Hardy-Weinberg Equilibrium and the Ternary Plot

The Hardy-Weinberg law, formulated about 100 years ago, states that under certain assumptions, the three genotypes AA, AB and BB at a bi-allelic locus are expected to occur in the proportions p2, 2pq, and q2 respectively, where p is the allele frequency of A, and q = 1-p. There are many statistical tests being used to check whether empirical marker data obeys the Hardy-Weinberg principle. Among these are the classical xi-square test (with or without continuity correction), the likelihood ratio test, Fisher's Exact test, and exact tests in combination with Monte Carlo and Markov Chain algorithms. Tests for Hardy-Weinberg equilibrium (HWE) are numerical in nature, requiring the computation of a test statistic and a p-value. There is however, ample space for the use of graphics in HWE tests, in particular for the ternary plot. Nowadays, many genetical studies are using genetical markers known as Single Nucleotide Polymorphisms (SNPs). SNP data comes in the form of counts, but from the counts one typically computes genotype frequencies and allele frequencies. These frequencies satisfy the unit-sum constraint, and their analysis therefore falls within the realm of compositional data analysis (Aitchison, 1986). SNPs are usually bi-allelic, which implies that the genotype frequencies can be adequately represented in a ternary plot. Compositions that are in exact HWE describe a parabola in the ternary plot. Compositions for which HWE cannot be rejected in a statistical test are typically “close" to the parabola, whereas compositions that differ significantly from HWE are “far". By rewriting the statistics used to test for HWE in terms of heterozygote frequencies, acceptance regions for HWE can be obtained that can be depicted in the ternary plot. This way, compositions can be tested for HWE purely on the basis of their position in the ternary plot (Graffelman & Morales, 2008). This leads to nice graphical representations where large numbers of SNPs can be tested for HWE in a single graph. Several examples of graphical tests for HWE (implemented in R software), will be shown, using SNP data from different human populations

Conceptual model for adaptable and extensible visual data exploration

Interactive visual representations complement traditional statistical and machine learning techniques for data analysis, allowing users to play a more active role in a knowledge discovery process and making the whole process more understandable. Though visual representations are applicable to several stages of the knowledge discovery process, a common use of visualization is in the initial stages to explore and organize a sometimes unknown and complex data set. In this context, the integrated and coordinated - that is, user actions should be capable of affecting multiple visualizations when desired - use of multiple graphical representations allows data to be observed from several perspectives and offers richer information than isolated representations. In this paper we propose an underlying model for an extensible and adaptable environment that allows independently developed visualization components to be gradually integrated into a user configured knowledge discovery application. Because a major requirement when using multiple visual techniques is the ability to link amongst them, so that user actions executed on a representation propagate to others if desired, the model also allows runtime configuration of coordinated user actions over different visual representations. We illustrate how this environment is being used to assist data exploration and organization in a climate classification problem.

Software for calculation of reservoir active capacity with the sequent-peak algorithm

It is presented a software developed with Delphi programming language to compute the reservoir's annual regulated active storage, based on the sequent-peak algorithm. Mathematical models used for that purpose generally require extended hydrological series. Usually, the analysis of those series is performed with spreadsheets or graphical representations. Based on that, it was developed a software for calculation of reservoir active capacity. An example calculation is shown by 30-years (from 1977 to 2009) monthly mean flow historical data, from Corrente River, located at São Francisco River Basin, Brazil. As an additional tool, an interface was developed to manage water resources, helping to manipulate data and to point out information that it would be of interest to the user. Moreover, with that interface irrigation districts where water consumption is higher can be analyzed as a function of specific seasonal water demands situations. From a practical application, it is possible to conclude that the program provides the calculation originally proposed. It was designed to keep information organized and retrievable at any time, and to show simulation on seasonal water demands throughout the year, contributing with the elements of study concerning reservoir projects. This program, with its functionality, is an important tool for decision making in the water resources management.

Avaliação da ferramenta de visualização de software SoftVisOAH como apoio à depuração de programas: um experimento controlado

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Imageamento da porosidade através de perfis geofísicos de poço

O imageamento da porosidade é uma representação gráfica da distribuição lateral da porosidade da rocha, estimada a partir de dados de perfis geofísicos de poço. Apresenta-se aqui uma metodologia para produzir esta imagem geológica, totalmente independente da intervenção do intérprete, através de um algoritmo, dito, interpretativo baseado em dois tipos de redes neurais artificiais. A primeira parte do algoritmo baseia-se em uma rede neural com camada competitiva e é construído para realizar uma interpretação automática do clássico gráfico o P_b - Φ_N, produzindo um zoneamento do perfil e a estimativa da porosidade. A segunda parte baseia-se em uma rede neural com função de base radial, projetado para realizar uma integração espacial dos dados, a qual pode ser dividida em duas etapas. A primeira etapa refere-se à correlação de perfis de poço e a segunda à produção de uma estimativa da distribuição lateral da porosidade. Esta metodologia ajudará o intérprete na definição do modelo geológico do reservatório e, talvez o mais importante, o ajudará a desenvolver de um modo mais eficiente as estratégias para o desenvolvimento dos campos de óleo e gás. Os resultados ou as imagens da porosidade são bastante similares às seções geológicas convencionais, especialmente em um ambiente deposicional simples dominado por clásticos, onde um mapa de cores, escalonado em unidades de porosidade aparente para as argilas e efetiva para os arenitos, mostra a variação da porosidade e a disposição geométrica das camadas geológicas ao longo da seção. Esta metodologia é aplicada em dados reais da Formação Lagunillas, na Bacia do Lago Maracaibo, Venezuela.

Caracterização do desempenho de escolares com e sem dificuldades de aprendizagem em tarefas de consciência fonológica

Learning to read and write at an early stage is the process of transferring the sound form of the spoken language for the graphical form of writing, a process, a time that in our system of alphabetical called writing, the letters are graphical representations in the level of phoneme. So that this representation occurs, it is necessary that the individual already can of some form perceive and manipulate the different sonorous segments of the word. This capacity of perception directed to the segments of the word calls Phonological Awareness. Thus, it was established had for objective to verify the pertaining to school performance of 1ª to 4ª series with and without of learning in Tests of Phonological Awareness. Fourth children with age average of 9 years and 3 months without learning disabilities had been submitted to the Protocol of Phonological Awareness (CIELO, 2002) using of this instrument had participated of this study 80 pertaining to school of both only the phonological tasks. The data received from quantiqualitative approach whose results were extracted inferences. The statistically significant results occurred in the tasks of Realism Face Detection, Syllables, Detecting Phonemes, Phonemic Synthesis and Reversal Phonemic. Based on the results we observed that children without learning difficulties performed better on all tasks mentioned above

Molecular determinants of caste differentiation in the highly eusocial honeybee Apis mellifera

Abstract Background In honeybees, differential feeding of female larvae promotes the occurrence of two different phenotypes, a queen and a worker, from identical genotypes, through incremental alterations, which affect general growth, and character state alterations that result in the presence or absence of specific structures. Although previous studies revealed a link between incremental alterations and differential expression of physiometabolic genes, the molecular changes accompanying character state alterations remain unknown. Results By using cDNA microarray analyses of >6,000 Apis mellifera ESTs, we found 240 differentially expressed genes (DEGs) between developing queens and workers. Many genes recorded as up-regulated in prospective workers appear to be unique to A. mellifera, suggesting that the workers' developmental pathway involves the participation of novel genes. Workers up-regulate more developmental genes than queens, whereas queens up-regulate a greater proportion of physiometabolic genes, including genes coding for metabolic enzymes and genes whose products are known to regulate the rate of mass-transforming processes and the general growth of the organism (e.g., tor). Many DEGs are likely to be involved in processes favoring the development of caste-biased structures, like brain, legs and ovaries, as well as genes that code for cytoskeleton constituents. Treatment of developing worker larvae with juvenile hormone (JH) revealed 52 JH responsive genes, specifically during the critical period of caste development. Using Gibbs sampling and Expectation Maximization algorithms, we discovered eight overrepresented cis-elements from four gene groups. Graph theory and complex networks concepts were adopted to attain powerful graphical representations of the interrelation between cis-elements and genes and objectively quantify the degree of relationship between these entities. Conclusion We suggest that clusters of functionally related DEGs are co-regulated during caste development in honeybees. This network of interactions is activated by nutrition-driven stimuli in early larval stages. Our data are consistent with the hypothesis that JH is a key component of the developmental determination of queen-like characters. Finally, we propose a conceptual model of caste differentiation in A. mellifera based on gene-regulatory networks.

O desenho no processo projetivo: estudo das representações gráficas de projetos de Paulo Mendes da Rocha

Há anos vem-se questionando o papel da representação gráfica na arquitetura, diante das novas tecnologias gráficas computacionais e novos processos projetivos delas decorrentes. Entretanto, o desenho à mão livre ainda se mostra atuante no processo projetivo, marcado por um olhar atento, uma percepção individual e um tempo de execução que permite imersão, entrega e reflexão. Este artigo apresenta uma análise a partir de um olhar mais atento ao desenho de projetos do arquiteto Paulo Mendes da Rocha, como contribuição para a discussão sobre o papel do desenho analógico no processo projetivo. Foram selecionados alguns projetos do arquiteto: Projeto para o Concurso de remodelação do centro urbano de Santiago (Chile); Estádio Serra Dourada; Edifício Jaraguá, Caetano de Campos; Ginásio do Clube Atlético Paulistano (1958); Residência no Butantã (1964); residência Fernando Millan (1970) e Museu Brasileiro da Escultura (1986). Este artigo apresenta estudos de leitura sobre os desenhos originais do arquiteto com o objetivo de detectar as intenções projetuais, conceitos e características do projeto. Foram feitas marcações gráficas sobre os desenhos originais, evidenciando uma leitura particular do pesquisador que permitiu uma melhor compreensão dos projetos.

O modelo tridimensional físico e seu papel na educação patrimonial

Este artigo versa sobre uma pesquisa integrante do Núcleo de Apoio à Pesquisa em Estudos de Linguagem em Arquitetura e Cidade (N.ELAC), que desenvolve pesquisas em Linguagem e Representação. Entre as diversas formas de representação em arquitetura, a presente pesquisa traz o modelo tridimensional físico como ferramenta que proporciona maior facilidade de leitura do projeto, sendo mais concreta que os desenhos técnicos. Objetiva-se, assim, destacar a importância do modelo físico como meio de aproximação da população ao patrimônio arquitetônico. Como estudo de caso, foi escolhido o Edifício E1, obra de Ernest Mange e Hélio Duarte. Localizado no campus da USP em São Carlos, é considerado patrimônio da cidade, entretanto, encontra-se praticamente enclausurado no interior do campus, dificultando maior contato da comunidade com o edifício. O projeto do edifício utilizou apenas o desenho como representação, não incluindo nenhum tipo de modelo tridimensional (físico ou digital). A partir de um levantamento das representações gráficas utilizadas pelos projetistas, foi possível fazer uma comparação entre o nível de compreensão do projeto apenas com as peças gráficas dos arquitetos e a partir do modelo físico, produzido pela pesquisadora. Foi realizado um pré-teste em escola pública municipal, despertando o interesse desses alunos pelo edifício em questão.

O uso da maquete física como ferramenta de leitura do patrimônio cultural

O presente artigo vincula-se às pesquisas do Núcleo de Apoio à Pesquisa em Estudos de Linguagem em Arquitetura e Cidade (N.ELAC), que atua na área de Linguagem e Representação. Diante das diversas formas de representação em arquitetura (desenho, maquete, modelos digitais), nesta pesquisa o modelo tridimensional físico é trazido como ferramenta que proporciona maior facilidade de leitura do projeto e tratado como meio de aproximação da comunidade ao patrimônio arquitetônico, envolvendo, sobretudo, a arquitetura moderna paulista. Como estudo de caso, escolheu-se o Edifício E1, obra de Ernest Mange e Hélio Duarte. Localizado no campus da USP em São Carlos, é considerado patrimônio da cidade, entretanto, encontra-se praticamente enclausurado no interior do campus, dificultando maior contato da comunidade com o edifício. Durante sua execução, foi utilizado apenas o desenho como ferramenta de representação de projeto, não incluindo nenhum tipo de modelo tridimensional (físico ou digital). A partir do levantamento das representações gráficas utilizadas, foi possível fazer uma comparação entre o nível de compreensão do projeto apenas com as peças gráficas dos arquitetos e a partir do modelo físico, produzido pela pesquisadora. Realizou-se um pré-teste em escola pública municipal, que indicou um aumento no interesse desses alunos pelo edifício em questão.

Data Quality Assessment of Ungated Flow Cytometry Data in High

Background: The recent development of semi-automated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical when developing new high throughput technologies and their associated information services. Our experience suggests that significant bottlenecks remain in the development of high throughput flow cytometry methods for data analysis and display. Especially, data quality control and quality assessment are crucial steps in processing and analyzing high throughput flow cytometry data. Methods: We propose a variety of graphical exploratory data analytic tools for exploring ungated flow cytometry data. We have implemented a number of specialized functions and methods in the Bioconductor package rflowcyt. We demonstrate the use of these approaches by investigating two independent sets of high throughput flow cytometry data. Results: We found that graphical representations can reveal substantial non-biological differences in samples. Empirical Cumulative Distribution Function and summary scatterplots were especially useful in the rapid identification of problems not identified by manual review. Conclusions: Graphical exploratory data analytic tools are quick and useful means of assessing data quality. We propose that the described visualizations should be used as quality assessment tools and where possible, be used for quality control.

Adaptive Rückmeldungen im intelligenten Tutorensystem LARGO

Das intelligente Tutorensystem LARGO für die Rechtswissenschaften soll Jurastudenten helfen, Argumentationsstrategien zu lernen. Im verwendeten Ansatz werden Gerichtsprotokolle als Lernmaterialien verwendet: Studenten annotieren diese und erstellen graphische Repräsentationen des Argumentationsverlaufs. Das System kann dabei zur Reflexion über die von Anwälten vorgebrachten Argumente anregen und Lernende auf mögliche Schwächen in ihrer Analyse des Disputs hinweisen. Zur Erkennung von Schwächen verwendet das System Graphgrammatiken und kollaborative Filtermechanismen. Dieser Artikel stellt dar, wie in LARGO auf Basis der Bestimmung eines „Benutzungskontextes“ die Rückmeldungen im System benutzungsadaptiv gestaltet werden. Weiterhin diskutieren wir auf Basis der Ergebnisse einer kontrollierten Studie mit dem System, welche mit Jurastudierenden an der University of Pittsburgh stattfand, in wie weit der automatisch bestimmte Benutzungskontext zur Vorhersage von Lernerfolgen bei Studenten verwendbar ist.

Tools for constraint visualization: The VIFID/TRIFID tool

Visualization of program executions has been used in applications which include education and debugging. However, traditional visualization techniques often fall short of expectations or are altogether inadequate for new programming paradigms, such as Constraint Logic Programming (CLP), whose declarative and operational semantics differ in some crucial ways from those of other paradigms. In particular, traditional ideas regarding the behavior of data often cannot be lifted in a straightforward way to (C)LP from other families of programming languages. In this chapter we discuss techniques for visualizing data evolution in CLP. We briefly review some previously proposed visualization paradigms, and also propose a number of (to our knowledge) novel ones. The graphical representations have been chosen based on the perceived needs of a programmer trying to analyze the behavior and characteristics of an execution. In particular, we concéntrate on the representation of the run-time valúes of the variables, and the constraints among them. Given our interest in visualizing large executions, we also pay attention to abstraction techniques, i.e., techniques which are intended to help in reducing the complexity of the visual information.

Some design issues in the visualization of constraint logic program execution

Visualization of program executions has been found useful in applications which include education and debugging. However, traditional visualization techniques often fall short of expectations or are altogether inadequate for new programming paradigms, such as Constraint Logic Programming (CLP), whose declarative and operational semantics differ in some crucial ways from those of other paradigms. In particular, traditional ideas regarding flow control and the behavior of data often cannot be lifted in a straightforward way to (C)LP from other families of programming languages. In this paper we discuss techniques for visualizing program execution and data evolution in CLP. We briefly review some previously proposed visualization paradigms, and also propose a number of (to our knowledge) novel ones. The graphical representations have been chosen based on the perceived needs of a programmer trying to analyze the behavior and characteristics of an execution. In particular, we concéntrate on the representation of the program execution behavior (control), the runtime valúes of the variables, and the runtime constraints. Given our interest in visualizing large executions, we also pay attention to abstraction techniques, Le., techniques which are intended to help in reducing the complexity of the visual information.

Tools for constraint visualisation: The VIFID/TRIFID tool

Visualisation of program executions has been used in applications which include education and debugging. However, traditional visualisation techniques often fall short of expectations or are altogether inadequate for new programming paradigms, such as Constraint Logic Programming (CLP), whose declarative and operational semantics differ in some crucial ways from those of other paradigms. In particular, traditional ideas regarding the behaviour of data often cannot be lifted in a straightforward way to (C)LP from other families of programming languages. In this chapter we discuss techniques for visualising data evolution in CLP. We briefly review some previously proposed visualisation paradigms, and also propose a number of (to our knowledge) novel ones. The graphical representations have been chosen based on the perceived needs of a programmer trying to analyse the behaviour and characteristics of an execution. In particular, we concentrate on the representation of the run-time values of the variables, and the constraints among them. Given our interest in visualising large executions, we also pay attention to abstraction techniques, i.e., techniques which are intended to help in reducing the complexity of the visual information.