Data analysis tools and methods for DNA microarray and high-throughput sequencing data

The recent rapid development of biotechnological approaches has enabled the production of large whole genome level biological data sets. In order to handle thesedata sets, reliable and efficient automated tools and methods for data processingand result interpretation are required. Bioinformatics, as the field of studying andprocessing biological data, tries to answer this need by combining methods and approaches across computer science, statistics, mathematics and engineering to studyand process biological data. The need is also increasing for tools that can be used by the biological researchers themselves who may not have a strong statistical or computational background, which requires creating tools and pipelines with intuitive user interfaces, robust analysis workflows and strong emphasis on result reportingand visualization. Within this thesis, several data analysis tools and methods have been developed for analyzing high-throughput biological data sets. These approaches, coveringseveral aspects of high-throughput data analysis, are specifically aimed for gene expression and genotyping data although in principle they are suitable for analyzing other data types as well. Coherent handling of the data across the various data analysis steps is highly important in order to ensure robust and reliable results. Thus,robust data analysis workflows are also described, putting the developed tools andmethods into a wider context. The choice of the correct analysis method may also depend on the properties of the specific data setandthereforeguidelinesforchoosing an optimal method are given. The data analysis tools, methods and workflows developed within this thesis have been applied to several research studies, of which two representative examplesare included in the thesis. The first study focuses on spermatogenesis in murinetestis and the second one examines cell lineage specification in mouse embryonicstem cells.

Examining sport commitment and intentions to participate in intramural sports : application of the Sport Commitment Model and the Theory of Planned Behaviour in a campus recreational sport setting

Fifty-six percent of Canadians, 20 years of age and older, are inactive (Canadian Community Health Survey, 200012001). Research has indicated that one of the most dramatic declines in population physical activity occurs between adolescence and young adulthood (Melina, 2001; Stephens, Jacobs, & White, 1985), a time when individuals this age are entering or attending college or university. Colleges and universities have generally been seen as environments where physical activity and sport can be promoted and accommodated as a result of the available resources and facilities (Archer, Probert, & Gagne, 1987; Suminski, Petosa, Utter, & Zhang, 2002). Intramural sports, one of the most common campus recreational sports options available for post-secondary students, enable students to participate in activities that are suited for different levels of ability and interest (Lewis, Jones, Lamke, & Dunn, 1998). While intramural sports can positively affect the physical activity levels and sport participation rates of post-secondary students, their true value lies in their ability to encourage sport participation after school ends and during the post-school lives of graduates (Forrester, Ross, Geary, & Hall, 2007). This study used the Sport Commitment Model (Scanlan et aI., 1993a) and the Theory of Planned Behaviour (Ajzen, 1991) with post secondary intramural volleyball participants in an effort to examine students' commitment to intramural sport and 1 intentions to participate in intramural sports. More specifically, the research objectives of this study were to: (1.) test the Sport Commitment Model with a sample of postsecondary intramural sport participants(2.) determine the utility of the sixth construct, social support, in explaining the sport commitment of post-secondary intramural sport participants; (3.) determine if there are any significant differences in the six constructs of IV the SCM and sport commitment between: gender, level of competition (competitive A vs. B), and number of different intramural sports played; (4.) determine if there are any significant differences between sport commitment levels and constructs from the Theory of Planned Behaviour (attitudes, subjective norms, perceived behavioural control, and intentions); (5.) determine the relationship between sport commitment and intention to continue participation in intramural volleyball, continue participating in intramurals and continuing participating in sport and physical activity after graduation; and (6.) determine if the level of sport commitment changes the relationship between the constructs from the Theory of Planned Behaviour. Of the 318 surveys distributed, there were 302 partiCipants who completed a usable survey from the sample of post-secondary intramural sport participants. There was a fairly even split of males and females; the average age of the students was twenty-one; 90% were undergraduate students; for approximately 25% of the students, volleyball was the only intramural sport they participated in at Brock and most were part of the volleyball competitive B division. Based on the post-secondary students responses, there are indications of intent to continue participation in sport and physical activity. The participation of the students is predominantly influenced by subjective norms, high sport commitment, and high sport enjoyment. This implies students expect, intend and want to 1 participate in intramurals in the future, they are very dedicated to playing on an intramural team and would be willing to do a lot to keep playing and students want to participate when they perceive their pursuits as enjoyable and fun, and it makes them happy. These are key areas that should be targeted and pursued by sport practitioners.

On some Density Theorems in Number Theory and Group Theory

Gowers, dans son article sur les matrices quasi-aléatoires, étudie la question, posée par Babai et Sos, de l'existence d'une constante $c>0$ telle que tout groupe fini possède un sous-ensemble sans produit de taille supérieure ou égale a $c|G|$. En prouvant que, pour tout nombre premier $p$ assez grand, le groupe $PSL_2(\mathbb{F}_p)$ (d'ordre noté $n$) ne posséde aucun sous-ensemble sans produit de taille $c n^{8/9}$, il y répond par la négative. Nous allons considérer le probléme dans le cas des groupes compacts finis, et plus particuliérement des groupes profinis $SL_k(\mathbb{Z}_p)$ et $Sp_{2k}(\mathbb{Z}_p)$. La premiére partie de cette thése est dédiée à l'obtention de bornes inférieures et supérieures exponentielles pour la mesure suprémale des ensembles sans produit. La preuve nécessite d'établir préalablement une borne inférieure sur la dimension des représentations non-triviales des groupes finis $SL_k(\mathbb{Z}/(p^n\mathbb{Z}))$ et $Sp_{2k}(\mathbb{Z}/(p^n\mathbb{Z}))$. Notre théoréme prolonge le travail de Landazuri et Seitz, qui considérent le degré minimal des représentations pour les groupes de Chevalley sur les corps finis, tout en offrant une preuve plus simple que la leur. La seconde partie de la thése à trait à la théorie algébrique des nombres. Un polynome monogéne $f$ est un polynome unitaire irréductible à coefficients entiers qui endengre un corps de nombres monogéne. Pour un nombre premier $q$ donné, nous allons montrer, en utilisant le théoréme de densité de Tchebotariov, que la densité des nombres premiers $p$ tels que $t^q -p$ soit monogéne est supérieure ou égale à $(q-1)/q$. Nous allons également démontrer que, quand $q=3$, la densité des nombres premiers $p$ tels que $\mathbb{Q}(\sqrt[3]{p})$ soit non monogéne est supérieure ou égale à $1/9$.

Does Chance hide Necessity? : a reevaluation of the debate ‘determinism - indeterminism’ in the light of quantum mechanics and probability theory

Dans cette thèse l’ancienne question philosophique “tout événement a-t-il une cause ?” sera examinée à la lumière de la mécanique quantique et de la théorie des probabilités. Aussi bien en physique qu’en philosophie des sciences la position orthodoxe maintient que le monde physique est indéterministe. Au niveau fondamental de la réalité physique – au niveau quantique – les événements se passeraient sans causes, mais par chance, par hasard ‘irréductible’. Le théorème physique le plus précis qui mène à cette conclusion est le théorème de Bell. Ici les prémisses de ce théorème seront réexaminées. Il sera rappelé que d’autres solutions au théorème que l’indéterminisme sont envisageables, dont certaines sont connues mais négligées, comme le ‘superdéterminisme’. Mais il sera argué que d’autres solutions compatibles avec le déterminisme existent, notamment en étudiant des systèmes physiques modèles. Une des conclusions générales de cette thèse est que l’interprétation du théorème de Bell et de la mécanique quantique dépend crucialement des prémisses philosophiques desquelles on part. Par exemple, au sein de la vision d’un Spinoza, le monde quantique peut bien être compris comme étant déterministe. Mais il est argué qu’aussi un déterminisme nettement moins radical que celui de Spinoza n’est pas éliminé par les expériences physiques. Si cela est vrai, le débat ‘déterminisme – indéterminisme’ n’est pas décidé au laboratoire : il reste philosophique et ouvert – contrairement à ce que l’on pense souvent. Dans la deuxième partie de cette thèse un modèle pour l’interprétation de la probabilité sera proposé. Une étude conceptuelle de la notion de probabilité indique que l’hypothèse du déterminisme aide à mieux comprendre ce que c’est qu’un ‘système probabiliste’. Il semble que le déterminisme peut répondre à certaines questions pour lesquelles l’indéterminisme n’a pas de réponses. Pour cette raison nous conclurons que la conjecture de Laplace – à savoir que la théorie des probabilités présuppose une réalité déterministe sous-jacente – garde toute sa légitimité. Dans cette thèse aussi bien les méthodes de la philosophie que de la physique seront utilisées. Il apparaît que les deux domaines sont ici solidement reliés, et qu’ils offrent un vaste potentiel de fertilisation croisée – donc bidirectionnelle.

Further investigations on doubly excited four-electron ions: beam-foil experiment and MCDF theory

In continuation of our previous work on the quintet transitions 1s2s2p^2 ^5 P-1s2s2p3d ^5 P^0, ^5 D^0, results on other n = 2 - n' = 3 quintet transitions for elements N, 0 and F are presented. Assignments have been established by comparison with Multi-Configuration Dirac-Fock calculations. High spectral resolution on beam-foil spectroscopy was essential for the identification of most of the lines. For some of the quintet lines decay curves were measured, and the lifetimes extracted were found to be in reasonable agreement with MCDF calculations.

On social networks and game theory, some research problems

Seminar given as part of social networking course, to give a brief overview of some applied examples game theory used in social network simulation

Data Science, Microsoft and You

In this session we'll explore how Microsoft uses data science and machine learning across it's entire business, from Windows and Office, to Skype and XBox. We'll look at how companies across the world use Microsoft technology for empowering their businesses in many different industries. And we'll look at data science technologies you can use yourselves, such as Azure Machine Learning and Power BI. Finally we'll discuss job opportunities for data scientists and tips on how you can be successful!

Shape complexity based on mutual information

Shape complexity has recently received attention from different fields, such as computer vision and psychology. In this paper, integral geometry and information theory tools are applied to quantify the shape complexity from two different perspectives: from the inside of the object, we evaluate its degree of structure or correlation between its surfaces (inner complexity), and from the outside, we compute its degree of interaction with the circumscribing sphere (outer complexity). Our shape complexity measures are based on the following two facts: uniformly distributed global lines crossing an object define a continuous information channel and the continuous mutual information of this channel is independent of the object discretisation and invariant to translations, rotations, and changes of scale. The measures introduced in this paper can be potentially used as shape descriptors for object recognition, image retrieval, object localisation, tumour analysis, and protein docking, among others