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.

Py-GC/MS(FID) assessed behavior of polysaccharides during kraft delignification of Eucalyptus globulus heartwood and sapwood

Eucalyptus globulus heartwood, sapwood and their delignified samples by kraft pulping at 130, 150 and 170 degrees C along time were characterized in respect to total carbohydrates by Py-GC/MS(FID). No significant differences between heartwood and sapwood were found in relation to pyrolysis products and composition. The main wood carbohydrate derived pyrolysis compounds were levoglucosan (25.1%), hydroxyacetaldehyde (12.5%), 2-oxo-propanal (10.3%) and acetic acid (8.7%). Levoglucosan decreased during the early stages of delignification and increased during the bulk and residual phases. Acetic acid decreased hydroxyacetaldehyde and 2-oxo-propanal increased, and 2-furaldehyde and hydroxypropanone remained almost constant during delignification. The C/L ratio was 3.2 in wood and remained rather constant in the first pulping periods until a loss of 15-25% in carbohydrate and 60% in lignin. Afterwards it increased sharply until 44 that correspond to the removal of 25-35% of carbohydrates and 95% of lignin. The pulping reactive selectivity to lignin vs. polysaccharides was the same for sapwood and heartwood. (C) 2013 Elsevier B.V. All rights reserved.

Measuring spatial interaction behavior in team sports using superimposed Voronoi diagrams

In team sports, the spatial distribution of players on the field is determined by the interaction behavior established at both player and team levels. The distribution patterns observed during a game emerge from specific technical and tactical methods adopted by the teams, and from individual, environmental and task constraints that influence players' behaviour. By understanding how specific patterns of spatial interaction are formed, one can characterize the behavior of the respective teams and players. Thus, in the present work we suggest a novel spatial method for describing teams' spatial interaction behaviour, which results from superimposing the Voronoi diagrams of two competing teams. We considered theoretical patterns of spatial distribution in a well-defined scenario (5 vs 4+ GK played in a field of 20x20m) in order to generate reference values of the variables derived from the superimposed Voronoi diagrams (SVD). These variables were tested in a formal application to empirical data collected from 19 Futsal trials with identical playing settings. Results suggest that it is possible to identify a number of characteristics that can be used to describe players' spatial behavior at different levels, namely the defensive methods adopted by the players.

Synthesis, characterization, electrochemical behavior and in vitro protein tyrosine kinase inhibitory activity of the cymene-halogenobenzohydroxamato [Ru(eta(6)-cymene)(bha)Cl] complexes

The ruthenium(II)-cymene complexes [Ru(eta(6)-cymene)(bha)Cl] with substituted halogenobenzohydroxamato (bha) ligands (substituents = 4-F, 4-Cl, 4-Br, 2,4-F-2, 3,4-F-2, 2,5-F-2, 2,6-F-2) have been synthesized and characterized by elemental analysis, IR, H-1 NMR, C-13 NMR, cyclic voltammetry and controlled-potential electrolysis, and density functional theory (DFT) studies. The compositions of their frontier molecular orbitals (MOs) were established by DFT calculations, and the oxidation and reduction potentials are shown to follow the orders of the estimated vertical ionization potential and electron affinity, respectively. The electrochemical E-L Lever parameter is estimated for the first time for the various bha ligands, which can thus be ordered according to their electron-donor character. All complexes exhibit very strong protein tyrosine kinase (PTK) inhibitory activity, even much higher than that of genistein, the clinically used PTK inhibitory drug. The complex containing the 2,4-difluorobenzohydroxamato ligand is the most active one, and the dependences of the PTK activity of the complexes and of their redox potentials on the ring substituents are discussed. (C) 2012 Elsevier B.V. All rights reserved.

Opportunistic feeding behavior of Diplodus argenteus (Perciformes, Sparidae) : human-fish interaction in two rocky reefs from SE and S Brazil

Comportamento alimentar oportunista do marimbá Diplodus argenteus (Perciformes, Sparidae): interação humana-peixe em dois sistemas de costões rochosos do SE e SU do Brasil. Esse artigo aborda dois tipos de comportamentos alimentares do marimbá Diplodus argenteus em dois sistemas de costões rochosos do Atlântico sul no Brasil. Essa espécie alimentou-se sobre o fundo e exibiu comportamentos ocasionais e oportunísticos.

Estudo da divergência entre duas vias que curvam em sentidos contrários

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Civil na Área de Especialização de Vias de Comunicação e Transportes

Static and hydrodynamic monitoring of citalopram based on its electro-oxidation behavior at a glassy-carbon surface

The electrooxidative behavior of citalopram (CTL) in aqueous media was studied by cyclic voltammetry (CV) and square-wave voltammetry (SWV) at a glassy-carbon electrode. The electrochemical behaviour of CTL involves two electrons and two protons in the irreversible and diffusion controlled oxidation of the tertiary amine group. The maximum analytical signal was obtained in a phosphate buffer (pH ¼ 8.2). For analytical purposes, an SWV method and a flow-injection analysis (FIA) system with amperometric detection were developed. The optimised SWV method showed a linear range between 1.10 10 5–1.20 10 4 molL 1, with a limit of detection (LOD) of 9.5 10 6 molL 1. Using the FIA method, a linear range between 2.00 10 6–9.00 10 5 molL 1 and an LODof 1.9 10 6 molL 1 were obtained. The validation of both methods revealed good performance characteristics confirming applicability for the quantification of CTL in several pharmaceutical products.

Validação da versão brasileira do Youth Risk Behavior Survey 2007

OBJETIVO: Validar as propriedades psicométricas da versão brasileira do questionário Youth Risk Behavior Survey (YRBS), versão 2007. MÉTODOS: Foram realizadas tradução para o português da versão original do YRBS2007 e retrotradução para o inglês. As versões do questionário foram analisadas por comitê de juízes. O comitê utilizou como critério de análise as equivalências semântica, idiomática, cultural e conceitual. Para identificação das propriedades psicométricas, a versão final do questionário YRBS2007 traduzida foi administrada em duas ocasiões com intervalo de duas semanas em amostra de 873 estudantes de ambos os sexos, do ensino médio, em Londrina, PR, em 2007. A confiabilidade teste-reteste foi analisada pelo cálculo do índice de concordância Kappa e da taxa de prevalência de cada comportamento de risco nas réplicas de aplicação. Teste de qui-quadrado foi empregado para identificar diferenças estatísticas entre a primeira e a segunda aplicações do questionário. RESULTADOS: Após discretas modificações apontadas nos processos de tradução, o comitê de juízes considerou que a versão para o idioma português do YRBS2007 apresentou equivalências semântica, idiomática, cultural e conceitual. Diferenças significativas entre as taxas de prevalências de ambas as aplicações foram observadas em 23,4% dos itens. A identificação de 91% dos itens com índice de concordância Kappa entre moderado a substancial e valor médio desse índice de 68,6% indicou a qualidade das propriedades psicométricas do YRBS2007 traduzido para o idioma português. CONCLUSÕES: A tradução, a adaptação transcultural e as qualidades psicométricas do questionário YRBS2007 foram satisfatórias, o que viabiliza sua aplicação em estudos epidemiológicos no Brasil.

Adsorption behavior of α-cypermethrin on cork and activated carbon

Studies were undertaken to determine the adsorption behavior of α-cypermethrin [R)-α-cyano-3-phenoxybenzyl(1S)-cis- 3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropanecarboxylate, and (S)-α-cyano-3-phenoxybenzyl (1R)-cis-3-(2,2-dichlorovinyl)-2,2- dimethylcyclopropanecarboxylate] in solutions on granules of cork and activated carbon (GAC). The adsorption studies were carried out using a batch equilibrium technique. A gas chromatograph with an electron capture detector (GC-ECD) was used to analyze α-cypermethrin after solid phase extraction with C18 disks. Physical properties including real density, pore volume, surface area and pore diameter of cork were evaluated by mercury porosimetry. Characterization of cork particles showed variations thereby indicating the highly heterogeneous structure of the material. The average surface area of cork particles was lower than that of GAC. Kinetics adsorption studies allowed the determination of the equilibrium time—24 hours for both cork (1–2 mm and 3–4 mm) and GAC. For the studied α-cypermethrin concentration range, GAC revealed to be a better sorbent. However, adsorption parameters for equilibrium concentrations, obtained through the Langmuir and Freundlich models, showed that granulated cork 1–2 mm have the maximum amount of adsorbed α-cypermethrin (qm) (303 μg/g); followed by GAC (186 μg/g) and cork 3-4 mm (136 μg/g). The standard deviation (SD) values, demonstrate that Freundlich model better describes the α-cypermethrin adsorption phenomena on GAC, while α-cypermethrin adsorption on cork (1-2 mm and 3-4 mm) is better described by the Langmuir. In view of the adsorption results obtained in this study it appears that granulated cork may be a better and a cheaper alternative to GAC for removing α-cypermethrin from water.

Symphysis-fundal height curve in the diagnosis of fetal growth deviations

OBJECTIVE: To validate a new symphysis-fundal curve for screening fetal growth deviations and to compare its performance with the standard curve adopted by the Brazilian Ministry of Health. METHODS: Observational study including a total of 753 low-risk pregnant women with gestational age above 27 weeks between March to October 2006 in the city of João Pessoa, Northeastern Brazil. Symphisys-fundal was measured using a standard technique recommended by the Brazilian Ministry of Health. Estimated fetal weight assessed through ultrasound using the Brazilian fetal weight chart for gestational age was the gold standard. A subsample of 122 women with neonatal weight measurements was taken up to seven days after estimated fetal weight measurements and symphisys-fundal classification was compared with Lubchenco growth reference curve as gold standard. Sensitivity, specificity, positive and negative predictive values were calculated. The McNemar χ2 test was used for comparing sensitivity of both symphisys-fundal curves studied. RESULTS: The sensitivity of the new curve for detecting small for gestational age fetuses was 51.6% while that of the Brazilian Ministry of Health reference curve was significantly lower (12.5%). In the subsample using neonatal weight as gold standard, the sensitivity of the new reference curve was 85.7% while that of the Brazilian Ministry of Health was 42.9% for detecting small for gestational age. CONCLUSIONS: The diagnostic performance of the new curve for detecting small for gestational age fetuses was significantly higher than that of the Brazilian Ministry of Health reference curve.

Health-related behavior and quality of life among the elderly: a population-based study

OBJECTIVE: To assess the association between health-related behaviors and quality of life among the elderly. METHODS: A population-based cross-sectional study was carried out including 1,958 elderly living in four areas in the state of São Paulo, southeastern Brazil, 2001/2002. Quality of life was assessed using the Medical Outcomes Study SF-36-Item Short Form Health Survey instrument. This instrument's eight subscales and two components were the dependent variables. Independent variables were physical activity, weekly frequency of alcohol consumption and smoking. Multiple linear regression models were used to control for the effect of gender, age, schooling, work, area of residence and number of chronic conditions. RESULTS: Physical activity was positively associated with the eight SF-36 subscales. The stronger associations were found for role-physical (β=11.9), physical functioning (β=11.3) and physical component. Elderly individuals who consumed alcohol at least once a week showed a better quality of life than those did not consume alcohol. Compared to non-smokers, smokers had a poorer quality of life for the mental component (β=-2.4). CONCLUSIONS: The study results showed that physical activity, moderate alcohol consumption and no smoking are positively associated with a better quality of life in the elderly.

Buying behavior and competition in the software market

In the actual world, the impact of the software buying decisions has a rising relevance in social and economic terms. This research tries to explain it focusing on the organizations buying decisions of Operating Systems and Office Suites for personal computers and the impact on the competition between incumbent and alternative players in the market in these software categories, although the research hypotheses and conclusions may extend to other software categories and platforms. We concluded that in this market beside brand image, product features or price, other factors could have influence in the buying choices. Network effect, switching costs, local network effect, lock-in or consumer heterogeneity all have influence in the buying decision, protecting the incumbent and making it difficult for the competitive alternatives, based mainly on product features and price, to gain market share to the incumbent. This happens in a stronger way in the Operating Systems category.

Influencing factors on the buying behavior in the software market

The case of desktop Operating System and Office Suite choices considering Proprietary and Open Source Software alternatives.

The Dark Side of Organizational Change: The Moderating Role of Political Behavior and Organizational Cynicism

Workplace aggression is a factor that shapes the interaction between individuals and their work environment and produces many undesirable outcomes, sometimes introducing heavy costs for organizations. Only through a comprehensive understanding of the genesis of workplace aggression is possible to develop strategies and interventions to minimize its nefarious effects. The existent body of knowledge has already identified several individual, situational and contextual antecedents of workplace aggression, although this is a research area where significant gaps occur and many issues were still not addressed Dupré and Barling (2006). According to Baron and Neuman (1998) one of these predictors is organizational change, since certain changes in the work environment (e.g., changes in management) can lead to increased aggression. This paper intends to contribute to workplace aggression research by studying its relationship with organizational change, considering a moderating role of political behaviors and organizational cynicism (Ammeter et al., 2002, Ferris et al., 2002). The literature review suggests that mediators and moderators that intervene in the relationships between workplace aggression and its antecedents are understudied topics. James (2005) sustains that organizational politics is related to cynicism and the empirical research of Miranda (2008) has identified leadership political behavior as an antecedent of cynicism but these two variables were not yet investigated regarding their relationship with workplace aggression. This investigation was operationalized using several scales including the Organizational Change Questionnaire-climate of change, processes, and readiness (Bouckenooghe, Devos and Broeck, 2009), a Workplace Aggression Scale (Vicente and D’Oliveira, 2008, 2009, 2010), an Organizational Cynicism Scale (Wanous, Reichers and Austin, 1994) and a Political Behavior Questionnaire (Yukl and Falbe, 1990). Participants representing a wide variety of jobs across many organizations were surveyed. The results of the study and its implications will be presented and discussed. This study contribution is also discussed in what concerns organizational change practices in organizations.

Workplace aggression in organizational changing processes: The mediation role of leader political (soft and hard) behavior

One of the main trends in workplace aggression research is studying its antecedents. But the literature also reveals that some predictors remain understudied, like organizational change [1]. Additionally, possible mediators of this relationship were not investigated. The main objective of this research is studding the mediating effect of the leader political behavior (soft and hard version) on the relationship between organizational change and workplace aggression. Participants representing a wide variety of jobs across many organizations were surveyed. The measures used in this research are an Organizational Change Questionnaire climate of change, processes, and readiness [2], a Workplace Aggression Scale [e.g. 3, 4] and a Political Behavior Questionnaire [5]. The results of the study and its theoretical and practical implications will be presented and discussed.