Model-based clustering in gene expression microarrays: An application to breast cancer data

In microarray studies, the application of clustering techniques is often used to derive meaningful insights into the data. In the past, hierarchical methods have been the primary clustering tool employed to perform this task. The hierarchical algorithms have been mainly applied heuristically to these cluster analysis problems. Further, a major limitation of these methods is their inability to determine the number of clusters. Thus there is a need for a model-based approach to these. clustering problems. To this end, McLachlan et al. [7] developed a mixture model-based algorithm (EMMIX-GENE) for the clustering of tissue samples. To further investigate the EMMIX-GENE procedure as a model-based -approach, we present a case study involving the application of EMMIX-GENE to the breast cancer data as studied recently in van 't Veer et al. [10]. Our analysis considers the problem of clustering the tissue samples on the basis of the genes which is a non-standard problem because the number of genes greatly exceed the number of tissue samples. We demonstrate how EMMIX-GENE can be useful in reducing the initial set of genes down to a more computationally manageable size. The results from this analysis also emphasise the difficulty associated with the task of separating two tissue groups on the basis of a particular subset of genes. These results also shed light on why supervised methods have such a high misallocation error rate for the breast cancer data.

Kinetic parameters associated with self-heating of New Zealand coals under adiabatic conditions

Adiabatic self-heating tests were carried out on five New Zealand coal samples ranging in rank from lignite to high-volatile bituminous. Kinetic parameters of oxidation were obtained front the self-heating curves assuming Arrhenius behaviour. The activation energy E (kJ mol(-1)) and the pre-exponential factor A (s(-1)) were determined in the temperature range of 70-140 degreesC. The activation energy exhibited a definite rank relationship with a minimum E of 55 kJ mol(-1) occurring at a Suggate rank of similar to6.2 corresponding to subbituminous C. Either side of this rank there was a noticeable increase in the activation energy indicating lower reactivity of the coal. A similar rank trend was also observed in the R-70 self-heating rate index values that were taken from the initial portion of the self-heating curve front 40 to 70 degreesC. From these results it is clear that the adiabatic method is capable of providing reliable kinetic parameters of coal oxidation.

Zygosity Diagnosis in the Absence of Genotypic Data: An Approach Using Latent Class Analysis

For zygosity diagnosis in the absence of genotypic data, or in the recruitment phase of a twin study where only single twins from same-sex pairs are being screened, or to provide a test for sample duplication leading to the false identification of a dizygotic pair as monozygotic, the appropriate analysis of respondents' answers to questions about zygosity is critical. Using data from a young adult Australian twin cohort (N = 2094 complete pairs and 519 singleton twins from same-sex pairs with complete responses to all zygosity items), we show that application of latent class analysis (LCA), fitting a 2-class model, yields results that show good concordance with traditional methods of zygosity diagnosis, but with certain important advantages. These include the ability, in many cases, to assign zygosity with specified probability on the basis of responses of a single informant (advantageous when one zygosity type is being oversampled); and the ability to quantify the probability of misassignment of zygosity, allowing prioritization of cases for genotyping as well as identification of cases of probable laboratory error. Out of 242 twins (from 121 like-sex pairs) where genotypic data were available for zygosity confirmation, only a single case was identified of incorrect zygosity assignment by the latent class algorithm. Zygosity assignment for that single case was identified by the LCA as uncertain (probability of being a monozygotic twin only 76%), and the co-twin's responses clearly identified the pair as dizygotic (probability of being dizygotic 100%). In the absence of genotypic data, or as a safeguard against sample duplication, application of LCA for zygosity assignment or confirmation is strongly recommended.

Systematic characterization of mutations in yeast acetohydroxyacid synthase: Interpretation of herbicide-resistance data

Acetohydroxyacid synthase (AHAS, EC 4.1.3.18) catalyses the first step in branched-chain amino acid biosynthesis and is the target for sulfonylurea and imidazolinone herbicides, which act as potent and specific inhibitors. Mutants of the enzyme have been identified that are resistant to particular herbicides. However, the selectivity of these mutants towards various sulfonylureas and imidazolinones has not been determined systematically. Now that the structure of the yeast enzyme is known, both in the absence and presence of a bound herbicide, a detailed understanding of the molecular interactions between the enzyme and its inhibitors becomes possible. Here we construct 10 active mutants of yeast AHAS, purify the enzymes and determine their sensitivity to six sulfonylureas and three imidazolinones. An additional three active mutants were constructed with a view to increasing imidazolinone sensitivity. These three variants were purified and tested for their sensitivity to the imidazolinones only. Substantial differences are observed in the sensitivity of the 13 mutants to the various inhibitors and these differences are interpreted in terms of the structure of the herbicide-binding site on the enzyme.

Model-based analysis of anaerobic acetate uptake by a mixed culture of polyphosphate-accumulating and glycogen-accumulating organisms

An increasing number of studies shows that the glycogen-accumulating organisms (GAOs) can survive and may indeed proliferate under the alternating anaerobic/aerobic conditions found in EBPR systems, thus forming a strong competitor of the polyphosphate-accumulating organisms (PAOs). Understanding their behaviors in a mixed PAO and GAO culture under various operational conditions is essential for developing operating strategies that disadvantage the growth of this group of unwanted organisms. A model-based data analysis method is developed in this paper for the study of the anaerobic PAO and GAO activities in a mixed PAO and GAO culture. The method primarily makes use of the hydrogen ion production rate and the carbon dioxide transfer rate resulting from the acetate uptake processes by PAOs and GAOs, measured with a recently developed titration and off-gas analysis (TOGA) sensor. The method is demonstrated using the data from a laboratory-scale sequencing batch reactor (SBR) operated under alternating anaerobic and aerobic conditions. The data analysis using the proposed method strongly indicates a coexistence of PAOs and GAOs in the system, which was independently confirmed by fluorescent in situ hybridization (FISH) measurement. The model-based analysis also allowed the identification of the respective acetate uptake rates by PAOs and GAOs, along with a number of kinetic and stoichiometric parameters involved in the PAO and GAO models. The excellent fit between the model predictions and the experimental data not involved in parameter identification shows that the parameter values found are reliable and accurate. It also demonstrates that the current anaerobic PAO and GAO models are able to accurately characterize the PAO/GAO mixed culture obtained in this study. This is of major importance as no pure culture of either PAOs or GAOs has been reported to date, and hence the current PAO and GAO models were developed for the interpretation of experimental results of mixed cultures. The proposed method is readily applicable for detailed investigations of the competition between PAOs and GAOs in enriched cultures. However, the fermentation of organic substrates carried out by ordinary heterotrophs needs to be accounted for when the method is applied to the study of PAO and GAO competition in full-scale sludges. (C) 2003 Wiley Periodicals, Inc.

A kinetic study of the thermally initiated free radical reactions of styrene with octanedithiol as a model for the reactions of multifunctional thiols with divinylbenzene

The kinetics of chain reactions of octanedithiol with styrene, thermally initiated with TX29B50 (a 50:50 wt% solution of TX29 diperoxy initiator in a phthalate plasticizer), have been studied over a range of initiator concentrations, a range of mixture formulations and a range of temperatures. This system has been investigated as a model system for the reactions of polyfunctional thiols with divinyl benzene. The reactions have been shown to follow first-order kinetics for both the thiol and the ene species and to be characterized by a dependence on the initiator concentration to the power of one half. The kinetic rate parameters have been shown to adhere to Arrhenius behaviour. A kinetic model for the chain reactions for this system has been proposed. (C) 2003 Society of Chemical Industry.

Data Mart para apoio ?? capacita????o em gest??o de pol??ticas p??blicas voltado para uma Escola de Administra????o P??blica

Este trabalho consiste num estudo de caso que se destina ao desenvolvimento de um Data Mart que possibilite a Escola Nacional de Administra????o P??blica ??? ENAP conhecer o perfil e o panorama geral da situa????o funcional dos servidores p??blicos federais que se capacitaram na Escola nos ??ltimos 7 anos. O aplicativo foi desenvolvido cruzando o banco de dados do sistema gerenciador dos cursos ministrados pela ENAP, onde est??o armazenadas informa????es sobre os alunos capacitados, os cursos realizados, os resultados alcan??ados, o perfil dos docentes e demais informa????es relativas ??s atividades da Escola, com os dados gerados pelo Sistema Integrado de Administra????o de Recursos Humanos ??? SIAPE, cuja extra????o de dados foi direcionada para os registros sobre a situa????o funcional, cargos, carreiras, fun????es, ??rg??os e alguns dados pessoais dos alunos, servidores p??blicos federais que se encontram registrados no SIAPE

New species of Bakeriella (Hymenoptera, Bethylidae) from the New World and new data on geographic distribution

Bakeriella lata sp. nov. (Brazil, Rondônia), Bakeriella aurata sp. nov. (Brazil, Amazonas) and Bakeriella sulcaticeps sp. nov. (Brazil, Amazonas) are described and illustrated. New geographic records and variation data for B. cristata Evans, 1964, B. floridana Evans, 1964, B. flavicornis Kieffer, 1910, B. incompleta Azevedo, 1994, B. mira Evans, 1997, B. montivaga (Kieffer, 1910), B. olmeca Evans, 1964 and B. subcarinata Evans, 1965 are provided. The male of B. incompleta is described for the first time.

Efeito da adição de extrato de casca de jabuticaba nas características físico-químicas e sensoriais de queijo petit suisse

A busca pela melhoria da qualidade de vida e a procura por alimentos naturais e funcionais são crescentes. A incorporação de prebióticos e corantes naturais pode agregar valor ao produto, por serem capazes de melhorar sua qualidade e por apresentarem grandes atrativos tecnológicos. Portanto, o objetivo deste trabalho foi avaliar o efeito da adição de prebióticos (inulina e oligofrutose) e corante natural (extrato de casca de jabuticaba) nas características de queijo petit suisse. Foi realizada análise da composição físico-química (extrato seco total, cinzas, proteínas, lipídeos, carboidratos e acidez titulável) logo após o processamento, análise do pH, colorimetria, teor de compostos bioativos e atividade antioxidante em diferentes tempos de armazenamento (0, 7, 14, 21 e 28 dias), análise do teor de fibras alimentares da formulação de queijo petit suisse com maior atividade antioxidante ao final da vida de prateleira e análises microbiológica e sensorial. O queijo petit suisse elaborado foi dividido em cinco formulações, de acordo com a concentração de corante natural incorporado, que foram 0%, 1,5%, 2,0%, 2,5% e 3,0%. Os dados obtidos com as análises realizadas logo após o processamento e análise sensorial foram submetidos à análise de variância e teste de Tukey, os dados obtidos com as análises realizadas em diferentes tempos de armazenamento foram submetidos à análise de variância e estudo do comportamento cinético, e a análise de fibras e microbiológica foi analisada por meio de estatística descritiva. Os valores de extrato seco total, proteínas, lipídeos, cinzas e carboidrato não diferiram significativamente (p>0,05) entre as formulações. A formulação sem adição de corante natural apresentou menor acidez (p≤0,05), e com o aumento da concentração de corante natural, maior foi a acidez do queijo. Os teores de antocianinas, fenólicos totais e capacidade antioxidante foram maiores com o aumento da concentração de corante incorporado, sendo que o teor de antocianinas reduziu com o decorrer do tempo de armazenamento. O valor encontrado de fibras para a formulação contendo 3,0% de corante natural foi baixo, e o produto não apresentou alegação de propriedade funcional. A fim de verificar se o queijo estava próprio para o consumo, foi realizada análise microbiológica para coliformes termotolerantes, estando todas as formulações de queijo petit suisse em condições sanitárias satisfatórias. A análise sensorial foi realizada em duas etapas. Na primeira etapa foi realizado teste de aceitação com avaliação dos atributos cor, sabor, consistência e impressão global, e intenção de compra para todas as formulações com incorporação de corante natural. Na segunda etapa foi realizado o teste de aceitação com informação nutricional do produto para a amostra mais aceita na primeira etapa. Como resultado, foi observado que o atributo cor foi o único que apresentou diferença significativa (p≤0,05) entre as formulações, sendo as mais aceitas com concentração 2,5% e 3,0%. De forma geral, todas as formulações foram bem aceitas, porém, a formulação com maior adição de corante natural foi a que xiii apresentou maiores notas. Assim, o queijo com maior concentração de corante natural foi o utilizado na segunda etapa sensorial, sendo observada influência das informações nos atributos cor e consistência (p≤0,05). Dessa forma, a utilização de prebióticos e corante natural de casca de jabuticaba em queijo petit suisse foi viável por não alterar a composição centesimal do produto, além de conferir ao produto uma coloração atrativa.

Privacy and Data Protection in Elderly Healthcare: Threats and Legal Warranties

The progressive aging of the population requires new kinds of social and medical intervention and the availability of different services provided to the elder population. New applications have been developed and some services are now provided at home, allowing the older people to stay home instead of having to stay in hospitals. But an adequate response to the needs of the users will imply a high percentage of use of personal data and information, including the building up and maintenance of user profiles, feeding the systems with the data and information needed for a proactive intervention in scheduling of events in which the user may be involved. Fundamental Rights may be at stake, so a legal analysis must also be considered.

The need for standardized tests to evaluate the reliability of data transport in wireless medical systems

Wireless medical systems are comprised of four stages, namely the medical device, the data transport, the data collection and the data evaluation stages. Whereas the performance of the first stage is highly regulated, the others are not. This paper concentrates on the data transport stage and argues that it is necessary to establish standardized tests to be used by medical device manufacturers to provide comparable results concerning the communication performance of the wireless networks used to transport medical data. Besides, it suggests test parameters and procedures to be used to produce comparable communication performance results.

A brief survey on online analysis of movement data

The increasing availability of mobility data and the awareness of its importance and value have been motivating many researchers to the development of models and tools for analyzing movement data. This paper presents a brief survey of significant research works about modeling, processing and visualization of data about moving objects. We identified some key research fields that will provide better features for online analysis of movement data. As result of the literature review, we suggest a generic multi-layer architecture for the development of an online analysis processing software tool, which will be used for the definition of the future work of our team.

COORDINSPECTOR: a tool for extracting coordination data from legacy code

More and more current software systems rely on non trivial coordination logic for combining autonomous services typically running on different platforms and often owned by different organizations. Often, however, coordination data is deeply entangled in the code and, therefore, difficult to isolate and analyse separately. COORDINSPECTOR is a software tool which combines slicing and program analysis techniques to isolate all coordination elements from the source code of an existing application. Such a reverse engineering process provides a clear view of the actually invoked services as well as of the orchestration patterns which bind them together. The tool analyses Common Intermediate Language (CIL) code, the native language of Microsoft .Net Framework. Therefore, the scope of application of COORDINSPECTOR is quite large: potentially any piece of code developed in any of the programming languages which compiles to the .Net Framework. The tool generates graphical representations of the coordination layer together and identifies the underlying business process orchestrations, rendering them as Orc specifications

Criminal Liability of Organizations, Corporations, Legal Persons, and Similar Entities on Law of Portuguese Cybercrime: A Brief Discussion on the Issue of Crimes of “False Information,” the “Damage on Other Programs or Computer Data,” the “Computer-Software Sabotage,” the “Illegitimate Access,” the “Unlawful Interception,” and “Illegitimate Reproduction of the Protected Program”

Abstract: in Portugal, and in much of the legal systems of Europe, «legal persons» are likely to be criminally responsibilities also for cybercrimes. Like for example the following crimes: «false information»; «damage on other programs or computer data»; «computer-software sabotage»; «illegitimate access»; «unlawful interception» and «illegitimate reproduction of protected program». However, in Portugal, have many exceptions. Exceptions to the «question of criminal liability» of «legal persons». Some «legal persons» can not be blamed for cybercrime. The legislature did not leave! These «legal persons» are v.g. the following («public entities»): legal persons under public law, which include the public business entities; entities utilities, regardless of ownership; or other legal persons exercising public powers. In other words, and again as an example, a Portuguese public university or a private concessionaire of a public service in Portugal, can not commit (in Portugal) any one of cybercrime pointed. Fair? Unfair. All laws should provide that all legal persons can commit cybercrimes. PS: resumo do artigo em inglês.