Gene expression databases and data mining.

The DNA microarray technology has arguably caught the attention of the worldwide life science community and is now systematically supporting major discoveries in many fields of study. The majority of the initial technical challenges of conducting experiments are being resolved, only to be replaced with new informatics hurdles, including statistical analysis, data visualization, interpretation, and storage. Two systems of databases, one containing expression data and one containing annotation data are quickly becoming essential knowledge repositories of the research community. This present paper surveys several databases, which are considered "pillars" of research and important nodes in the network. This paper focuses on a generalized workflow scheme typical for microarray experiments using two examples related to cancer research. The workflow is used to reference appropriate databases and tools for each step in the process of array experimentation. Additionally, benefits and drawbacks of current array databases are addressed, and suggestions are made for their improvement.

Conceptual models for designing information systems supporting the strategic analysis of technology environments

1 6 STRUCTURE OF THIS THESIS -Chapter I presents the motivations of this dissertation by illustrating two gaps in the current body of knowledge that are worth filling, describes the research problem addressed by this thesis and presents the research methodology used to achieve this goal. -Chapter 2 shows a review of the existing literature showing that environment analysis is a vital strategic task, that it shall be supported by adapted information systems, and that there is thus a need for developing a conceptual model of the environment that provides a reference framework for better integrating the various existing methods and a more formal definition of the various aspect to support the development of suitable tools. -Chapter 3 proposes a conceptual model that specifies the various enviromnental aspects that are relevant for strategic decision making, how they relate to each other, and ,defines them in a more formal way that is more suited for information systems development. -Chapter 4 is dedicated to the evaluation of the proposed model on the basis of its application to a concrete environment to evaluate its suitability to describe the current conditions and potential evolution of a real environment and get an idea of its usefulness. -Chapter 5 goes a step further by assembling a toolbox describing a set of methods that can be used to analyze the various environmental aspects put forward by the model and by providing more detailed specifications for a number of them to show how our model can be used to facilitate their implementation as software tools. -Chapter 6 describes a prototype of a strategic decision support tool that allow the analysis of some of the aspects of the environment that are not well supported by existing tools and namely to analyze the relationship between multiple actors and issues. The usefulness of this prototype is evaluated on the basis of its application to a concrete environment. -Chapter 7 finally concludes this thesis by making a summary of its various contributions and by proposing further interesting research directions.

Importance of influx and efflux systems and xenobiotic metabolizing enzymes in intratumoral disposition of anticancer agents.

In this review, intratumoral drug disposition will be integrated into the wide range of resistance mechanisms to anticancer agents with particular emphasis on targeted protein kinase inhibitors. Six rules will be established: 1. There is a high variability of extracellular/intracellular drug level ratios; 2. There are three main systems involved in intratumoral drug disposition that are composed of SLC, ABC and XME enzymes; 3. There is a synergistic interplay between these three systems; 4. In cancer subclones, there is a strong genomic instability that leads to a highly variable expression of SLC, ABC or XME enzymes; 5. Tumor-expressed metabolizing enzymes play a role in tumor-specific ADME and cell survival and 6. These three systems are involved in the appearance of resistance (transient event) or in the resistance itself. In addition, this article will investigate whether the overexpression of some ABC and XME systems in cancer cells is just a random consequence of DNA/chromosomal instability, hypo- or hypermethylation and microRNA deregulation, or a more organized modification induced by transposable elements. Experiments will also have to establish if these tumor-expressed enzymes participate in cell metabolism or in tumor-specific ADME or if they are only markers of clonal evolution and genomic deregulation. Eventually, the review will underline that the fate of anticancer agents in cancer cells should be more thoroughly investigated from drug discovery to clinical studies. Indeed, inhibition of tumor expressed metabolizing enzymes could strongly increase drug disposition, specifically in the target cells resulting in more efficient therapies.

Recommendations for locus-specific databases and their curation.

Expert curation and complete collection of mutations in genes that affect human health is essential for proper genetic healthcare and research. Expert curation is given by the curators of gene-specific mutation databases or locus-specific databases (LSDBs). While there are over 700 such databases, they vary in their content, completeness, time available for curation, and the expertise of the curator. Curation and LSDBs have been discussed, written about, and protocols have been provided for over 10 years, but there have been no formal recommendations for the ideal form of these entities. This work initiates a discussion on this topic to assist future efforts in human genetics. Further discussion is welcome.

Evaluation of a mixed approach combining stationary and wearable systems to monitor gait over long distance.

Thanks to decades of research, gait analysis has become an efficient tool. However, mainly due to the price of the motion capture systems, standard gait laboratories have the capability to measure only a few consecutive steps of ground walking. Recently, wearable systems were proposed to measure human motion without volume limitation. Although accurate, these systems are incompatible with most of existing calibration procedures and several years of research will be necessary for their validation. A new approach consisting of using a stationary system with a small capture volume for the calibration procedure and then to measure gait using a wearable system could be very advantageous. It could benefit from the knowledge related to stationary systems, allow long distance monitoring and provide new descriptive parameters. The aim of this study was to demonstrate the potential of this approach. Thus, a combined system was proposed to measure the 3D lower body joints angles and segmental angular velocities. It was then assessed in terms of reliability towards the calibration procedure, repeatability and concurrent validity. The dispersion of the joint angles across calibrations was comparable to those of stationary systems and good reliability was obtained for the angular velocities. The repeatability results confirmed that mean cycle kinematics of long distance walks could be used for subjects' comparison and pointed out an interest for the variability between cycles. Finally, kinematics differences were observed between participants with different ankle conditions. In conclusion, this study demonstrated the potential of a mixed approach for human movement analysis.

Adaptive search and information updating in sequential mate choice

Classical treatments of problems of sequential mate choice assume that the distribution of the quality of potential mates is known a priori. This assumption, made for analytical purposes, may seem unrealistic, opposing empirical data as well as evolutionary arguments. Using stochastic dynamic programming, we develop a model that includes the possibility for searching individuals to learn about the distribution and in particular to update mean and variance during the search. In a constant environment, a priori knowledge of the parameter values brings strong benefits in both time needed to make a decision and average value of mate obtained. Knowing the variance yields more benefits than knowing the mean, and benefits increase with variance. However, the costs of learning become progressively lower as more time is available for choice. When parameter values differ between demes and/or searching periods, a strategy relying on fixed a priori information might lead to erroneous decisions, which confers advantages on the learning strategy. However, time for choice plays an important role as well: if a decision must be made rapidly, a fixed strategy may do better even when the fixed image does not coincide with the local parameter values. These results help in delineating the ecological-behavior context in which learning strategies may spread.

Information provision and information needs in adult survivors of childhood cancer.

BACKGROUND: Knowledge about their past medical history is central for childhood cancer survivors to ensure informed decisions in their health management. Knowledge about information provision and information needs in this population is still scarce. We thus aimed to assess: (1) the information survivors reported to have received on disease, treatment, follow-up, and late effects; (2) their information needs in these four domains and the format in which they would like it provided; (3) the association with psychological distress and quality of life (QoL). PROCEDURE: As part of the Follow-up survey of the Swiss Childhood Cancer Survivor Study, we sent a questionnaire to all survivors (≥18 years) who previously participated to the baseline survey, were diagnosed with cancer after 1990 at an age of <16 years. RESULTS: Most survivors had received oral information only (on illness: oral: 82%, written: 38%, treatment: oral: 79%, written: 36%; follow-up: oral: 77%, written: 23%; late effects: oral: 68%, written: 14%). Most survivors who had not previously received any information rated it as important, especially information on late effects (71%). A large proportion of survivors reported current information needs and would like to receive personalized information especially on late effects (44%). Survivors with higher information needs reported higher psychological distress and lower QoL. CONCLUSIONS: Survivors want to be more informed especially on possible late effects, and want to receive personalized information. Improving information provision, both qualitatively and quantitatively, will allow survivors to have better control of their health and to become better decision makers.

Heat capacity measurements on the equiatomic compounds in Ni-X (X = Al, In, Si, Ge and Bi) and M-Sb (with M = Ni, Co and Fe) systems

Molar heat capacities of the binary compounds NiAl, NiIn, NiSi, NiGe, NiBi, NiSb, CoSb and FeSb were determined every 10 K by differential scanning calorimetry in the temperature range 310-1080 K. The experimental results have been fitted versus temperature according to C-p = a + b . T + c . T-2 + d . T-2. Results are given, discussed and compared to estimations found in the literature. Two compounds, NiBi and FeSb, are subject to transformations between 460 and 500 K. (C) 1999 Elsevier Science Ltd. All rights reserved.

Strategic Enterprise Architecture Management - Challenges, Best Practices, and Future Developments

The discipline of Enterprise Architecture Management (EAM) deals with the alignment of business and information systems architectures. While EAM has long been regarded as a discipline for IT managers this book takes a different stance: It explains how top executives can use EAM for leveraging their strategic planning and controlling processes and how EAM can contribute to sustainable competitive advantage. Based on the analysis of best practices from eight leading European companies from various industries the book presents crucial elements of successful EAM. It outlines what executives need to do in terms of governance, processes, methodologies and culture in order to bring their management to the next level. Beyond this, the book points how EAM might develop in the next decade allowing today's managers to prepare for the future of architecture management.

Limitations and information needs for engineered nanomaterial-specific exposure estimation and scenarios: recommendations for improved reporting practices

The aim of this paper is to describe the process and challenges in building exposure scenarios for engineered nanomaterials (ENM), using an exposure scenario format similar to that used for the European Chemicals regulation (REACH). Over 60 exposure scenarios were developed based on information from publicly available sources (literature, books, and reports), publicly available exposure estimation models, occupational sampling campaign data from partnering institutions, and industrial partners regarding their own facilities. The primary focus was on carbon-based nanomaterials, nano-silver (nano-Ag) and nano-titanium dioxide (nano-TiO2), and included occupational and consumer uses of these materials with consideration of the associated environmental release. The process of building exposure scenarios illustrated the availability and limitations of existing information and exposure assessment tools for characterizing exposure to ENM, particularly as it relates to risk assessment. This article describes the gaps in the information reviewed, recommends future areas of ENM exposure research, and proposes types of information that should, at a minimum, be included when reporting the results of such research, so that the information is useful in a wider context.

Impacts des technologies de l'information sur les modes de coordination à travers quatre études en systèmes d'information

L'évolution de l'environnement économique, des chaînes de valeur et des modèles d'affaires des organisations augmentent l'importance de la coordination, qui peut être définie comme la gestion des interdépendances entre des tâches réalisées par des acteurs différents et concourants à un objectif commun. De nombreux moyens sont mis en oeuvre au sein des organisations pour gérer ces interdépendances. A cet égard, les activités de coordination bénéficient massivement de l'appui des technologies de l'information et de communication (TIC) qui sont désormais disséminées, intégrées et connectées sous de multiples formes tant dans l'environnement privé que professionnel. Dans ce travail, nous avons investigué la question de recherche suivante : comment l'ubiquité et l'interconnec- tivité des TIC modifient-elles les modes de coordination ? A travers quatre études en systèmes d'information conduites selon une méthodologie design science, nous avons traité cette question à deux niveaux : celui de l'alignement stratégique entre les affaires et les systèmes d'information, où la coordination porte sur les interdépendances entre les activités ; et celui de la réalisation des activités, où la coordination porte sur les interdépendances des interactions individuelles. Au niveau stratégique, nous observons que l'ubiquité et l'interconnectivité permettent de transposer des mécanismes de coordination d'un domaine à un autre. En facilitant différentes formes de coprésence et de visibilité, elles augmentent aussi la proximité dans les situations de coordination asynchrone ou distante. Au niveau des activités, les TIC présentent un très fort potentiel de participation et de proximité pour les acteurs. De telles technologies leur donnent la possibilité d'établir les responsabilités, d'améliorer leur compréhension commune et de prévoir le déroulement et l'intégration des tâches. La contribution principale qui émerge de ces quatre études est que les praticiens peuvent utiliser l'ubiquité et l'interconnectivité des TIC pour permettre aux individus de communi-quer et d'ajuster leurs actions pour définir, atteindre et redéfinir les objectifs du travail commun. -- The evolution of the economic environment and of the value chains and business models of organizations increases the importance of coordination, which can be defined as the management of interdependences between tasks carried out by different actors and con-tributing to a common goal. In organizations, a considerable number of means are put into action in order to manage such interdependencies. In this regard, information and communication technologies (ICT), whose various forms are nowadays disseminated, integrated and connected in both private and professional environments, offer important support to coordination activities. In this work, we have investigated the following research question: how do the ubiquity and the interconnectivity of ICT modify coordination mechanisms? Throughout four information systems studies conducted according to a design science methodology, we have looked into this question at two different levels: the one of strategic alignment between business and information systems strategy, where coordination is about interdependencies between activities; and the one of tasks, where coordination is about interdependencies between individual interactions. At the strategic level, we observe that ubiquity and interconnectivity allow for transposing coordination mechanisms from one field to another. By facilitating various forms of copresence and visibility, they also increase proximity in asynchronous or distant coordination situations. At the tasks level, ICTs offer the actors a very high potential for participation and proximity. Such technologies make it possible to establish accountability, improve common understanding and anticipate the unfolding and integration of tasks. The main contribution emerging from these four studies is that practitioners can use the ubiquity and interconnectivity of ICT in order to allow individuals to communicate and adjust their actions to define, reach and redefine the goals of common work.