NCube/papyrus huggingface dataset:
Morphologie évolutive et fonctionnelle des hémichordés

The phylum Hemichordata comprises the classes  Enteropneusta and Pterobranchia. Together with echinoderms, hemichordates are the sister-group to chordates. Enteropneusts are worm-shaped solitary deposit feeders. Pterobranchs are colonial filter feeders that live in a secreted collagenous domicile called a coenecium. In this thesis, three studies are presented. These studies are based on observations of extant hemichordates, and adress a variety of issues relating to the evolution of hemichordates, chordates, and the super-phylum to which they belong: Deuterostomia.    Our first study demonstrates that the gill slits, pre-oral ciliary organ (POCO), and lining of the pharynx of the enteropneust Protoglossus graveolens are used in filter feeding. The filter-feeding system of P. graveolens enables particle capture down to 1.3 um, at a rate up to 4.05 mm.s-1, with a power consumption of 0.009 uW. Structural and functional similarities with the cephalochordate filter-feeding system suggest that pharyngeal filter-feeding is ancestral to the deuterostomes.  In our second study, we address the hypothesis that the enteropneust POCO, a putative chemosensory structure located anterior to the mouth, is homologous to the cephalochordate wheel organ and vertebrate adenohypophysis. We characterized the expression pattern of the adenohypophysis-specific transcription factor Pit-1 in the adult enteropneust Saccoglossus pusillus with immunohistochemistry. Pit-1 is expressed in sensory cells of the POCO and in scattered epithelial cells of the proboscis, collar and trunk. This expression pattern does not allow to confirm or reject the homology of the POCO with the vertebrate adenohypophysis.   In our third study, we characterized the ultrastructure of the coenecium of the pterobranchs Cephalodiscus hodgsoni, Cephalodiscus nigrescens and Cephalodiscus densus using transmission and scanning electron microscopy. Cephalodiscus is the sister-group to the Graptolithina, which includes the extinct graptolites and the extant pterobranch genus Rhabdopleura. We described the fibril types, size and organization, as well as the general organization of the coenecium. We demonstrated that the coenecium of Cephalodiscus shows similarities with the graptolite eucortex, paracortex and pseudocortex. The cortical-like organization of the coenecium of Cephalodiscus suggests that the cortex is ancestral to the Pterobranchia.  Together, these three studies illustrate different axes of  hemichordate research, and show how integrating morphological, functional and molecular data allows us toinfer key events in the evolution of deuterostomes.

Keyphrases: Coenecium, Pharynx, Pit-1, Adenohypophysis, Coenecium, Deuterostomes, Enteropneusts, Filter feeding, Pre-oral ciliary organ, Pharynx, Pit-1, Pterobranchs, Evolution
Développement et évaluation d’un environnement informatisé d’apprentissage pour faciliter l’intégration des sciences et de la technologie

Through this research we will fully assess the benefits brought by the ExAO (Computer Assisted Experimentation) in school laboratories of science and technology in Lebanon. We would also like to mention its contribution in a tangible way in laboratory research of Pedagogic Robotic from Montreal University, particularly in the development of ExAO µlaboratory. We wanted to test the capabilities of the ExAO, its use in the classroom such as: 1. A replacement of a traditional laboratory in the use of the experimental method. 2. A scientific investigation tool.  3. An integration tool of experimental sciences and mathematics. 4. An integration tool of experimental sciences, mathematics and technology in the technoscientific learning. To do so, we have mobilized 13 group classes, designated teachers to experiment themselves along with their students in order to assess, in a more realistic way, the benefits of implementing this micro computer laboratory at school.  Different testing, evaluated using the results of learning activities undertaken by students, their responses to a questionnaire and feedback from teachers, show that:     1. The replacement of a traditional laboratory with an ExAO µlaboratory does not seem to pose problem, expected that students have adapted to it in only ten minutes, indicating that the speed with which data were graphed was more productive.  2. In order to investigate a physical phenomenon, the usability of the tutorial associated with the ability to amplify the phenomenon before its graph representation, has allowed students to design and implement quickly and independently an experiment to verify their prediction.   3. The integration of mathematics into an experimental approach can quickly grasp the phenomenon. In addition, it gives more autonomy and a meaning to the graphs and algebraic representations allowing to use them as a cognitive tool to interpret this phenomenon. 4. The approach made by the students to design and construct a technological object, showed that this activity was easily carried out by the use of universal sensors, amplifiers to offset the graphical modeling tool, and the tutorial ability to transform any measured variable by another variable (for instance, the resistance variation in temperature change, …). This educational activity shows that students had no difficulty integrating in a single learning activity the mathematics, experimental sciences and technology, in order to design and implement a functional piece of technology. The ExAO µlaboratory, by offering new educational opportunities, such as the ability to design, produce and validate a technological object, in order to do so, new capacities to boost measures, modeling physical phenomena, developing new sensors, is an  important addition to the experiments being conducted in ExAO.

Keyphrases: ExAO, ExAO, teaching, integration, Lebanese schools
Capacité de deux accéléromètres (SenseWear Armband et l’Actical) à estimer la dépense énergétique totale chez les adultes sains

The increase in energy expenditure by the increase of physical activity contributes to maintaining and improving health. The large-scale measurement of total energy expenditure in general and physical activity in particular, is faced with difficulties of data collection, validity and cost. Although literature suggests that many accelerometers are used to estimate total energy expenditure, there are still limits as to the measurement of the intensity of physical activity, which is one of the factors that influences the energy balance and health benefits of physical activity. In addition, few comparisons between the different accelerometers are available. This study aimed to evaluate the ability of two accelerometers (Actical and SensWear Armband) to estimate total energy expenditure compared with the technique of doubly labelled water; to assess the correlation between the two accelerometers in the measurement of resting energy expenditure, compared with the technique of indirect calorimetry and finally to assess energy expenditure linked to physical (walking and cycling) at different intensities, in comparison with the indirect calorimetry technique. The results show a very good correlation between indirect calorimetry and the two accelerometers(r > 0.80, p<0.001) in the measurement of resting energy expenditure and a good correlation between accelerometers and the gold standard technique (doubly labeled water) in the measurement of total energy expenditure(r>0.75, p<0.001). To measure the intensity of physical activity, Actical is more accurate than SensWear Armband(r=0.80, p<0.001) at low intensity while the SensWear Armband is better at higher intensity (r=0.80, p<0.001). This study provides evidence that these two accelerometers are suitable alternatives for measuring energy expenditure.

Keyphrases: Energy expenditure, Indirect calorimetry, Doubly labelled water, Accelerometers, Healthy Adults
Étude structurale du mode de liaison des protéines Whirly de plantes à l’ADN monocaténaire

Plants must protect the integrity of three genomes located respectively in the nucleus, the chloroplasts and the mitochondria. Although DNA repair mechanisms in the nucleus are the subject of multiple studies, little attention has been paid to DNA repair mechanisms in chloroplasts and mitochondria. This is unfortunate since mutations in the chloroplast or the mitochondrial genome can lead to altered plant growth and development. Our laboratory has identified a new family of proteins, the Whirlies, whose members are located in plant mitochondria and chloroplasts. These proteins form tetramers that bind single-stranded DNA and play various roles associated with DNA metabolism. In Arabidopsis, two Whirly proteins maintain chloroplast genome stability. Whether or not these proteins are involved in DNA repair has so far not been investigated.  Our studies in Arabidopsis demonstrate that DNA double-strand breaks are repaired in both mitochondria and chloroplasts through a microhomology-mediated repair pathway and indicate that Whirly proteins affect this pathway. In particular, the role of Whirly proteins would be to promote accurate repair of organelle DNA by preventing the repair of DNA double-strand breaks by the microhomology-dependant pathway. To understand how Whirly proteins mediate this function, we solved the crystal structure of Whirly-DNA complexes. These structures show that Whirly proteins bind single-stranded DNA with low sequence specificity. The DNA is maintained in an extended conformation between the β-sheets of adjacent protomers, thus preventing spurious annealing with a complementary strand. In turn, this prevents formation of DNA rearrangements and favors accurate DNA repair. We also show that upon binding long ssDNA sequences, Whirly proteins assemble into higher order structures, or hexamers of tetramers, thus forming spherical particles of twelve nanometers in diameter. We also demonstrate that a lysine residue conserved among plant Whirly proteins is important for the stability of these higher order structures as well as for cooperative binding to DNA and for DNA repair. Overall, our study elucidates some of the mechanisms of DNA repair in plant organelles as well as the roles of Whirly proteins in this process.

Keyphrases: Plant organelles, Chloroplastic and mitochondrial genomes, DNA repair, DNA rearrangements mediated by very short repeated sequences, Single-stranded DNA binding proteins, Whirly proteins, Protein oligomerization, X-ray crystallography
Optimisation et approximation adiabatique

The adiabatic approximation in quantum mechanics states that if the Hamiltonian of a physical system evolves slowly enough, then it will remain in the instantaneous eigenstate related to the initial eigenstate. Recently, two researchers found an inconsistency in the application of the approximation. A discussion about the limit of this idea will be presented.  Our goal is to optimize the probability to be in the instantaneous eigenstate related to the initial eigenstate knowing the initial and final system, with the total time of the experiment fixed to $T$. This last condition prevents us from being slow enough to use the adiabatic approximation.  To solve this problem, we turn to the calculus of variation. We suppose the ideal evolution is known and we add a small variation to it. We take the result, put it in the probability to be adiabatic and expand in powers of the variation. The first order term must be zero. This enables us to derive a criterion which will give us conditions on the ideal Hamiltonian. Those conditions should define the ideal Hamiltonian.   Time dependent quantum systems are very complicated. To simplify the problem, we will start by considering systems with time independent energies. Afterward, the general case will be treated.

Keyphrases: quantum mechanics, adiabatic theorem, calculus of variation, quantum computing
Analyse des attitudes envers les sciences chez des élèves du secondaire d'origine haïtienne de milieux défavorisés de la région de Montréal

Having in perspective the slight representativeness of students, from Haitian background, from the most unprivileged sections of the great region of Montreal in the scientific fields in High School and in the choices of career, this study intends to examine the effect of the individual characteristics as well as the associated factors related to the familial, scholastic, socio-economic, and cultural environment upon the attitudes of those students toward sciences. The analysis of the datum is based on the results of a questionnaire focusing on the socio-demographic profile of a group of students from fourth and fifth year attending two multiethnic High Shools of the  North-Crown of Montreal as well as on the interviews with fifteen of those students who are from a haitian background.  There were also interviews with some parents, a member of a community organism, some staff members of some schools as well as some Haitian-Quebecer professionals and scientists, in order to have a critical viewpoint upon the different positions expressed by the fifteen students. The Bronfenbrenner’s ecosystemic model (1979, 1986) has been used as scope of reference allowing to draw the prominent aspects from the attitudes toward science in the students, from haitian background. The synthesis of ideas expressed by different interviewee reveals the existence of a environment not much enhancing the value of sciences around of students, from Haitian background. The socio-economic conditions, the familial practices, the ethnocultural status as well as some individual representations of sciences contribute to create and maintain some attitudes very little committed to sciences in those students. The study shows how much it is urgent to demystify the sciences by breaking with some stereotypes that prevent some categories of students from acceding to sciences. It also commands to politicians, concerning education, to be more open to ethnocultural differences and to explore some dynamic ways in order to make the scientific culture accessible to all social groups.

Keyphrases: immigration, science learning, attitudes toward science, multiethnicity, environmental factors, High School students, ecosystemic model, immigration, socio-economic status, haitian background, econominically disadvantaged area
Étude de cohorte rétrospective analytique et descriptive des résultats échocardiographiques et cliniques de la chirurgie valvulaire tricuspidienne

Abstract - Data regarding surgical management of tricuspid valve disease are based on small cohort studies, and only few of them report echocardiographic results or risk factors for mortality and morbidity. A retrospective descriptive and analytic cohort study was performed in order to analyze the Montreal Heart Institute experience regarding tricuspid valve surgery. Data was extracted from the medical files of patients. During the 1977-2008 period, 792 tricuspid valve repairs and 134 tricuspid valve replacements were performed (median age of patients: 62 years). Operative mortality was 13.8%. Actuarial survival rates at 5, 10, and 15 years were 67±2%, 47±2%, and 29±2%, respectively. At last follow-up, 31% of patients who underwent repair and 12% of patients who underwent replacement had tricuspid regurgitation ≥3/4 (p<0,001). NYHA functional class improved significantly at last follow-up compared to baseline (p<0,001). Propensity score analysis showed that a replacement was associated with increased operative and late mortality rates compared to repair, but with less tricuspid regurgitation ≥2/4 or ≥3/4 at follow-up. The study shows that despite substantial mortality rates, patients experience a significant functional improvement following tricuspid valve surgery. Risk factors for mortality and morbidity are described, and sub-group analyses for triple valve surgery and for isolated tricuspid valve surgery are exposed.

Keyphrases: Valve tricuspide, Annuloplastie, Cohort study, Tricuspid valve, Cardiac valves, Valvular disease, Cardiac surgery, Valvular prosthesis, Annuloplasty, Epidemiology, Cardiology, Surgical outcomes
Étude de l'association supramoléculaire à l'état solide des fullerènes C60 et C70 avec des dérivés triptycényles fonctionnalisés

The fullerene C60 is a spherical molecule made up exclusively of carbon atoms. The surface of this compound is homogenous, convex and aromatic. As a result, C60 can associate with other aromatic molecules via non-covalent π-stacking interactions to form supramolecular assemblies. The triptycene is a "Y"-shaped molecule with concave aromatic surfaces. This molecule can thereby interact with C60 and form crystals through amplified π-stacking interactions resulting from the concave/convex complementary arrangement. In the course of our work, we made a series of new triptycene derivatives with functional groups added to the periphery of the aromatic core. In particular, we found that methyl groups, as well as atoms of chlorine, bromine and iodine, can be placed on the extremities of the triptycene core to expand the concave cavities available to interact with C60 and C70. We studied the non-covalent interactions between fullerenes and triptycene derivatives using X-ray crystallography. Furthermore, Hirshfeld surfaces have been used to map the interaction patterns around fullerene surfaces. In addition, we have found that aromatic solvents that are properly functionalized with halogen atoms and methyl groups have a special ability to solubilize C60.

Keyphrases: Fullerene, C60, C60, C70, C70, Triptycene, Supramolecular association, co-cristals, X-ray diffraction, Hirshfeld surface
Les tests de causalité en variance entre deux séries chronologiques multivariées

Time series models with conditionnaly heteroskedastic variances have become almost inevitable to model financial time series. In many applications,    to confirm the existence of a relationship between two  time series is very  important. In this Master thesis, we generalize in several directions and in a multivariate framework, the method developed by Cheung and Ng (1996) designed to examine causality in variance in the case of two univariate series. Based on the work of El Himdi and Roy (1997) and Duchesne (2004), we propose a test based on residual cross-correlation matrices of squared residuals and cross-products of these residuals. Under the null hypothesis of no causality in variance, we establish that  the test statistics converge in distribution to  chi-square random variables. In a second approach, we define as in Ling and Li (1997)  a transformation of the residuals for each  residual time series. The test statistics are built from the cross-correlations of these transformed residuals. In both approaches,  test statistics at   individual lags are presented and also portmanteau-type test statistics. That methodology is also used to determine the direction of causality in variance. The simulation results show that the proposed tests provide satisfactory empirical properties. An application with real data is also presented  to illustrate the methods

Keyphrases: Tests, Causality, Heteroscedasticity, Portmanteau, Correlation, Test, Variances, Multivariate, Time, Series, Conditionnal, Variance
De la formulation à l’implantation :
expérience de la mise en oeuvre d’un projet éducatif et d’un plan de réussite d’une école primaire de la grande région de Montréal

Using the analytical framework of Honig (2006) which studies the implementation of public policy from dimensions that are location, policy and actors, this research explores the relationship between implementation and formulation of public policy. Introduced in education by the adoption of Bill 124 (Quebec, 2002) in 2002, the results-based management framework has led to the development of a strategic plan for the school board and a success plan from an educational project for the school. However, the study of single case of this research which is part of a project led by Professor Martial Dembélé on results-based management framework at the primary level of education in Quebec (FQRSC, 2007-2008; SSHRC 2007-2010) examines the relationship formulation - implementation of the educational project/success plan of a primary school located in the greater Montreal area. The results of this research show that the formulation of a policy has an impact on its implementation, but this aspect is not exclusive to an effective implementation. Other dimensions that are the actors and place have as much effect: one or two dimensions can compensate for the weakness of the third one.

Keyphrases: Public policy, Formulation, Implementation, Planification scolaire, School planning, Educational project, Success plan
Développement et caractérisation de nouveaux 
modèles du cancer épithélial de l’ovaire

The epithelial ovarian cancer (EOC) is the most lethal of gynecological cancers. This complexe and heterogenous disease progresses rapidly and is almost asymptomatic in early stages. The survival rate of patients with late stage diagnosis remains low albeit cytoreductive surgery and chemotherapy. In order to study the EOC disease in an ex vivo context, the use of different cellular models is necessary. EOC cell lines derived from long-term passages of malignant ovarian cancers are useful tools for molecular and cellular research but it is not clear how culture conditions affect overall gene expression and oncogenic potential as compared to the original tumor. The main goal of this research was to develo and characterize new in vitro model systems that will recapitulate more closely some of the growth conditions encountered by tumor cells in vivo. In order to develop an in vitro tridimensional EOC spheroid model, we have used cell lines previously established in our laboratory. Spheroids were generated using the hanging droplet method, which was innovative for the culture of cancer cells. Comparative gene expression profile analysis of monolayer cultures, 3D spheroids and in vivo xenografts were performed and we have shown that the spheroid transcriptome more closely reflects expression patterns of the in vivo model compared to that of monolayer cultures. Among the best candidates, S100A6 gene over-expressed in the 3D models versus monolayer cultures was chosen for further analysis. To begin to address how S100A6 might affect EOC growth parameters, we have inhibited its expression in our in vitro models. The loss of S100A6 in the spheroid model results in an reduction of cellular migration, which seems to be in line with previous in vivo results published by other researchers. Always with the objective of developing the most relevant to the in vivo disease model systems, we have also succeeded in developing a unique EOC cell lines derived from patients with the most frequently diagnosed serous type of cancer. Very few cell lines derived from this type of cancers and from chemotherapy naïve patients are available. Moreover, we characterize for the first time EOC serous type cell lines derived from the ascites and the solid tumor of the same patient.

Keyphrases: S100A6, Spheroid, Ovarian cancer, Model systems, Cell lines
Étude des débats menant à l’adoption du projet de loi no 38 sur la gouvernance des universités québécoises

This thesis aims to understand the social issues that have animated the social field of higher education at the formulation stage of Bill no. 38 on university governance. Also it aims to highlight the role and influence of various categories of social actors involved in these debates, each trying to impose its definition of issues according to their interests. The debates that took place around the bill are to be treated as the product of an action system, which presents these debates as a typology of issues, each corresponding to three levels of social action: fondamentals issues, organizational issues and political issues. The analysis of the debates indicate a conflictual relationship between the actors 'external' to the university and the actors involved in the academic community whose object is the organization and exercise of power between actors and bodies within academic institutions.

Keyphrases: Policy analysis