Epidemiological studies in the information and genomics era: experience of the Clinical Genome of Cancer Project in São Paulo, Brazil

Genomics is expanding the horizons of epidemiology, providing a new dimension for classical epidemiological studies and inspiring the development of large-scale multicenter studies with the statistical power necessary for the assessment of gene-gene and gene-environment interactions in cancer etiology and prognosis. This paper describes the methodology of the Clinical Genome of Cancer Project in São Paulo, Brazil (CGCP), which includes patients with nine types of tumors and controls. Three major epidemiological designs were used to reach specific objectives: cross-sectional studies to examine gene expression, case-control studies to evaluate etiological factors, and follow-up studies to analyze genetic profiles in prognosis. The clinical groups included patients' data in the electronic database through the Internet. Two approaches were used for data quality control: continuous data evaluation and data entry consistency. A total of 1749 cases and 1509 controls were entered into the CGCP database from the first trimester of 2002 to the end of 2004. Continuous evaluation showed that, for all tumors taken together, only 0.5% of the general form fields still included potential inconsistencies by the end of 2004. Regarding data entry consistency, the highest percentage of errors (11.8%) was observed for the follow-up form, followed by 6.7% for the clinical form, 4.0% for the general form, and only 1.1% for the pathology form. Good data quality is required for their transformation into useful information for clinical application and for preventive measures. The use of the Internet for communication among researchers and for data entry is perhaps the most innovative feature of the CGCP. The monitoring of patients' data guaranteed their quality.

Time to volume through efficient multi-site ramp-up

The aim of this thesis was to create a process for all multi-site ramp-up (MSRU) projects in the case company in order to have simultaneous ramp-ups early in the market. The research was done through case study in one company and semi-structured interviews. There are already processes, which are now in use in MSRU-cases. Interviews of 20 ramp-up specialists revealed topics to be improved. Those were project team set up, roles and responsibilities and recommended project organization, communication, product change management practices, competence and know how transfer practices and support model. More R&D support and involvement is needed in MSRU-projects. DCM’s role is very important in the MSRU-projects among PMT-team; he should be the business owner of the project. Recommendation is that product programs could take care of the product and repair training of new products in volume factories. R&D’s participation in competence transfers is essential important in MSRU-projects. Communication in projects could be shared through special intranet commune. Blogging and tweeting could be considered in the communication plan. If hundreds of change notes are open in ramp-up phase, it should be considered not to approve the product into volume ramp-up. PMTs’ supports are also important and MSRU-projects should be planned, budgeted and executed together. Finally a new MSRU-process is presented in this thesis to be used in all MSRU-projects.

Effects of genotype and environment on grain yield and quality traits in bread wheat (T. aestivum L.)

Genotype (G), environment (E) and their interaction (GEI) play an important role in the final expression of grain yield and quality attributes. A multi-environment trial in wheat was conducted to evaluate the magnitude of G, E and GEI effects on grain yield and quality of wheat genotypes under the three rainfed locations (hereafter environment) of Central Anatolian Plateau of Turkey, during the 2012-2013 cropping season. Grain yield (GY) and analyses of test weight (TW), protein content (PC), wet gluten content (WGC), grain hardness (GH), thousand kernel weight (TKW) and Zeleny sedimentation volume (ZSV) were determined. Allelic variations of high and low molecular weight glutenin subunits (HMW-GS and LMW-GS) and 1B/1R translocation were determined in all genotypes evaluated. Both HMW-Glu-1, 17+18, 5+10 and LMW-Glu-3 b, b, b corresponded to genotypes possessing medium to good quality attributes. Large variability was found among most of the quality attributes evaluated; wider ranges of quality traits were observed in the environments than among the genotypes. The importance of the growing environment effects on grain quality was proved, suggesting that breeders' quality objectives should be adapted to the targeted environments.

Control of multi-actuator system by an electrically driven hydraulic pump-motor

The awareness and concern of our environment together with legislation have set more and more tightening demands for energy efficiency of non-road mobile machinery (NRMM). Integrated electro-hydraulic energy converter (IEHEC) has been developed in Lappeenranta University of Technology (LUT). The elimination of resistance flow, and the recuperation of energy makes it very efficient alternative. The difficulties of IEHEC machine to step to the market has been the requirement of one IEHEC machine per one actuator. The idea is to switch IEHEC between two actuators of log crane using fast on/off valves. The control system architecture is introduced. The system has been simulated in co-simulation using two different software. The simulated responses of pump-controlled system is compared to the responses of the conventional valve-controlled system.

Boulevard to broken dreams, Part 1: the Polonoroeste road project in the Brazilian Amazon, and the World Bank's environmental and indigenous peoples' norms

ABSTRACT Before the mid 1980s the World Bank conceived "nature" as something to be "conquered" and "environment" as a source of resources for "development". By the late 1980s the Bank incorporated norms of environmental sustainability and indigenous peoples' protection into its mandate, and other development-oriented IOs followed. This two-part paper describes how a fight over the Polonoroeste road project in the Brazilian Amazon - inside the Bank, between the Bank and NGOs supported by the US Congress, and between the Bank and the government of Brazil -helped to generate the far-reaching change of policy norms. The first part describes how the project was designed as an innovation in sustainable development in rainforests; and how it provoked a firestorm inside the Bank as it moved towards project approval.

Automated UI testing. WBCT, a computer-automated user test environment tool.

Today, the user experience and usability in software application are becoming a major design issue due to the adaptation of many processes using new technologies. Therefore, the study of the user experience and usability might be included in every software development project and, thus, they should be tested to get traceable results. As a result of different testing methods to evaluate the concepts, a non-expert on the topic might have doubts on which option he/she should opt for and how to interpret the outcomes of the process. This work aims to create a process to ease the whole testing methodology based on the process created by Seffah et al. and a supporting software tool to follow the procedure of these testing methods for the user experience and usability.

Developmental patterns of individiuals within a sensory-based learning environment in art education : insights emerging from a case study /

My research permitted me to reexamine my recent evaluations of the Leaf Project given to the Foundation Year students during the fall semester of 1997. My personal description of the drawing curriculum formed part of the matrix of the Foundation Core Studies at the Ontario College of Art and Design. Research was based on the random selection of 1 8 students distributed over six of my teaching groups. The entire process included a representation of all grade levels. The intent of the research was to provide a pattern of alternative insights that could provide a more meaningful method of evaluation for visual learners in an art education setting. Visual methods of learning are indeed complex and involve the interplay of many sensory modalities of input. Using a qualitative method of research analysis, a series of queries were proposed into a structured matrix grid for seeking out possible and emerging patterns of learning. The grid provided for interrelated visual and linguistic analysis with emphasis in reflection and interconnectedness. Sensory-based modes of learning are currently being studied and discussed amongst educators as alternative approaches to learning. As patterns emerged from the research, it became apparent that a paradigm for evaluation would have to be a progressive profile of the learning that would take into account many of the different and evolving learning processes of the individual. A broader review of the student's entire development within the Foundation Year Program would have to have a shared evaluation through a cross section of representative faculty in the program. The results from the research were never intended to be conclusive. We realized from the start that sensory-based learning is a difficult process to evaluate from traditional standards used in education. The potential of such a process of inquiry permits the researcher to ask for a set of queries that might provide for a deeper form of evaluation unique to the students and their related learning environment. Only in this context can qualitative methods be used to profile their learning experiences in an expressive and meaningful manner.

Six-month outcomes of a multi-campus smoking cessation contest

Background: Up to 40% of North American post-secondary students smoke at least occasionally, and most want to quit. Given students' preferences for free, easy-to-access, self-directed, convenient cessation methods, a motivational, incentive-based cessation contest may be an effective way to assist students to quit. The current study describes 3- and 6-month outcomes experienced by post-secondary student smokers who entered the 'Let's Make A Deal!' contest. Methodology: Contestants from five university campuses who chose to quit completely ('Quit For Good') or reduce their tobacco consumption by 50% ('Keep The Count') were invited to participate in a study of the contest. Three and six months after registration, participants were contacted by phone to assess their smoking and quitting behaviours. Qualitative and quantitative measures were collected, including weekly tobacco consumption, efficacy to resist temptations to smoke, use of quitting aids, and strategies to cope with withdrawal. Quitting was assessed using 7-day point prevalence and continuous abstinence. Results: Seventy-four (64.9%) of the 114 participants recruited for the study completed the follow-ups. Over 31 % of participants who entered Quit For Good and 23.5% of participants who entered Keep The Count were identified as quitters at the 6-month follow-up. Among the quitters, 45.5% experienced sustained abstinence from smoking for the 6-month duration of the study. Keep The Count contestants reduced their tobacco consumption by 57.2% at 3-month follow-up and sustained some of this reduction through to the 6-month follow-up. Qualitative data provides insights into how quitters coped with withdrawal and what hampered continuing smokers' efforts to quit. Significance: A motivational, incentive-based contest for post-secondary students can facilitate both smoking cessation and harm reduction. The contest environment, incentives, resources, and "buddies" provide positive structural and social supports to help smokers overcome potential barriers to quitting, successfully stop smoking, and manage potential triggers to relapse. The contest cessation rates are higher than the typical 5-7% associated with unassisted quitting.

What gets plans off the shelf? : a multi-site case study of the factors influencing municipal recreation plan implementation

Municipalities that engage in recreation planning have the potential to use their resources more effectively. However, successful planning means getting the plan off the shelf and implemented. This study investigated the factors that influenced municipal recreation plan implementation in three municipalities. Interviews were conducted with eleven key informants (recreation directors, planning consultants, a city councillor, and members of plan steering committees). The findings of this study suggested that because the implementation of recreation plans occurs in a highly political environment, recreation professionals will need effective strategies to get their plans implemented and that implementation can be facilitated by developing or expanding strategies that: (l) build the power of the recreation department within the municipal government structure; (2) build support for recreation within the local community; and (3) build the political and organizational capacity in the recreation department.

Generating Aesthetically Pleasing Images in a Virtual Environment using Particle Swarm Optimization

This research focuses on generating aesthetically pleasing images in virtual environments using the particle swarm optimization (PSO) algorithm. The PSO is a stochastic population based search algorithm that is inspired by the flocking behavior of birds. In this research, we implement swarms of cameras flying through a virtual world in search of an image that is aesthetically pleasing. Virtual world exploration using particle swarm optimization is considered to be a new research area and is of interest to both the scientific and artistic communities. Aesthetic rules such as rule of thirds, subject matter, colour similarity and horizon line are all analyzed together as a multi-objective problem to analyze and solve with rendered images. A new multi-objective PSO algorithm, the sum of ranks PSO, is introduced. It is empirically compared to other single-objective and multi-objective swarm algorithms. An advantage of the sum of ranks PSO is that it is useful for solving high-dimensional problems within the context of this research. Throughout many experiments, we show that our approach is capable of automatically producing images satisfying a variety of supplied aesthetic criteria.

A research capacity strengthening project for infectious diseases in Honduras: experience and lessons learned

Background: In Honduras, research capacity strengthening (RCS) has not received sufficient attention, but an increase in research competencies would enable local scientists to advance knowledge and contribute to national priorities, including the Millennium Development Goals (MDGs). Objective: This project aimed at strengthening research capacity in infectious diseases in Honduras, focusing on the School of Microbiology of the National Autonomous University of Honduras (UNAH). The primary objective was the creation of a research-based graduate program for the continued training of researchers. Parallel objectives included institutional strengthening and the facilitation of partnerships and networks. Methods: Based on a multi-stakeholder consultation, an RCS workplan was designed and undertaken from 2007 to 2012. Due to unexpected adverse circumstances, the first 2 years were heavily dedicated to implementing the project's flagship, an MSc program in infectious and zoonotic diseases (MEIZ). In addition, infrastructure improvements and demand-driven continuing education opportunities were facilitated; biosafety and research ethics knowledge and practices were enhanced, and networks fostering collaborative work were created or expanded. Results: The project coincided with the peak of UNAH's radical administrative reform and an unprecedented constitutional crisis. Challenges notwithstanding, in September 2009, MEIZ admitted the first cohort of students, all of whom undertook MDG-related projects graduating successfully by 2012. Importantly, MEIZ has been helpful in expanding the School of Microbiology's traditional etiology-based, disciplinary model to infectious disease teaching and research. By fulfilling its objectives, the project contributed to a stronger research culture upholding safety and ethical values at the university. Conclusions: The resources and strategic vision afforded by the project enhanced UNAH's overall research capacity and its potential contribution to the MDGs. Furthermore, increased research activity and the ensuing improvement in performance indicators at the prime Honduran research institution invoke the need for a national research system in Honduras.

Choosing Wisely: The Natural Multi-Bidding Mechanism

Pérez-Castrillo and Wettstein (2002) propose a multi-bidding mechanism to determine a winner from a set of possible projects. The winning project is implemented and its surplus is shared among the agents. In the multi-bidding mechanism each agent announces a vector of bids, one for each possible project, that are constrained to sum up to zero. In addition, each agent chooses a favorite a object which is used as a tie-breaker if several projects receive the same highest aggregate bid. Since more desirable projects receive larger bids, it is natural to consider the multi-bidding mechanism without the announcement of favorite projects. We show that the merits of the multi-bidding mechanism appear not to be robust to this natural simplification. Specifically, a Nash equilibrium exists if and only if there are at least two individually optimal projects and all individually optimal projects are efficient.

Structure et dynamique des communautés multi-espèces : le rôle de l’espace

Cette thèse porte sur le rôle de l’espace dans l’organisation et dans la dynamique des communautés écologiques multi-espèces. Deux carences peuvent être identifiées dans les études théoriques actuelles portant sur la dimension spatiale des communautés écologiques : l’insuffisance de modèles multi-espèces représentant la dimension spatiale explicitement, et le manque d’attention portée aux interactions positives, tel le mutualisme, en dépit de la reconnaissance de leur ubiquité dans les systèmes écologiques. Cette thèse explore cette problématique propre à l’écologie des communautés, en utilisant une approche théorique s’inspirant de la théorie des systèmes complexes et de la mécanique statistique. Selon cette approche, les communautés d’espèces sont considérées comme des systèmes complexes dont les propriétés globales émergent des interactions locales entre les organismes qui les composent, et des interactions locales entre ces organismes et leur environnement. Le premier objectif de cette thèse est de développer un modèle de métacommunauté multi-espèces, explicitement spatial, orienté à l’échelle des individus et basé sur un réseau d’interactions interspécifiques générales comprenant à la fois des interactions d’exploitation, de compétition et de mutualisme. Dans ce modèle, les communautés locales sont formées par un processus d’assemblage des espèces à partir d’un réservoir régional. La croissance des populations est restreinte par une capacité limite et leur dynamique évolue suivant des mécanismes simples de reproduction et de dispersion des individus. Ces mécanismes sont dépendants des conditions biotiques et abiotiques des communautés locales et leur effet varie en fonction des espèces, du temps et de l’espace. Dans un deuxième temps, cette thèse a pour objectif de déterminer l’impact d’une connectivité spatiale croissante sur la dynamique spatiotemporelle et sur les propriétés structurelles et fonctionnelles de cette métacommunauté. Plus précisément, nous évaluons différentes propriétés des communautés en fonction du niveau de dispersion des espèces : i) la similarité dans la composition des communautés locales et ses patrons de corrélations spatiales; ii) la biodiversité locale et régionale, et la distribution locale de l’abondance des espèces; iii) la biomasse, la productivité et la stabilité dynamique aux échelles locale et régionale; et iv) la structure locale des interactions entre les espèces. Ces propriétés sont examinées selon deux schémas spatiaux. D’abord nous employons un environnement homogène et ensuite nous employons un environnement hétérogène où la capacité limite des communautés locales évoluent suivant un gradient. De façon générale, nos résultats révèlent que les communautés écologiques spatialement distribuées sont extrêmement sensibles aux modes et aux niveaux de dispersion des organismes. Leur dynamique spatiotemporelle et leurs propriétés structurelles et fonctionnelles peuvent subir des changements profonds sous forme de transitions significatives suivant une faible variation du niveau de dispersion. Ces changements apparaissent aussi par l’émergence de patrons spatiotemporels dans la distribution spatiale des populations qui sont typiques des transitions de phases observées généralement dans les systèmes physiques. La dynamique de la métacommunauté présente deux régimes. Dans le premier régime, correspondant aux niveaux faibles de dispersion des espèces, la dynamique d’assemblage favorise l’émergence de communautés stables, peu diverses et formées d’espèces abondantes et fortement mutualistes. La métacommunauté possède une forte diversité régionale puisque les communautés locales sont faiblement connectées et que leur composition demeure ainsi distincte. Par ailleurs dans le second régime, correspondant aux niveaux élevés de dispersion, la diversité régionale diminue au profit d’une augmentation de la diversité locale. Les communautés locales sont plus productives mais leur stabilité dynamique est réduite suite à la migration importante d’individus. Ce régime est aussi caractérisé par des assemblages incluant une plus grande diversité d’interactions interspécifiques. Ces résultats suggèrent qu’une augmentation du niveau de dispersion des organismes permet de coupler les communautés locales entre elles ce qui accroît la coexistence locale et favorise la formation de communautés écologiques plus riches et plus complexes. Finalement, notre étude suggère que le mutualisme est fondamentale à l’organisation et au maintient des communautés écologiques. Les espèces mutualistes dominent dans les habitats caractérisés par une capacité limite restreinte et servent d’ingénieurs écologiques en facilitant l’établissement de compétiteurs, prédateurs et opportunistes qui bénéficient de leur présence.

Projets des logements à la suite des désastres : analyse du système organisationnel et évaluation de la satisfaction des usagers dans un projet de reconstruction dans la région du Maghreb

Plusieurs études ont révélé des problèmes récurrents au niveau de la performance et de la gestion des projets de reconstruction à la suite des catastrophes dans les pays en voie de développement (PEVD). Ces projets doivent faire face à des conditions de vulnérabilité des habitants, engendrées par des facteurs politiques, économiques, sociaux et culturels. Les divers participants - contraints par un accès limité à l’information - sont confrontés à travailler dans un contexte hostile ayant un niveau d’incertitude élevé. Ce niveau d’incertitude augmente les risques du projet de reconstruction, particulièrement le risque d’insatisfaction des usagers. Ce travail vise à mettre en parallèle l’analyse du système organisationnel adopté pour la conduite d’un projet de reconstruction et celle du niveau de satisfaction des usagers. Il émet l’hypothèse suivante: deux facteurs organisationnels influencent largement le niveau de satisfaction de la part des bénéficiaires d’un projet de reconstruction de logements à la suite d’un désastre en PEVD: (i) le niveau de centralisation de la prise de décisions (jumelée au manque d’information) au sein de la Multi-Organisation Temporaire (MOT); et (ii) la capacité de la structure organisationnelle de la MOT d’impliquer la participation active des usagers au niveau de la planification, de la gestion, du financement et du design du projet. Afin d’atteindre cet objectif, une recherche empirique fut menée pour analyser le cas des inondations ayant eu lieu en 2003 dans une ville dans la région du Maghreb. Le niveau de satisfaction des usagers a été déterminé grâce à des indicateurs de transfert de technologie qui se basent sur l’analyse du « Cadre Logique » - une méthode d’évaluation largement utilisée dans le domaine du développement international. Les résultats de la recherche ne visent pas à identifier une relation de cause à effet entre les deux variables étudiées (la structure organisationnelle et la satisfaction des usagers). Cependant, ils mettent en évidence certains principes du montage et de la gestion des projets qui peuvent être mis en place pour l’amélioration des pratiques de reconstruction.

Calibration de systèmes de caméras et projecteurs dans des applications de création multimédia

Ce mémoire s'intéresse à la vision par ordinateur appliquée à des projets d'art technologique. Le sujet traité est la calibration de systèmes de caméras et de projecteurs dans des applications de suivi et de reconstruction 3D en arts visuels et en art performatif. Le mémoire s'articule autour de deux collaborations avec les artistes québécois Daniel Danis et Nicolas Reeves. La géométrie projective et les méthodes de calibration classiques telles que la calibration planaire et la calibration par géométrie épipolaire sont présentées pour introduire les techniques utilisées dans ces deux projets. La collaboration avec Nicolas Reeves consiste à calibrer un système caméra-projecteur sur tête robotisée pour projeter des vidéos en temps réel sur des écrans cubiques mobiles. En plus d'appliquer des méthodes de calibration classiques, nous proposons une nouvelle technique de calibration de la pose d'une caméra sur tête robotisée. Cette technique utilise des plans elliptiques générés par l'observation d'un seul point dans le monde pour déterminer la pose de la caméra par rapport au centre de rotation de la tête robotisée. Le projet avec le metteur en scène Daniel Danis aborde les techniques de calibration de systèmes multi-caméras. Pour son projet de théâtre, nous avons développé un algorithme de calibration d'un réseau de caméras wiimotes. Cette technique basée sur la géométrie épipolaire permet de faire de la reconstruction 3D d'une trajectoire dans un grand volume à un coût minime. Les résultats des techniques de calibration développées sont présentés, de même que leur utilisation dans des contextes réels de performance devant public.