April 25, 2012

Geneva Henry, Executive Director of the Center for Digital Scholarship, Rice University. Data rights and ownership of digital research data can impact how you use data, how others use data you've collected, and how rights are determined in collaborative research. Copyright rules governing data vary from one country to the next, making data ownership in international collaborations particularly murky. Licensing the use of data sets from the start is one way to address these issues early and provide a means for easily sharing datasets that can be cited and properly attributed. This talk with introduce issues associated with digital research data governance and how to protect your rights with data you work with.

INTEGRATIVE BIOMARKER IDENTIFICATION AND CLASSIFICATION USING HIGH THROUGHPUT ASSAYS

It is well accepted that tumorigenesis is a multi-step procedure involving aberrant functioning of genes regulating cell proliferation, differentiation, apoptosis, genome stability, angiogenesis and motility. To obtain a full understanding of tumorigenesis, it is necessary to collect information on all aspects of cell activity. Recent advances in high throughput technologies allow biologists to generate massive amounts of data, more than might have been imagined decades ago. These advances have made it possible to launch comprehensive projects such as (TCGA) and (ICGC) which systematically characterize the molecular fingerprints of cancer cells using gene expression, methylation, copy number, microRNA and SNP microarrays as well as next generation sequencing assays interrogating somatic mutation, insertion, deletion, translocation and structural rearrangements. Given the massive amount of data, a major challenge is to integrate information from multiple sources and formulate testable hypotheses. This thesis focuses on developing methodologies for integrative analyses of genomic assays profiled on the same set of samples. We have developed several novel methods for integrative biomarker identification and cancer classification. We introduce a regression-based approach to identify biomarkers predictive to therapy response or survival by integrating multiple assays including gene expression, methylation and copy number data through penalized regression. To identify key cancer-specific genes accounting for multiple mechanisms of regulation, we have developed the integIRTy software that provides robust and reliable inferences about gene alteration by automatically adjusting for sample heterogeneity as well as technical artifacts using Item Response Theory. To cope with the increasing need for accurate cancer diagnosis and individualized therapy, we have developed a robust and powerful algorithm called SIBER to systematically identify bimodally expressed genes using next generation RNAseq data. We have shown that prediction models built from these bimodal genes have the same accuracy as models built from all genes. Further, prediction models with dichotomized gene expression measurements based on their bimodal shapes still perform well. The effectiveness of outcome prediction using discretized signals paves the road for more accurate and interpretable cancer classification by integrating signals from multiple sources.

Deep drilling of glaciers: Russian projects in the Arctic (1975-1995)

The data collection "Deep Drilling of Glaciers: Soviet-Russian projects in Arctic, 1975-1995" was collected by the following basic considerations: - compilation of deep (>100 m) drilling projects on Arctic glaciers, using data of (a) publications; (b) archives of IGRAN; (c) personal communication of project participants; - documentation of parameters, references. Accuracy of data and techniques applied to determine different parameters are not evaluated. The accuracy of some geochemical parameters (up to 1984 and heavy metalls) is uncertain. Most reconstructions of ice core age and of annual layer thickness are discussed; - digitizing of published diagrams (in case, when original numerical data were lost) and subsequent data conversion to equal range series and adjustment to the common units. Therefore, the equal-range series were calculated from original data or converted from digitized chart values as indicated in the metadata. For the methodological purpose, the equal-range series obtained from original and reconstructed data were compared repeatedly; the systematic difference was less then 5-7%. Special attention should be given to the fact, that the data for individual ice core parameters varies, because some parameters were originally measured or registered. Parameters were converted in equal-range series using 2 m steps; - two or more parameter values were determined, then the mean-weighted (i.e. accounting the sample length) value is assigned to the entire interval; - one parameter value was determined, measured or registered independently from the parameter values in depth intervals which over- and underlie it, then the value is assigned to the entire interval; - one parameter value was determined, measured or registered for two adjoining depth intervals, then the specific value is assigned to the depth interval, which represents >75% of sample length ; if each of adjoining depth intervals represents <75% of sample length, then the correspondent parameter value is assigned to both intervals of depth. This collection of ice core data (version 2000) was made available through the EU funded QUEEN project by S.M. Arkhipov, Moscow.

30 years of synoptic observations from Neumayer Station with links to datasets

The analysis of research data plays a key role in data-driven areas of science. Varieties of mixed research data sets exist and scientists aim to derive or validate hypotheses to find undiscovered knowledge. Many analysis techniques identify relations of an entire dataset only. This may level the characteristic behavior of different subgroups in the data. Like automatic subspace clustering, we aim at identifying interesting subgroups and attribute sets. We present a visual-interactive system that supports scientists to explore interesting relations between aggregated bins of multivariate attributes in mixed data sets. The abstraction of data to bins enables the application of statistical dependency tests as the measure of interestingness. An overview matrix view shows all attributes, ranked with respect to the interestingness of bins. Complementary, a node-link view reveals multivariate bin relations by positioning dependent bins close to each other. The system supports information drill-down based on both expert knowledge and algorithmic support. Finally, visual-interactive subset clustering assigns multivariate bin relations to groups. A list-based cluster result representation enables the scientist to communicate multivariate findings at a glance. We demonstrate the applicability of the system with two case studies from the earth observation domain and the prostate cancer research domain. In both cases, the system enabled us to identify the most interesting multivariate bin relations, to validate already published results, and, moreover, to discover unexpected relations.

Reference list of 269 sources used for exploratory search

Today's digital libraries (DLs) archive vast amounts of information in the form of text, videos, images, data measurements, etc. User access to DL content can rely on similarity between metadata elements, or similarity between the data itself (content-based similarity). We consider the problem of exploratory search in large DLs of time-oriented data. We propose a novel approach for overview-first exploration of data collections based on user-selected metadata properties. In a 2D layout representing entities of the selected property are laid out based on their similarity with respect to the underlying data content. The display is enhanced by compact summarizations of underlying data elements, and forms the basis for exploratory navigation of users in the data space. The approach is proposed as an interface for visual exploration, leading the user to discover interesting relationships between data items relying on content-based similarity between data items and their respective metadata labels. We apply the method on real data sets from the earth observation community, showing its applicability and usefulness.

Usability-Oriented Software Development Process

Usability is the capability of the software product to be understood, learned, used and attractive to the user, when used under specified conditions. Many studies demonstrate the benefits of usability, yet to this day software products continue to exhibit consistently low levels of this quality attribute. Furthermore, poor usability in software systems contributes largely to software failing in actual use. One of the main disciplines involved in usability is that of Human-Computer Interaction (HCI). Over the past two decades the HCI community has proposed specific features that should be present in applications to improve their usability, yet incorporating them into software continues to be far from trivial for software developers. These difficulties are due to multiple factors, including the high level of abstraction at which these HCI recommendations are made and how far removed they are from actual software implementation. In order to bridge this gap, the Software Engineering community has long proposed software design solutions to help developers include usability features into software, however, the problem remains an open research question. This doctoral thesis addresses the problem of helping software developers include specific usability features into their applications by providing them with a structured and tangible guidance in the form of a process, which we have termed the Usability-Oriented Software Development Process. This process is supported by a set of Software Usability Guidelines that help developers to incorporate a set of eleven usability features with high impact on software design. After developing the Usability-oriented Software Development Process and the Software Usability Guidelines, they have been validated across multiple academic projects and proven to help software developers to include such usability features into their software applications. In doing so, their use significantly reduced development time and improved the quality of the resulting designs of these projects. Furthermore, in this work we propose a software tool to automate the application of the proposed process. In sum, this work contributes to the integration of the Software Engineering and HCI disciplines providing a framework that helps software developers to create usable applications in an efficient way.

Métodos acotados de aplicación de reglas de evolución para la implementación de Sistemas P de Transición

La característica fundamental de la Computación Natural se basa en el empleo de conceptos, principios y mecanismos del funcionamiento de la Naturaleza. La Computación Natural -y dentro de ésta, la Computación de Membranas- surge como una posible alternativa a la computación clásica y como resultado de la búsqueda de nuevos modelos de computación que puedan superar las limitaciones presentes en los modelos convencionales. En concreto, la Computación de Membranas se originó como un intento de formular un nuevo modelo computacional inspirado en la estructura y el funcionamiento de las células biológicas: los sistemas basados en este modelo constan de una estructura de membranas que actúan a la vez como separadores y como canales de comunicación, y dentro de esa estructura se alojan multiconjuntos de objetos que evolucionan de acuerdo a unas determinadas reglas de evolución. Al conjunto de dispositivos contemplados por la Computación de Membranas se les denomina genéricamente como Sistemas P. Hasta el momento los Sistemas P sólo han sido estudiados a nivel teórico y no han sido plenamente implementados ni en medios electrónicos, ni en medios bioquímicos, sólo han sido simulados o parcialmente implementados. Por tanto, la implantación de estos sistemas es un reto de investigación abierto. Esta tesis aborda uno de los problemas que debe ser resuelto para conseguir la implantación de los Sistemas P sobre plataformas hardware. El problema concreto se centra en el modelo de los Sistemas P de Transición y surge de la necesidad de disponer de algoritmos de aplicación de reglas que, independientemente de la plataforma hardware sobre la que se implementen, cumplan los requisitos de ser no deterministas, masivamente paralelos y además su tiempo de ejecución esté estáticamente acotado. Como resultado se ha obtenido un conjunto de algoritmos (tanto para plataformas secuenciales, como para plataformas paralelas) que se adecúan a las diferentes configuraciones de los Sistemas P. ABSTRACT The main feature of Natural Computing is the use of concepts, principles and mechanisms inspired by Nature. Natural Computing and within it, Membrane Computing emerges as an potential alternative to conventional computing and as from the search for new models of computation that may overcome the existing limitations in conventional models. Specifically, Membrane Computing was created to formulate a new computational paradigm inspired by the structure and functioning of biological cells: it consists of a membrane structure, which acts as separators as well as communication channels, and within this structure are stored multisets of objects that evolve according to certain evolution rules. The set of computing devices addressed by Membrane Computing are generically known P systems. Up to now, no P systems have been fully implemented yet in electronic or biochemical means. They only have been studied in theory, simulated or partially implemented. Therefore, the implementation of these systems is an open research challenge. This thesis addresses one of the problems to be solved in order to deploy P systems on hardware platforms. This specific problem is focused on the Transition P System model and emerges from the need of providing application rules algorithms that independently on the hardware platform on which they are implemented, meets the requirements of being nondeterministic, massively parallel and runtime-bounded. As a result, this thesis has developed a set of algorithms for both platforms, sequential and parallel, adapted to all possible configurations of P systems.

Quality of experience and HTTP adaptive streaming: a review of subjective studies

HTTP adaptive streaming technology has become widely spread in multimedia services because of its ability to provide adaptation to characteristics of various viewing devices and dynamic network conditions. There are various studies targeting the optimization of adaptation strategy. However, in order to provide an optimal viewing experience to the end-user, it is crucial to get knowledge about the Quality of Experience (QoE) of different adaptation schemes. This paper overviews the state of the art concerning subjective evaluation of adaptive streaming QoE and highlights the challenges and open research questions related to QoE assessment.

Subjective QoE Analysis of HTTP Adaptive Streaming Applications

Actualmente la optimization de la calidad de experiencia (Quality of Experience- QoE) de HTTP Adaptive Streaming (HAS) de video recibe una atención creciente. Este incremento de interés proviene fundamentalmente de las carencias de las soluciones actuales HAS, que, al no ser QoE-driven, no incluyen la percepción de la calidad de los usuarios finales como una parte integral de la lógica de adaptación. Por lo tanto, la obtención de información de referencia fiable en QoE en HAS presenta retos importantes, ya que las metodologías de evaluación subjetiva de la calidad de vídeo propuestas en las normas actuales no son adecuadas para tratar con la variación temporal de la calidad que es consustancial de HAS. Esta tesis investiga la influencia de la adaptación dinámica en la calidad de la transmisión de vídeo considerando métodos de evaluación subjetiva. Tras un estudio exhaustivo del estado del arte en la evaluación subjetiva de QoE en HAS, se han resaltado los retos asociados y las líneas de investigación abiertas. Como resultado, se han seleccionado dos líneas principales de investigación: el análisis del impacto en la QoE de los parámetros de las técnicas de adaptación y la investigación de las metodologías de prueba subjetiva adecuada para evaluación de QoE en HAS. Se han llevado a cabo un conjunto de experimentos de laboratorio para investigar las cuestiones planteadas mediante la utilización de diferentes metodologáas para pruebas subjetivas. El análisis estadístico muestra que no son robustas todas las suposiciones y reivindicaciones de las referencias analizadas, en particular en lo que respecta al impacto en la QoE de la frecuencia de las variaciones de calidad, de las adaptaciones suaves o abruptas y de las oscilaciones de calidad. Por otra parte, nuestros resultados confirman la influencia de otros parámetros, como la longitud de los segmentos de vídeo y la amplitud de las oscilaciones de calidad. Los resultados también muestran que tomar en consideración las características objetivas de los contenidos puede ser beneficioso para la mejora de la QoE en HAS. Además, todos los resultados han sido validados mediante extensos análisis experimentales que han incluido estudio tanto en otros laboratorios como en crowdsourcing Por último, sobre los aspectos metodológicos de las pruebas subjetivas de QoE, se ha realizado la comparación entre los resultados experimentales obtenidos a partir de un método estandarizado basado en estímulos cortos (ACR) y un método semi continuo (desarrollado para la evaluación de secuencias prolongadas de vídeo). A pesar de algunas diferencias, el resultado de los análisis estadísticos no muestra ningún efecto significativo de la metodología de prueba. Asimismo, aunque se percibe la influencia de la presencia de audio en la evaluación de degradaciones del vídeo, no se han encontrado efectos estadísticamente significativos de dicha presencia. A partir de la ausencia de influencia del método de prueba y de la presencia de audio, se ha realizado un análisis adicional sobre el impacto de realizar comparaciones estadísticas múltiples en niveles estadísticos de importancia que aumentan la probabilidad de los errores de tipo-I (falsos positivos). Nuestros resultados muestran que, para obtener un efectos sólido en el análisis estadístico de los resultados subjetivos, es necesario aumentar el número de sujetos de las pruebas claramente por encima de los tamaños de muestras propuestos por las normas y recomendaciones actuales. ABSTRACT Optimizing the Quality of Experience (QoE) of HTTP adaptive video streaming (HAS) is receiving increasing attention nowadays. The growth of interest is mainly caused by the fact that current HAS solutions are not QoE-driven, i.e. end-user quality perception is not integral part of the adaptation logic. However, obtaining the necessary reliable ground truths on HAS QoE faces substantial challenges, since the subjective video quality assessment methodologies as proposed by current standards are not well-suited for dealing with the time-varying quality properties that are characteristic for HAS. This thesis investigates the influence of dynamic quality adaptation on the QoE of streaming video by means of subjective evaluation approaches. Based on a comprehensive survey of related work on subjective HAS QoE assessment, the related challenges and open research questions are highlighted and discussed. As a result, two main research directions are selected for further investigation: analysis of the QoE impact of different technical adaptation parameters, and investigation of testing methodologies suitable for HAS QoE evaluation. In order to investigate related research issues and questions, a set of laboratory experiments have been conducted using different subjective testing methodologies. Our statistical analysis demonstrates that not all assumptions and claims reported in the literature are robust, particularly as regards the QoE impact of switching frequency, smooth vs. abrupt switching, and quality oscillation. On the other hand, our results confirm the influence of some other parameters such as chunk length and switching amplitude on perceived quality. We also show that taking the objective characteristics of the content into account can be beneficial to improve the adaptation viewing experience. In addition, all aforementioned findings are validated by means of an extensive cross-experimental analysis that involves external laboratory and crowdsourcing studies. Finally, to address the methodological aspects of subjective QoE testing, a comparison between the experimental results obtained from a (short stimuli-based) ACR standardized method and a semi-continuous method (developed for assessment of long video sequences) has been performed. In spite of observation of some differences, the result of statistical analysis does not show any significant effect of testing methodology. Similarly, although the influence of audio presence on evaluation of video-related degradations is perceived, no statistically significant effect of audio presence could be found. Motivating by this finding (no effect of testing method and audio presence), a subsequent analysis has been performed investigating the impact of performing multiple statistical comparisons on statistical levels of significance which increase the likelihood of Type-I errors (false positives). Our results show that in order to obtain a strong effect from the statistical analysis of the subjective results, it is necessary to increase the number of test subjects well beyond the sample sizes proposed by current quality assessment standards and recommendations.

INTERVENÇÕES DE PSICÓLOGOS NAS UNIDADES BÁSICAS DE SAÚDE DO GRANDE ABC

Este trabalho tem como objetivo fazer um levantamento das intervenções que são realizadas pelos psicólogos que atuam nas Unidades Básicas de Saúde (UBS) do Grande ABC, bem como traçar um perfil destes profissionais. Pretendeu-se fazer na Região do Grande ABC este levantamento, baseando-se na tradição que a Psicologia tem de pesquisar-se como profissão, nos últimos trinta anos. A análise dos dados da pesquisa se deu através de quatro categorias levantadas a partir das mudanças que o exercício da profissão nas UBS requer: 1) do âmbito do atendimento, do individual para o coletivo; 2) do atendimento em consultório para instituição pública; 3) do enfoque do trabalho, do curativo para o preventivo; 4) da área de atuação, da saúde mental para a psicologia da saúde. Os resultados apresentados são oriundos de trinta e oito entrevistas realizadas com psicólogos das UBS s da Região do Grande ABC, no decorrer do ano de 2002, que trazem as dificuldades para o desenvolvimento das atividades. Dentre elas, destaca-se as de ordem política, econômica e social, que independem do desejo dos profissionais. Além destas, constatou-se dificuldades frente à formação profissional e à compreensão do papel e da função do psicólogo nas UBS s.

INTERVENÇÕES DE PSICÓLOGOS NAS UNIDADES BÁSICAS DE SAÚDE DO GRANDE ABC

Este trabalho tem como objetivo fazer um levantamento das intervenções que são realizadas pelos psicólogos que atuam nas Unidades Básicas de Saúde (UBS) do Grande ABC, bem como traçar um perfil destes profissionais. Pretendeu-se fazer na Região do Grande ABC este levantamento, baseando-se na tradição que a Psicologia tem de pesquisar-se como profissão, nos últimos trinta anos. A análise dos dados da pesquisa se deu através de quatro categorias levantadas a partir das mudanças que o exercício da profissão nas UBS requer: 1) do âmbito do atendimento, do individual para o coletivo; 2) do atendimento em consultório para instituição pública; 3) do enfoque do trabalho, do curativo para o preventivo; 4) da área de atuação, da saúde mental para a psicologia da saúde. Os resultados apresentados são oriundos de trinta e oito entrevistas realizadas com psicólogos das UBS s da Região do Grande ABC, no decorrer do ano de 2002, que trazem as dificuldades para o desenvolvimento das atividades. Dentre elas, destaca-se as de ordem política, econômica e social, que independem do desejo dos profissionais. Além destas, constatou-se dificuldades frente à formação profissional e à compreensão do papel e da função do psicólogo nas UBS s.

Clinica psicanalítica: o sentimento de solidão e a saúde mental de mulheres casadas

Este trabalho teve como objetivo principal investigar o sentimento de solidão e a saúde mental de mulheres casadas, procurando comparar a maneira de compreender e vivenciar este sentimento em mulheres solteiras e casadas, bem como verificar em que medida este sentimento pode ser mitigado pela presença do outro no casamento (coabitação) e em que condições isto ocorria. Partiu-se da hipótese de que esse sentimento é compartilhado por todas as pessoas, já que o ser humano é uno e individual. Logo, a separação eterna do outro, que se inicia quando o bebê percebe que é diferente da mãe e, assim, um indivíduo único, está associado a uma sensação de solidão que acompanha o ser humano por toda a vida. Desta forma, é muito comum ver pessoas se envolver em relacionamentos para diminuir este sentimento, que se vê intensificado a cada dia em função da superficialidade dos vínculos emocionais. A presença de outrem pode ser aproveitada numa relação interpessoal quando se diminui a intensidade da hostilidade, associada ao sentimento de solidão. O antídoto contra tal sentimento vem do fortalecimento do auto-conhecimento, da autonomia, e da amizade por um companheiro que mostra aceitação incondicional pelo verdadeiro self. Para análise deste sentimento em mulheres casadas, foi realizada uma pesquisa quantitativa e qualitativa com mulheres solteiras e universitárias. A escolha da amostra foi aleatória e por conglomerado, em três estágios. Participaram do estudo 184 mulheres, 38% casadas, 7,6% separadas e 52,7% solteiras. Da pesquisa quantitativa foi possível analisar que a percepção das mulheres sobre a solidão vem, em muitos aspectos, de encontro com a teoria psicanalítica. Pelas respostas encontradas percebeu-se que a grande maioria das participantes tem um baixo sentimento de solidão (58,7%) e 41,3% se classificaram com um escore de alto a médio sentimento de solidão, nestes dois grupos a maioria são de mulheres casadas e separadas, sendo que quanto mais nova a mulher maior a tendência a buscar um relacionamento para fugir da solidão, sendo entre as casadas também que isto ocorre com mais freqüência. A partir destes escores, 18 mulheres foram convidadas a participar de uma entrevista diagnóstica. Destas dezoito, seis mulheres apresentavam alto sentimento de solidão, sendo duas casadas, duas solteiras e duas separadas. Da mesma forma as mulheres com média e baixa solidão. Os resultados encontrados nestas entrevistas foram que todas as mulheres que apresentaram um alto sentimento de solidão demonstram uma adaptação ineficaz perante a vida, enquanto que aquelas que apresentaram médio ou baixo sentimento de solidão dificilmente apresentam adaptação ineficaz. Do grupo de médio sentimento de solidão, três mulheres apresentaram adaptação eficaz, e do grupo de baixo sentimento de solidão apenas uma participante apresentou adaptação ineficaz leve. Com isso concluímos que a solidão, quando em alta medida, além de dolorosa indica uma grande dificuldade do indivíduo em lidar com seus aspectos emocionais e produtivos, necessitando de ajuda psíquica.