Grid computing solutions for distributed repositories of protein folding and unfolding simulations

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data and a data warehouse. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular we look at two aspects, first how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories --- this is an important and challenging aspect of P-found because the data volumes involved are too large to be centralised. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling new scientific discoveries.

Business Intelligence: comparação de ferramentas

Cada vez mais o tempo acaba sendo o diferencial de uma empresa para outra. As empresas, para serem bem sucedidas, precisam da informação certa, no momento certo e para as pessoas certas. Os dados outrora considerados importantes para a sobrevivência das empresas hoje precisam estar em formato de informações para serem utilizados. Essa é a função das ferramentas de “Business Intelligence”, cuja finalidade é modelar os dados para obter informações, de forma que diferencie as ações das empresas e essas consigam ser mais promissoras que as demais. “Business Intelligence” é um processo de coleta, análise e distribuição de dados para melhorar a decisão de negócios, que leva a informação a um número bem maior de usuários dentro da corporação. Existem vários tipos de ferramentas que se propõe a essa finalidade. Esse trabalho tem como objetivo comparar ferramentas através do estudo das técnicas de modelagem dimensional, fundamentais nos projetos de estruturas informacionais, suporte a “Data Warehouses”, “Data Marts”, “Data Mining” e outros, bem como o mercado, suas vantagens e desvantagens e a arquitetura tecnológica utilizada por estes produtos. Assim sendo, foram selecionados os conjuntos de ferramentas de “Business Intelligence” das empresas Microsoft Corporation e Oracle Corporation, visto as suas magnitudes no mundo da informática.

Metrics to support the evaluation of association rule clustering

Many topics related to association mining have received attention in the research community, especially the ones focused on the discovery of interesting knowledge. A promising approach, related to this topic, is the application of clustering in the pre-processing step to aid the user to find the relevant associative patterns of the domain. In this paper, we propose nine metrics to support the evaluation of this kind of approach. The metrics are important since they provide criteria to: (a) analyze the methodologies, (b) identify their positive and negative aspects, (c) carry out comparisons among them and, therefore, (d) help the users to select the most suitable solution for their problems. Some experiments were done in order to present how the metrics can be used and their usefulness. © 2013 Springer-Verlag GmbH.

Plataforma de evaluación de algoritmos para la identificación de usuarios

La minería de datos es un campo de las ciencias de la computación referido al proceso que intenta descubrir patrones en grandes volúmenes de datos. La minería de datos busca generar información similar a la que podría producir un experto humano. Además es el proceso de descubrir conocimientos interesantes, como patrones, asociaciones, cambios, anomalías y estructuras significativas a partir de grandes cantidades de datos almacenadas en bases de datos, data warehouses o cualquier otro medio de almacenamiento de información. El aprendizaje automático o aprendizaje de máquinas es una rama de la Inteligencia artificial cuyo objetivo es desarrollar técnicas que permitan a las computadoras aprender. De forma más concreta, se trata de crear programas capaces de generalizar comportamientos a partir de una información no estructurada suministrada en forma de ejemplos. La minería de datos utiliza métodos de aprendizaje automático para descubrir y enumerar patrones presentes en los datos. En los últimos años se han aplicado las técnicas de clasificación y aprendizaje automático en un número elevado de ámbitos como el sanitario, comercial o de seguridad. Un ejemplo muy actual es la detección de comportamientos y transacciones fraudulentas en bancos. Una aplicación de interés es el uso de las técnicas desarrolladas para la detección de comportamientos fraudulentos en la identificación de usuarios existentes en el interior de entornos inteligentes sin necesidad de realizar un proceso de autenticación. Para comprobar que estas técnicas son efectivas durante la fase de análisis de una determinada solución, es necesario crear una plataforma que de soporte al desarrollo, validación y evaluación de algoritmos de aprendizaje y clasificación en los entornos de aplicación bajo estudio. El proyecto planteado está definido para la creación de una plataforma que permita evaluar algoritmos de aprendizaje automático como mecanismos de identificación en espacios inteligentes. Se estudiarán tanto los algoritmos propios de este tipo de técnicas como las plataformas actuales existentes para definir un conjunto de requisitos específicos de la plataforma a desarrollar. Tras el análisis se desarrollará parcialmente la plataforma. Tras el desarrollo se validará con pruebas de concepto y finalmente se verificará en un entorno de investigación a definir. ABSTRACT. The data mining is a field of the sciences of the computation referred to the process that it tries to discover patterns in big volumes of information. The data mining seeks to generate information similar to the one that a human expert might produce. In addition it is the process of discovering interesting knowledge, as patterns, associations, changes, abnormalities and significant structures from big quantities of information stored in databases, data warehouses or any other way of storage of information. The machine learning is a branch of the artificial Intelligence which aim is to develop technologies that they allow the computers to learn. More specifically, it is a question of creating programs capable of generalizing behaviors from not structured information supplied in the form of examples. The data mining uses methods of machine learning to discover and to enumerate present patterns in the information. In the last years there have been applied classification and machine learning techniques in a high number of areas such as healthcare, commercial or security. A very current example is the detection of behaviors and fraudulent transactions in banks. An application of interest is the use of the techniques developed for the detection of fraudulent behaviors in the identification of existing Users inside intelligent environments without need to realize a process of authentication. To verify these techniques are effective during the phase of analysis of a certain solution, it is necessary to create a platform that support the development, validation and evaluation of algorithms of learning and classification in the environments of application under study. The project proposed is defined for the creation of a platform that allows evaluating algorithms of machine learning as mechanisms of identification in intelligent spaces. There will be studied both the own algorithms of this type of technologies and the current existing platforms to define a set of specific requirements of the platform to develop. After the analysis the platform will develop partially. After the development it will be validated by prove of concept and finally verified in an environment of investigation that would be define.

An authoring tool for decision support systems in context questions of ecological knowledge

Decision support systems (DSS) support business or organizational decision-making activities, which require the access to information that is internally stored in databases or data warehouses, and externally in the Web accessed by Information Retrieval (IR) or Question Answering (QA) systems. Graphical interfaces to query these sources of information ease to constrain dynamically query formulation based on user selections, but they present a lack of flexibility in query formulation, since the expressivity power is reduced to the user interface design. Natural language interfaces (NLI) are expected as the optimal solution. However, especially for non-expert users, a real natural communication is the most difficult to realize effectively. In this paper, we propose an NLI that improves the interaction between the user and the DSS by means of referencing previous questions or their answers (i.e. anaphora such as the pronoun reference in “What traits are affected by them?”), or by eliding parts of the question (i.e. ellipsis such as “And to glume colour?” after the question “Tell me the QTLs related to awn colour in wheat”). Moreover, in order to overcome one of the main problems of NLIs about the difficulty to adapt an NLI to a new domain, our proposal is based on ontologies that are obtained semi-automatically from a framework that allows the integration of internal and external, structured and unstructured information. Therefore, our proposal can interface with databases, data warehouses, QA and IR systems. Because of the high NL ambiguity of the resolution process, our proposal is presented as an authoring tool that helps the user to query efficiently in natural language. Finally, our proposal is tested on a DSS case scenario about Biotechnology and Agriculture, whose knowledge base is the CEREALAB database as internal structured data, and the Web (e.g. PubMed) as external unstructured information.

Modernizing Secure OLAP Applications with a Model-Driven Approach

The majority of the organizations store their historical business information in data warehouses which are queried to make strategic decisions by using online analytical processing (OLAP) tools. This information has to be correctly assured against unauthorized accesses, but nevertheless there are a great amount of legacy OLAP applications that have been developed without considering security aspects or these have been incorporated once the system was implemented. This work defines a reverse engineering process that allows us to obtain the conceptual model corresponding to a legacy OLAP application, and also analyses and represents the security aspects that could have established. This process has been aligned with a model-driven architecture for developing secure OLAP applications by defining the transformations needed to automatically apply it. Once the conceptual model has been extracted, it can be easily modified and improved with security, and automatically transformed to generate the new implementation.

Sistema de referenciação geográfica

Nos dias de hoje o acesso à informação por parte das empresas é vital para o bom desempenho das suas funções. As empresas de telecomunicações não fogem à regra, a sua posição no mercado está dependente das decisões que são tomadas com base na avaliação dessa informação. Para suportar os processos de apoio à decisão é coerente recorrer-se a Data Warehouses que permitem integrar informação de diversas fontes, verificando a sua qualidade, actualização e coerência, organizando-a para um fácil acesso e consulta de vários pontos de vista. Numa empresa de telecomunicações móvel, um Data Mart geográfico baseado na informação de tráfego da companhia que pode identificar as localizações preferenciais dos utilizadores na rede é muito importante porque fornece indicadores muito úteis para o departamento de marketing e negócio da empresa de maneira a que se saiba onde e como actuar para permitir que esta se desenvolva e ganhe vantagem no mercado. ABSTRACT: Today the access to information by enterprises is vital for the company’s performance. Telecommunications companies are no exception. Their position in the market is dependent on the decisions that are taken based on the evaluation of such information. To support the decision making process Data Warehouse is today an extremely useful tool; it integrates information from different sources, checking on its validity, quality and update, coherence, organizing it for an easy access and search from various perspectives. ln a mobile telecommunications company a geographical Data Mart-based traffic information that can identify the preferential locations of users on the network is very important It provides useful indicators to the Department of Marketing and Business there by allowing you to know where and how to act and boosting the development of the company.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

[gait Speed, Grip Strength And Self-rated Health Among The Elderly: Data From The Fibra Campinas Network, São Paulo, Brazil].

The article seeks to investigate patterns of performance and relationships between grip strength, gait speed and self-rated health, and investigate the relationships between them, considering the variables of gender, age and family income. This was conducted in a probabilistic sample of community-dwelling elderly aged 65 and over, members of a population study on frailty. A total of 689 elderly people without cognitive deficit suggestive of dementia underwent tests of gait speed and grip strength. Comparisons between groups were based on low, medium and high speed and strength. Self-related health was assessed using a 5-point scale. The males and the younger elderly individuals scored significantly higher on grip strength and gait speed than the female and oldest did; the richest scored higher than the poorest on grip strength and gait speed; females and men aged over 80 had weaker grip strength and lower gait speed; slow gait speed and low income arose as risk factors for a worse health evaluation. Lower muscular strength affects the self-rated assessment of health because it results in a reduction in functional capacity, especially in the presence of poverty and a lack of compensatory factors.

Correlation Between Cephalometric Data And Severity Of Sleep Apnea.

Obstructive sleep apnea syndrome has a high prevalence among adults. Cephalometric variables can be a valuable method for evaluating patients with this syndrome. To correlate cephalometric data with the apnea-hypopnea sleep index. We performed a retrospective and cross-sectional study that analyzed the cephalometric data of patients followed in the Sleep Disorders Outpatient Clinic of the Discipline of Otorhinolaryngology of a university hospital, from June 2007 to May 2012. Ninety-six patients were included, 45 men, and 51 women, with a mean age of 50.3 years. A total of 11 patients had snoring, 20 had mild apnea, 26 had moderate apnea, and 39 had severe apnea. The distance from the hyoid bone to the mandibular plane was the only variable that showed a statistically significant correlation with the apnea-hypopnea index. Cephalometric variables are useful tools for the understanding of obstructive sleep apnea syndrome. The distance from the hyoid bone to the mandibular plane showed a statistically significant correlation with the apnea-hypopnea index.

Censored Linear Regression Models For Irregularly Observed Longitudinal Data Using The Multivariate-t Distribution.

In acquired immunodeficiency syndrome (AIDS) studies it is quite common to observe viral load measurements collected irregularly over time. Moreover, these measurements can be subjected to some upper and/or lower detection limits depending on the quantification assays. A complication arises when these continuous repeated measures have a heavy-tailed behavior. For such data structures, we propose a robust structure for a censored linear model based on the multivariate Student's t-distribution. To compensate for the autocorrelation existing among irregularly observed measures, a damped exponential correlation structure is employed. An efficient expectation maximization type algorithm is developed for computing the maximum likelihood estimates, obtaining as a by-product the standard errors of the fixed effects and the log-likelihood function. The proposed algorithm uses closed-form expressions at the E-step that rely on formulas for the mean and variance of a truncated multivariate Student's t-distribution. The methodology is illustrated through an application to an Human Immunodeficiency Virus-AIDS (HIV-AIDS) study and several simulation studies.

[evaluation Of Data On Live Birth Certificates From The Information System On Live Births (sinasc) In Campinas, São Paulo, 2009].

To assess the completeness and reliability of the Information System on Live Births (Sinasc) data. A cross-sectional analysis of the reliability and completeness of Sinasc's data was performed using a sample of Live Birth Certificate (LBC) from 2009, related to births from Campinas, Southeast Brazil. For data analysis, hospitals were grouped according to category of service (Unified National Health System, private or both), 600 LBCs were randomly selected and the data were collected in LBC-copies through mothers and newborns' hospital records and by telephone interviews. The completeness of LBCs was evaluated, calculating the percentage of blank fields, and the LBCs agreement comparing the originals with the copies was evaluated by Kappa and intraclass correlation coefficients. The percentage of completeness of LBCs ranged from 99.8%-100%. For the most items, the agreement was excellent. However, the agreement was acceptable for marital status, maternal education and newborn infants' race/color, low for prenatal visits and presence of birth defects, and very low for the number of deceased children. The results showed that the municipality Sinasc is reliable for most of the studied variables. Investments in training of the professionals are suggested in an attempt to improve system capacity to support planning and implementation of health activities for the benefit of maternal and child population.

Augmented Mixed Models For Clustered Proportion Data.

Often in biomedical research, we deal with continuous (clustered) proportion responses ranging between zero and one quantifying the disease status of the cluster units. Interestingly, the study population might also consist of relatively disease-free as well as highly diseased subjects, contributing to proportion values in the interval [0, 1]. Regression on a variety of parametric densities with support lying in (0, 1), such as beta regression, can assess important covariate effects. However, they are deemed inappropriate due to the presence of zeros and/or ones. To evade this, we introduce a class of general proportion density, and further augment the probabilities of zero and one to this general proportion density, controlling for the clustering. Our approach is Bayesian and presents a computationally convenient framework amenable to available freeware. Bayesian case-deletion influence diagnostics based on q-divergence measures are automatic from the Markov chain Monte Carlo output. The methodology is illustrated using both simulation studies and application to a real dataset from a clinical periodontology study.

Cephalometric And Anthropometric Data Of Obstructive Apnea In Different Age Groups.

Patients with obstructive sleep apnea syndrome usually present with changes in upper airway morphology and/or body fat distribution, which may occur throughout life and increase the severity of obstructive sleep apnea syndrome with age. To correlate cephalometric and anthropometric measures with obstructive sleep apnea syndrome severity in different age groups. A retrospective study of cephalometric and anthropometric measures of 102 patients with obstructive sleep apnea syndrome was analyzed. Patients were divided into three age groups (≥20 and <40 years, ≥40 and <60 years, and ≥60 years). Pearson's correlation was performed for these measures with the apnea-hypopnea index in the full sample, and subsequently by age group. The cephalometric measures MP-H (distance between the mandibular plane and the hyoid bone) and PNS-P (distance between the posterior nasal spine and the tip of the soft palate) and the neck and waist circumferences showed a statistically significant correlation with apnea-hypopnea index in both the full sample and in the ≥40 and <60 years age group. These variables did not show any significant correlation with the other two age groups (<40 and ≥60 years). Cephalometric measurements MP-H and PNS-P and cervical and waist circumferences correlated with obstructive sleep apnea syndrome severity in patients in the ≥40 and <60 age group.

Two Novel Mutations In The Thyroid Hormone Receptor β In Patients With Resistance To Thyroid Hormone (rth β): Clinical, Biochemical, And Molecular Data.

The syndrome of resistance to thyroid hormone (RTH β) is an inherited disorder characterized by variable tissue hyposensitivity to 3,5,30-l-triiodothyronine (T3), with persistent elevation of free-circulating T3 (FT3) and free thyroxine (FT4) levels in association with nonsuppressed serum thyrotropin (TSH). Clinical presentation is variable and the molecular analysis of THRB gene provides a short cut diagnosis. Here, we describe 2 cases in which RTH β was suspected on the basis of laboratory findings. The diagnosis was confirmed by direct THRB sequencing that revealed 2 novel mutations: the heterozygous p.Ala317Ser in subject 1 and the heterozygous p.Arg438Pro in subject 2. Both mutations were shown to be deleterious by SIFT, PolyPhen, and Align GV-GD predictive methods.