A mobile testing application using Unity was developed to analyse what impact button sizes and button layouts has on the accuracy of touch as well as the time to finish a labyrinth. This was tested on a Nexus 4 phone. 28 users navigated a small object through a labyrinth in which they collect keys to open the door to the exit. Each participant did the test 6 times with different combinations of button size and button layout each time, done in a random order. Hits, misses, completion time, order of button size and order of button layout was collected and then visualized using R. A mixed model analysis was used to analyse the data. The model to estimate what impact button size has on time is found to be poor while the model to estimate accuracy is assumed to be good. Results show that a button size larger than 6.0mm is required for the average user to have satisfactory accuracy. / En testapplikation för mobila enheter utvecklades i Unity för att analysera vilken påverkan knappstorlekar och gränssnitt har på träffsäkerheten och tiden att slutföra en labyrint. Detta testades på en Nexus 4 telefon. 28 användare navigerade ett litet objekt genom en labyrint i vilken de samlar nycklar för att öppna dörren till utgången. Varje deltagare utförde testet 6 gånger med annorlunda kombination av knappstorlek och gränssnittsdesign varje gång, detta i slumpmässig ordning. Träffar, missar, slutföringstid, vilken ordning som knappstorlek och gränssnittsdesign presenterades för användaren samlades in och visualiserades med R. En blandmodell användes för att analysera data. Modellen för vilken påverkan som knappstorlekar har på slutföringstiden ansågs otillräcklig medan modellen för hur träffsäkerheten påverkas av knappstorlekar ansågs god. Resultaten visar att en knappstorlek större än 6,0mm krävs för den genomsnittliga användaren ska ha en tillfredställande träffsäkerhet.

La détection de gènes est une étape importante dans la compréhension des effets de l'information génétique d'un individu sur ses caractères phénotypiques. Durant mon doctorat, j'ai étudié les méthodes statistiques pour conduire les analyses de génétique d'association, avec les hybrides de maïs comme modèle d'application. Je me suis tout d'abord intéressé à l'estimation des paramètres d'apparentement entre individus à partir de données de marqueurs bialléliques. Cette estimation est réalisée dans le cadre d'un modèle de mélange paramétrique. J'ai étudié l'identifiabilité de ce modèle dans un cadre général mais aussi dans un cadre plus spécifique où les individus étudiés étaient issus de croisements entre lignées, cadre représentatif des plans de croisement classiquement utilisés en génétique végétale. Je me suis ensuite intéressé à l'estimation des paramètres des modèles mixtes à plusieurs composantes de variance et plus particulièrement à la performance des algorithmes pour tester l'effet de très nombreux marqueurs. J'ai comparé pour cela des logiciels existants et optimisé un algorithme Min-Max. La pertinence des différentes méthodes développées a finalement été illustrée dans le cadre de la détection de QTL à travers une analyse d'association réalisée sur un panel d'hybrides de maïs. / The detection of genes is a first step to understand the impact of the genetic information of individuals on their phenotypes. During my PhD, I studied statistical methods to perform genome-wide association studies, with maize hybrids as an application case. Firstly, I studied the inference of relatedness coefficients between individuals from biallelic marker data. This estimation is based on a parametric mixture model. I studied the identifiability of this model in the generic case but also in the specific case of mating design where observed individuals are obtained by crossing lines, a representative case of classical mating design in plant genetics. Then I studied inference of variance component mixed model parameters and particularly the performance of algorithms to test effects of numerous markers. I compared existing programs and I optimized a Min-Max algorithm. Relevance of developed methods had been illustrated for the detection of QTLs through a genome-wide association analysis in a maize hybrids panel.

The current study investigated vowel quality in Miami Cuban Spanish, looking specifically at the influence of English on the Spanish vowel system. The vowel production of eleven Miami Cubans from three generations is investigated. Subjects include six males and five females. Three different elicitation instruments were used. The first was a brief sociolinguistic interview, the second was a story that the participants were asked to read aloud. Carrier words were embedded into the story in order to obtain multiple samples of both stressed and unstressed vowels. For the third instrument, subjects were asked to read a list of words with careful attention to their pronunciation. The reading list contained the same words that were embedded in the story of the first task. These three instruments were repeated in both Spanish and in English in order to investigate possible English influence in the Spanish vowel system of these bilinguals.

Despite known associations between fitness and recurrent cardiovascular events, changes in cardiorespiratory fitness (CRF) and muscle strength with long-term cardiac rehabilitation (CR) have not been extensively examined in men, and data in women is absent in the literature. The purpose of this thesis was to estimate changes in CRF and muscle strength associated with long-term CR program enrollment in men and women, and to examine the influence of baseline fitness and age on these fitness trajectories in men. Our methods and interpretations of the findings are discussed in the thesis, but in brief, using mixed model analyses we observed important fitness benefits over long-term CR enrollment in men and women and influences of baseline fitness and age on the trajectories in men. Our data provide new evidence of improved fitness trajectories in men and women after long-term CR enrollment and highlight the importance of long-term exercise-based CR after the completion of short-term programs. Larger prospective cohort studies are warranted to confirm the observations, and to identify potential mechanisms underlying these findings. / Dissertation / Doctor of Philosophy (PhD)

Pathway is a set of genes which are predefined and serve a particular celluar or physiological function. Ranking pathways relevant to a particular phenotype can help researchers focus on a few sets of genes in pathways. In this thesis, a Bayesian hierarchical latent model was proposed using generalized linear random effects model. The advantage of the approach was that it can easily incorporate prior knowledges when the sample size was small and the number of genes was large. For the covariance matrix of a set of random variables, two Gaussian random processes were considered to construct the dependencies among genes in a pathway. One was based on the polynomial kernel and the other was based on the Gaussian kernel. Then these two kernels were compared with constant covariance matrix of the random effect by using the ratio, which was based on the joint posterior distribution with respect to each model. For mixture models, log-likelihood values were computed at different values of the mixture proportion, compared among mixtures of selected kernels and point-mass density (or constant covariance matrix). The approach was applied to a data set (Mootha et al., 2003) containing the expression profiles of type II diabetes where the motivation was to identify pathways that can discriminate between normal patients and patients with type II diabetes. / Master of Science

Sex ratio is very important for the evolution of dioecious plants. It can influence the reproductive success of plants. Sex ratio bias is common among reproductive individuals. Studying the reproductive traits can help to understand possible mechanisms that could influence the generation and maintenance of sex ratio bias. However, few studies have reported the relationship between reproductive traits and sex ratio bias. We investigated 29 full-sib families of the dwarf willow Salix herbacea L. S.herbacea exhibits an overall female sex ratio bias but also strong variation in sex ratio among families. We used variance component analysis to investigate from which morphological level the variation of reproductive traits (cumulative catkin number over four growth periods, annual catkin number in the fourth growth period, flower number, ovule number) came from. And we used mixed models to test the influence of family, sex and the sex by family interaction on reproductive traits. Besides that, we also tested the correlation between sex ratio and reproductive traits. Our results suggest that genetic factors can influence the degree of sexual dimorphism of S. herbacea in the different families Flowers from families with higher sex ratios had more ovules, sex ratio and the ovule number co-varied across families.

京都大学 / 新制・課程博士 / 博士(情報学) / 甲第25426号 / 情博第864号 / 新制||情||145(附属図書館) / 京都大学大学院情報学研究科知能情報学専攻 / (主査)准教授 水原 啓暁, 教授 西田 眞也, 教授 熊田 孝恒 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DFAM

Introduction and objectives In Vietnam, the forest resources have been declining and degrading severely in recent years. The degradation has decreased the natural forest area, changed the forest structure seriously and reduced timber volume and biodiversity. From 1999 to 2005, the rich forest area has decreased 10.2%, whereas the poor secondary forest has increased dramatically by 20.7%. Forest structure plays an important role in forestry research. Understanding forest structure will unlock an understanding of the history, function and future of a forest ecosystem (Spies, 1998). The forest structure is an excellent basis for restoration measures. Therefore, this research is necessary to contribute to improving forest area and quality, reducing difficulties in forest management. The study also enhances the grasp of forest structure, structure changes after harvesting and fills serious gaps in knowledge. In addition, the research results will contribute to improving and rescuing the poor secondary forest and restoring it, approaching the old-growth forest in Vietnam. Material and methods The study was conducted in Kon Ka Kinh national park. The park is located in the Northeastern region of Gia Lai province, 50 km from Pleiku city center to the Northeast. The park is distributed over seven different communes in three districts: K’Bang, Mang Yang and Đăk Đoa. Data were collected from 10 plots of secondary forests (Type IIb) and 10 plots of primeval forests (Type IV). Stratified random sampling was applied to select plot locations. 1 ha plots were used to investigate gaps. 2000 m2 plots were used to measure overstorey trees such as diameter at breast height, total height, crown width and species names. 500 m2 subplots were used to record tree positions. For regeneration, 25 systematic 4 m2 subplots were established inside 1 ha plots. After data were collected in the field, data analyses were conducted by using R and Excel. Firstly, some stand information, such as density, volume and so on, was calculated, and then descriptive statistics were computed for diameter and height variables. Linear mixed effect models were applied to analyze the difference of diameter and height and to check the effect of random factor between the two forest types. Diameter and height frequency distributions were also generated and compared by using permutational analysis of variance (PERMANOVA). Non-linear regression models were analyzed for diameter and height variables. Similar analyses were implemented for gaps. Regarding spatial point patterns of overstorey trees, replicated point pattern analysis techniques were applied in this research. For biodiversity, some calculations were run such as richness and biodiversity indices, comparison of biodiversity indices by using linear mixed models and biodiversity differences between two forest types tested again by permutational analysis of variance. In terms of regeneration, some analyses were implemented such as: height frequency distribution generation, frequency difference testing, biodiversity indices for the regeneration and spatial distribution checking by using a nonrandomness index. Results and discussion After analyzing the data, some essential findings were obtained as follows: Hypothesis H1 “The overstorey structure of secondary forests is more homogeneous and uniform than old-growth forests” is accepted. In other words, the secondary forest density is about 1.8 times higher than the jungle. However, the volume is only 0.56 times as large. The average diameter and height of the secondary forest is smaller by 5.71 cm and 3.73 m than the old-growth forest, respectively. Linear mixed effect model results indicate that this difference is statistically different and the effect of the random factor (Section) is not important. Type IIb has many small trees and the diameter frequency distribution is quite homogeneous. The old-growth forest has more big trees. For both forest stages, the height frequency distribution is positively skewed. PERMANOVA results illustrate that the frequency distribution is statistically different between the two forest types. Regression functions are also more variant and diverse in the old-growth forest, because all standard deviations of the parameters are greater there. Gap analysis results indicate that the number of gaps in the young forest is slightly higher, while the average gap size is much smaller. The gap frequency distribution is statistically different between the two types. In terms of the spatial point pattern of overlayer trees, the G-test and the pair correlation function results show that trees distribute randomly in the secondary forest. In contrast, the spatial point patterns of trees are more regular and diverse in the old-growth forest. The spatial point pattern difference is not significant, and this is proved by a permutational t-test for pair correlation function (pcf). Envelope function results indicate that the variation of pcf in young forests is much lower than in the primary forests. Hypothesis H2 “The overstorey species biodiversity of the secondary forest is less than in the old-growth forest” is rejected. Results show that the number of species of the secondary forest is much greater than in the old-growth forest, especially richness. The richness of the secondary forest is 1.16 times higher. The Simpson and Shannon indices are slightly smaller in the secondary forest. The average Simpson index for both forest stages is 0.898 and 0.920, respectively. However, the difference is not significant. Species accumulation curves become relatively flatter on the right, meaning a reasonable number of plots have been observed. Estimated number of species from accumulation curves in two forest types are 105 and 95/ha. PERMANOVA results show that number of species and proportion of individuals in each species are significantly different between forest types. Hypothesis H3 “The number regenerating species of the secondary forest is less and they distribute more regularly, compared to the old-growth forest” is rejected. There are both similarities and differences between the two types. The regeneration density of the stage IIb is 22,930 seedlings/ha, greater than the old forest by 9,030 seedlings. The height frequency distribution shows a decreasing trend. Similar to overstorey, the richness of the secondary forest is 141 species, higher than the old-growth forest by 9 species. Biodiversity indices are not statistically different between two types. PERMANOVA results indicate that the number of species and the proportion of individuals for each species are also not significantly different from observed forest types. Nonrandomness index results show that the regeneration distributes regularly. Up to 95% of the plots reflect this distribution trend. Hypothesis H4 “Restoration measures (with and without human intervention) could be implemented in the regenerating forest” is accepted. The investigated results show that the secondary forest still has mother trees, and it has enough seedlings to restore. Therefore, restoration solutions with and without human intervention can be implemented. Firstly, forest protection should be applied. This measure is relevant to national park regulations in Vietnam. Rangers and other related organizations will be responsible for carrying out protection activities. These activities will protect forest resources from illegal logging, grazing and tourist activities. Environmental education and awareness-raising activities for indigenous people is also important. Another measure is additional and enrichment planting. It should focus on exclusive species of the overstorey in Type IIb or exclusive species of the primary forest. Selection of these species will lead to species biodiversity increase in the future. This also meets the purpose of the maximum biodiversity solution. Conclusion Forest resources play a very important role in human life as well as maintaining the sustainability of ecosystems. However, at present, they are under serious threat, particularly in Vietnam. Central Highland, Vietnam, where forest resources are still relatively good, is also threatened by illegal logging, lack of knowledge of people and so on. Therefore, it needs the hands of the people, especially foresters and researchers. Through research, scientists can provide the knowledge and understanding of the forest, including the structure and forest restoration. This study has obtained important findings. The secondary forest is more homogeneous and uniform, while the old-growth forest is very diverse. Biodiversity of the overstorey in the secondary forest is more than the primary. The number of regenerating species in the secondary forest is higher, but other indices are not statistically different between two types. The regeneration distribute regularly on the ground. The secondary forest still has mother trees and sufficient regeneration, so some restoration measures can be applied here. Findings of the study contribute to improve people’s understanding of the structure and the structural changes after harvesting in Kon Ka Kinh national park, Gia Lai. That is a key to have better understandings of the history and values of the forests. These findings and the proposed restoration measures address rescuing degraded forests in Central Highland in particular and Vietnam in general. And further, this is a promising basis for the management and sustainable use of forest resources in the future.

Domaine en plein développement, le transfert des connaissances (TC) se définit, comme l’ensemble des activités, des mécanismes et des processus favorisant l’utilisation de connaissances pertinentes (tacites et empiriques) par un public cible tel que les intervenants psychosociaux. Cette recherche vise à améliorer l’efficacité des méthodes linéaires écrites de TC en identifiant mieux les besoins d’information des intervenants en protection de la jeunesse. Notons que les méthodes linéaires écrites de TC désignent des outils d’information écrits unidirectionnels tels que les revues, les publications, les sites Internet, etc. Le premier objectif est de déterminer les catégories de besoins exprimés par les intervenants, c’est-à-dire déterminer si les besoins rapportés par des intervenants se regroupent en types ou sortes de besoins. Le deuxième objectif est d’établir l’importance relative de chacune de ces catégories. Enfin, cette étude vise à déterminer si ces besoins diffèrent selon les caractéristiques des intervenants ou de l’environnement. Deux facteurs sont étudiés, l’expérience de l’intervenant et la direction pour laquelle celui-ci travaille (Direction des services milieu à l’enfance ou Direction des services milieu à l’adolescence et ressources). Un devis mixte séquentiel exploratoire a été développé. Lors de la première étape, une analyse thématique a été effectuée à partir des réponses à une question ouverte posée aux membres de trois équipes et à partir d’un document résumant les requêtes effectuées auprès de l’équipe de la bibliothèque du Centre jeunesse de Montréal. Les résultats permettent de répondre au premier objectif de ce mémoire. En effet, les analyses ont permis de créer un arbre thématique comprenant 42 éléments classés hiérarchiquement. Les besoins se regroupent en deux thèmes généraux, soit les besoins qui concernent les « opérations » (c’est-à-dire l’action de l’intervenant) et les besoins concernant les « systèmes » (c’est-à-dire les éléments sur lesquels peuvent porter l’intervention). Cette dernière catégorie se subdivise entre l’usager, ses environnements et le contexte culturel et sociétal. Lors de la deuxième étape, une analyse de la variance (ANOVA) et une analyse de variance multivariée (MANOVA) ont été effectuées à partir des réponses de 82 intervenants à un questionnaire en ligne structuré selon les catégories de besoins d’informations déterminées à l’étape qualitative précédente. Les résultats permettent de répondre au deuxième objectif de ce mémoire et de mesurer le degré de force ou d’importance de chacune des catégories de besoins, identifiées lors de la première étape, selon les intervenants eux-mêmes. Les besoins ont ainsi pu être classés par ordre décroissant d’importance. Il a été possible de définir un groupe de neuf besoins prioritaires (portant sur l’animation, les caractéristiques personnelles des usagers, les caractéristiques des parents et leurs relations avec l’enfant, ainsi que l’intervention interculturelle et les problématiques sociales) et un autre groupe de sept besoins moins élevés (portant sur les autres « opérations » et les services professionnels dont a bénéficié l’usager). L’interprétation de ces résultats indique que les besoins en TC des intervenants se limitent aux informations qui concernent directement leur mandat, leur pratique ou les problématiques rencontrées. Les résultats de cette étape ont également permis de répondre au troisième objectif de ce mémoire. En effet, les résultats indiquent que l’importance ressentie des besoins (sur une échelle de 1 à 7) ne diffère pas significativement selon la direction pour laquelle travaille l’intervenant, mais elle diffère significativement selon l’expérience de ce dernier (moins de 10 ans ou plus de 10 ans). Cette différence est discutée et plusieurs hypothèses explicatives sont envisagées telles que l’accumulation de connaissances liée à l’expérience ou les changements cognitifs liés à l’expertise. Enfin, dans la discussion, les résultats sont mis en contexte parmi les autres types de besoins existants et les autres caractéristiques des connaissances qui doivent être prises en considération. Cela permet de formuler des recommandations pour améliorer la production de documents écrits ainsi que pour poursuivre la recherche dans le domaine de l’évaluation des besoins de TC. Bien que présentant certaines limites méthodologiques, cette recherche ouvre la voie au développement de meilleurs outils d’évaluation des besoins et à l’amélioration des techniques de transfert linéaires écrites. / Knowledge transfer (KT) is an expanding academic field that includes the study of activities, mechanisms, and processes leading workers, such as staff member performing psychosocial interventions at the department of youth protection (DYP), to adequately use knowledge whether it is empirical or tacit. The purpose of this study is to foster more efficiency in linear written tools of KT (e.g.: academic journals, publications, and websites) by identifying more adequately the needs of DYP workers. Our first goal is to qualitatively determine categories of needs that can be investigated quantitatively. Second, using statistical methods, we seek to validate the categories resulting from qualitative investigation. A third goal is to determine if other factors might influence these needs. In this study, two other factors have been investigated: work experience and department affiliation (i.e.: childhood services or adolescence services). To investigate these three objectives, we developed a 2-Step sequential exploratory mixed model. In the qualitative phase, we conducted a content analysis on a single open-question administrated to three different work teams as well as a document summarizing the request formulated to the DYP’s library. The results shed light on the first objective of this memoir: identifying if the needs of field workers in psychosocial intervention could be classified by type. Our analysis produced a thematic tree comprising 2 greater categories: needs related to the steps in intervention and needs related intervention itself. The category of needs related to intervention itself can be divided in 3 sub-categories: Needs related to intervention on the child/adolescent; Needs related to intervening on his environment; and Need related to intervention on the greater sociocultural context. Moreover, a more in-depth analysis produced up to 42 factors distributed in these 2 broader categories. Secondly, 82 participants filled out an electronic administrated questionnaire based on the previous categories identified. To analyze these data, we performed an ANOVA and a MANOVA to reach our second objective: determine the intensity of each categories identified in the qualitative phase. The needs identified were summed up in 16 groups and were classified in decreasing order: 9 groups of high-level needs (animation, individual characteristics of children/adolescents, characteristics of their parents, parent-child relationships, intercultural intervention, and social problems) and 7 low-level needs (other steps of intervention and professional services). The results indicate that the needs of DWP staff working in psychosocial intervention are mainly centered on their mandate, their clinical practice, and the clinical problems they face. Finally, we met our third objective: determine if the identified need vary according to work experience or department affiliation. Our results suggest that department affiliation is not significantly associated with needs in KT. However, in our analyses, experience (10 years or less and more than 10) was significantly associated with differences in KT needs. These differences are discussed in the result section and explanatory hypothesis such as the accumulation of knowledge due to work experience or cognitive changes related to expertise are formulated. The discussion contextualizes our result by comparing them to other needs identified and other characteristics of knowledge that should be took into consideration. Recommendations based on our results are formulated to foster better efficiency in written documents designed for professional in psychosocial intervention and to explore further more KT. Notwithstanding certain limitations, these results pave the way to developing better KT assessment tool as well as better implementation of KT techniques in written tools to enhance their use and efficiency.

of the diploma thesis Title: Computational Methods for Maximum Likelihood Estimation in Generalized Linear Mixed Models Author: Bc. Martin Otava Department: Department of Probability and Mathematical Statistics Supervisor: RNDr. Arnošt Komárek, Ph.D., Department of Probability and Mathematical Statistics Abstract: Using maximum likelihood method for generalized linear mixed models, the analytically unsolvable problem of maximization can occur. As solution, iterative and ap- proximate methods are used. The latter ones are core of the thesis. Detailed and general introducing of the widely used methods is emphasized with algorithms useful in practical cases. Also the case of non-gaussian random effects is discussed. The approximate methods are demonstrated using the real data sets. Conclusions about bias and consistency are supported by the simulation study. Keywords: generalized linear mixed model, penalized quasi-likelihood, adaptive Gauss- Hermite quadrature 1