligomeric assembly, transport to a particular subcellular compartment, or disposal by degradation. Molecular chaperones do not convey steric information specifying correct folding: instead, they prevent incorrect interactions within and between nonnative peptides, thus typically increasing the yield but not the rate of folding reactions. Molecular chaperones are ubiquitous and comprise several protein families that are structurally unrelated (Hartl and Hayer-Hartl 2009). The Hsp70s and the Chaperonin families have been extensively studied.

A similarity measure for music signals

One of the goals in the field of Music Information Retrieval is to obtain a measure of similarity between two musical recordings. Such a measure is at the core of automatic classification, query, and retrieval systems, which have become a necessity due to the ever increasing availability and size of musical databases. This paper proposes a method for calculating a similarity distance between two music signals. The method extracts a set of features from the audio recordings, models the features, and determines the distance between models. While further work is needed, preliminary results show that the proposed method has the potential to be used as a similarity measure for musical signals.

Os preços de transferência e o âmbito de intervenção do auditor: abordagem e enquadramento

Dissertação de Mestrado apresentado ao Instituto de Contabilidade e Administração do obtenção do grau de Mestre em Auditoria Auditoria, sob orientação de Adalmiro Álvaro Malheiro de Castro Andrade