The ade4 Package: Implementing the Duality Diagram for Ecologists

Multivariate analyses are well known and widely used to identify and understand structures of ecological communities. The ade4 package for the R statistical environment proposes a great number of multivariate methods. Its implementation follows the tradition of the French school of "Analyse des Donnees" and is based on the use of the duality diagram. We present the theory of the duality diagram and discuss its implementation in ade4. Classes and main functions are presented. An example is given to illustrate the ade4 philosophy.

Nonparametric estimation of the conditional distribution of the inter-jumping times for piecewise-deterministic Markov processes

This paper presents a nonparametric method for estimating the conditional density associated to the jump rate of a piecewise-deterministic Markov process. In our framework, the estimation needs only one observation of the process within a long time interval. Our method relies on a generalization of Aalen's multiplicative intensity model. We prove the uniform consistency of our estimator, under some reasonable assumptions related to the primitive characteristics of the process. A simulation example illustrates the behavior of our estimator

A Determination of the Trade Creation and Diversion Effects of Regional Trade Agreements in the Western Hemisphere

With the recent proliferation of Regional Trade Agreements (RTAs) the tendency world-wide has been seemingly toward trade liberalization. This thesis is primarily concerned with the impacts RTAs have had in the Western Hemisphere regarding agricultural trade flows. Utilizing the framework of the Gravity Model, agricultural trade flows for 24 Western Hemisphere Nations were examined. In the course of the study it was expected that if RTAs were to have an effect it would be a positive Trade Creation Effect and a negative Trade Diversion Effect with positive effects for GDP of importer/exporter and population size of importer/exporter and a negative effect for that of distance. Of the five agreements examined (NAFTA, AC, MERCO, LAIA, and CACM), NAFTA and LAIA were the only positive (but non-significant) as to Trade Creation effects while AC, MERCO, and CACM were all negative (but non-significant). It was also interesting to note that of the agreements, NAFTA, had both a positive and significant (p=0.023) diversionary effect with the remaining agreements all being negative (as expected) and significant regarding trade diversion. It was also concluded that GDP (importer) and distance also had the expected signs (+, respectively) with distance also being significant (p=0.0001). It was concluded that RTAs had a more pronounced effect on inter-industry trade versus intra-industry trade and that with the passage of more time, further analysis may substantiate the claim of a positive RTA effect on agricultural bilateral trade flows.International Relations/Trade,

The ade4 Package: Implementing the Duality Diagram for Ecologists

Multivariate analyses are well known and widely used to identify and understand structures of ecological communities. The ade4 package for the R statistical environment proposes a great number of multivariate methods. Its implementation follows the tradition of the French school of "Analyse des Donnees" and is based on the use of the duality diagram. We present the theory of the duality diagram and discuss its implementation in ade4. Classes and main functions are presented. An example is given to illustrate the ade4 philosophy

La motivation aux interventions et programmes correctionnels chez les détenus canadiens des pénitenciers fédéraux

Malgré l’importance de la motivation pour le maintien des détenus dans les programmes visant leur réadaptation, les connaissances sur leur motivation demeurent insuffisantes. Les études passées comportent des limites affectant leur possibilité de généralisation et de comparaison. Les facteurs associés à la motivation ne sont pas explorés systématiquement et sont parfois inconsistants. De plus, la compréhension de la motivation parmi les détenus canadiens est limitée par le fait que le Service correctionnel Canada (SCC) n’utilise pas d’instrument évaluant exclusivement leur motivation à l’égard des interventions. Les évaluations du SCC qui considèrent la motivation ont rarement été examinées en recherche et ne l’ont pas été de manière interactive. Une recension approfondie des écrits sur la motivation en milieu carcéral et une méthodologie plus détaillée de la thèse sont d’abord décrites. L’étude comporte deux volets incluant 562 hommes détenus, condamnés à une première ou nouvelle sentence de deux ans et plus, incarcérés pour des délits variés à travers tous les pénitenciers fédéraux du Québec. Dans le premier, des évaluations de leur santé mentale ont été effectuées avec plusieurs instruments cliniques. Dans le deuxième, une collecte de données a été entreprise dans leurs dossiers carcéraux afin d’obtenir des informations sur les services reçus en établissement. Par exemple, des programmes correctionnels sur la prévention de la violence, la prévention de la violence familiale, la délinquance sexuelle, la toxicomanie, les compétences psychosociales et le maintien des acquis sont pris en compte. Le premier article explore l’association et la cohérence entre les mesures de la motivation aux interventions et programmes correctionnels, l’évolution de la motivation au cours des programmes, ainsi que l'impact de la motivation sur la complétion d’un programme et la réhabilitation. Le second article se penche sur l’identification des prédicteurs principaux de la motivation aux interventions. Les résultats montrent (1) le lien et la différence entre les mesures de la motivation aux interventions évaluées par des intervenants distincts et ayant des cibles différentes, (2) l’augmentation de la motivation au cours d’un programme complété, (3) la similarité de la motivation entre des programmes ciblant la même problématique, (4) la différence de motivation entre des programmes ciblant une problématique distincte, (5) la prédiction de la complétion et réussite d’un programme par la motivation évaluée avant programme, (6) la prédiction de la révocation par la motivation évaluée après un programme complété et, (7) après avoir considéré plusieurs éléments ayant été liés à la motivation lors d’études antérieures, l’identification de plus de quinze prédicteurs de la motivation des détenus en établissant leur importance respective dans des modèles considérant les mesures de la motivation du SCC. Plusieurs implications sont ensuite discutées. Cette thèse permet de guider la manière dont la motivation aux interventions pourrait être considérée et évaluée en cours d’incarcération pour encourager la réussite des programmes. Elle permet aussi d’identifier des prédicteurs de la motivation qui pourraient être ciblés pour motiver les détenus et aider à sélectionner ceux nécessitant des interventions motivationnelles avant et pendant les programmes. Enfin, elle permet de cibler des pistes pour les recherches futures.Despite the importance of inmates’ motivation for retention in programs designed to rehabilitate them, knowledge about their motivation remains insufficient. Past studies have limitations affecting their potential for generalization and comparison. Factors associated with motivation are not systematically explored and are sometimes inconsistent. In addition, the understanding of motivation among Canadian inmates is limited by the fact that Correctional Service Canada (CSC) does not use instruments that exclusively evaluate motivation for interventions. CSC’s evaluations of motivation have rarely been considered in research and have not been examined interactively. Detailed review of the literature on motivation in correctional institutions and methodology of the thesis are first described. The study has two parts and includes 562 male inmates who were sentenced to a first or new sentence of two years or more. These inmates were incarcerated for various offenses across all federal penitentiaries in Quebec. In the first part, mental health assessments were conducted using several clinical instruments. In the second part, data collection was undertaken within correctional files to obtain information about services received in institutions. For example, correctional programs targeting violence prevention, family violence prevention, sex offending, substance abuse, living skills and community maintenance were taken into account. The first article explores the association and coherence between measures of motivation towards correctional interventions and programs, the evolution of motivation during programs, as well as the impact of motivation on program completion and rehabilitation. The second article targets the identification of motivation’s main predictors for interventions. Results show (1) the link and difference between measures of motivation towards interventions with different targets while evaluated by different professionals, (2) increased motivation within a completed program, (3) the similarity in motivation between programs targeting the same issue, (4) the difference in motivation between programs targeting distinct issues, (5) the prediction of program completion and success by the motivation evaluated before program, (6) the prediction of revocation by the motivation evaluated after program completion and, (7) after considering several elements that were related to inmates’ motivation in previous studies, the identification of more than fifteen predictors of inmates’ motivation while establishing their respective importance in models considering CSC’s measures of motivation. Various implications are then discussed. For example, this thesis provides guidance on how motivation towards interventions could be considered and assessed throughout incarceration to encourage the success of programs. It also helps identify predictors of motivation that could be targeted to motivate inmates and aid in selection of those requiring motivational interventions before and during programs. Finally, it identifies directions for future research

La laïcité et la presse écrite canadienne: le cas de la Loi sur la laïcité de l’État

Ce mémoire se penche sur le traitement médiatique de la Loi sur la laïcité de l’État pendant la première année de mandat de la Coalition avenir Québec (CAQ). En effet, cette dernière a été élue avec, entre autres, la promesse de bannir le port de symboles religieux pour les employés de l’État en position d’autorité, incluant les enseignants du primaire et du secondaire. Cette façon d’aménager le religieux dans l’espace public correspond à la laïcité, soit la séparation de l’État et de la religion. Deux grandes idées derrière ce principe s’affrontent. Elles sont communément appelées « laïcité libérale » et « laïcité républicaine », cette dernière correspondant aux visées de la loi adoptée par le gouvernement caquiste. La Loi sur la laïcité de l’État est de même une législation unique au Canada, où la laïcité d’inspiration libérale est généralement davantage prisée. Étant un sujet polarisant, cette loi a été l’objet de très nombreuses publications à travers le pays. Une analyse de contenu des chroniques et des éditoriaux anglophones et francophones de dix grands médias canadiens a permis de comprendre la façon dont la loi a été perçue à travers les journaux. Également, la perception de la loi a été mise en rapport avec la relation historiquement tendue entre le Québec francophone et le Canada anglais. Hormis la langue, les traditions religieuses sont également différentes. Au Québec, l’Église catholique a joué un rôle particulièrement marquant dans l’évolution de la société, notamment dans les services sociaux tels la santé, l’éducation et la charité publique. L’identité québécoise s’est donc forgée à travers la présence du catholicisme pour, par la suite, faire un virage à la suite de la Révolution tranquille. Nos résultats ont entre autres mis en lumière le fait que la quasi-totalité des chroniques et éditoriaux anglophones ont véhiculé une image négative de la loi. Au Québec francophone, les résultats étaient davantage partagés. Toutefois, les conclusions obtenues à travers divers sondages ne correspondaient pas à nos résultats. Il était effectivement montré que, malgré une plus grande proportion d’anglophones qui étaient contre la loi, il y avait malgré tout une proportion non négligeable qui se prononçait plutôt en sa faveur. On a ainsi pu constater que les écrits des chroniqueurs et éditorialistes ne reflètent pas correctement l’opinion publique

Consensus genetic structuring and typological value of markers using multiple co-inertia analysis

Working with weakly congruent markers means that consensus genetic structuring of populations requires methods explicitly devoted to this purpose. The method, which is presented here, belongs to the multivariate analyses. This method consists of different steps. First, single-marker analyses were performed using a version of principal component analysis, which is designed for allelic frequencies (%PCA). Drawing confidence ellipses around the population positions enhances %PCA plots. Second, a multiple co-inertia analysis (MCOA) was performed, which reveals the common features of single-marker analyses, builds a reference structure and makes it possible to compare single-marker structures with this reference through graphical tools. Finally, a typological value is provided for each marker. The typological value measures the efficiency of a marker to structure populations in the same way as other markers. In this study, we evaluate the interest and the efficiency of this method applied to a European and African bovine microsatellite data set. The typological value differs among markers, indicating that some markers are more efficient in displaying a consensus typology than others. Moreover, efficient markers in one collection of populations do not remain efficient in others. The number of markers used in a study is not a sufficient criterion to judge its reliability. "Quantity is not quality"

Poisson (co)homology and isolated singularities

To each polynomial \v\in\F[x,y,z] is associated a Poisson structure on \F^3, a surface and a Poisson structure on this surface. When \v is weight homogeneous with an isolated singularity, we determine the Poisson cohomology and homology of the two Poisson varieties obtained.Comment: 27 page

Targeting renal cell carcinoma with NVP-BEZ235, a dual PI3K/mTOR inhibitor, in combination with sorafenib

Background: Targeted therapies for metastatic renal cell carcinoma (RCC), including mammalian target of rapamycin (mTOR) inhibitors and small-molecule multikinase inhibitors, have produced clinical effects. However, most patients acquire resistance over time. Thus, new therapeutic strategies need to be developed. Here, we evaluated the effect of the dual PI3K/mTOR inhibitor NVP-BEZ235, in combination with the multikinase inhibitor sorafenib on renal cancer cell proliferation and survival in vitro as well as on tumor growth in vivo.Methods: The renal carcinoma cell lines 786-0 and Caki-1 were treated with NVP-BEZ235 or sorafenib, either alone or in combination. Tumor cell proliferation and apoptosis were investigated in vitro. The anticancer efficacy of NVP-BEZ235 alone, or in combination with sorafenib, was also evaluated on RCC xenografts in nude mice.Results: Treatment of 786-0 and Caki-1 cells with NVP-BEZ235 or sorafenib resulted in reduced tumor cell proliferation and increased tumor cell apoptosis in vitro. The combination of NVP-BEZ235 and sorafenib was more effective than each compound alone. Similarly, in vivo, NVP-BEZ235 or sorafenib reduced the growth of xenografts generated from 786-0 or Caki-1 cells. The antitumor efficacy of NVP-BEZ235 in combination with sorafenib was superior to NVP-BEZ235 or sorafenib alone.Conclusions: Our findings indicate that the simultaneous use of NVP-BEZ235 and sorafenib has greater antitumor benefit compared to either drug alone and thus provides a treatment strategy in RCC

Sensory-based nutrition pilot intervention for women

Negative effects of restrained eating (ie, concerns about dieting and weight control) have been observed in eating behaviors. Such findings underscore the need to develop more positive approaches to promote healthy eating behaviors. The objectives of this pilot randomized controlled trial were to investigate and determine whether sensory-based intervention influenced eating-related attitudes and behaviors among restrained women, as well as reliance on physical signals for hunger and satiety. Between January and September 2011, data were collected using validated questionnaires (Restraint Scale, Three-Factor Eating Questionnaire, Mindful Eating Questionnaire, and Intuitive Eating Scale) at baseline (T=1), the end of the intervention period (T=2), and 12 weeks post intervention (T=3). At T=1, women (n=50) from Quebec City, Canada, were randomly assigned to an intervention group (sensory-based intervention) or a waiting list control group. Statistical analyses were conducted using mixed models, including the group, time, and group-by-time interaction. Women from the intervention group showed a significant decrease in Three-Factor Eating Questionnaire-Disinhibition and a significant increase in Mindful Eating Questionnaire-Disinhibition at T=2 vs T=3 (P=0.02 and P=0.02, respectively) and at T=3 vs T=1 (P=0.003 and P=0.002, respectively). Women from the intervention group also showed a significant increase in Intuitive Eating Scale-Unconditional Permission to Eat at T=2 vs T=1 (P<0.0001) and at T=3 vs T=1 (P<0.0001). These preliminary data suggest that sensory-based intervention can be a promising approach to improve eating-related attitudes and behaviors among restrained women, without exacerbating other behaviors such as restrained eating