NCube/papyrus huggingface dataset:
Fonction de l'AmtB dans la régulation de la nitrogénase chez Rhodobacter capsulatus

The reduction of diatomic nitrogen is a very important biological process given the need of all organisms for fixed nitrogen for the biosynthesis of basic key molecules such as, amino acids, nucleic acids, etc.. The reduction of nitrogen to ammonia is catalyzed by nitrogenase, an enzyme with high energy demands since it requires 20 to 30 moles of ATP for the reduction of one mole of nitrogen. Therefore a strict control is required to minimize energy waste. Several systems of regulation are known, both at the translational and post-translational level.        In the purple non-sulfur photosynthetic bacterium R. capsulatus, the post-translational regulation of nitrogenase activity requires an array of proteins, including; the membrane protein AmtB, implicated in the perception and transport of ammonium, and PII proteins, which play key roles in the regulation of nitrogen assimilation. Following the addition of ammonium to the medium nitrogenase activity is reversibly inhibited (nitrogenase switch-off) via a mechanism of ADP-ribosylation of nitrogenase. Sequestration of GlnK (PII protein) by AmtB allows DraT, an ADP-ribosyltransferase, to add an ADP-ribose group to the Fe protein preventing it from forming a complex with the MoFe protein and nitrogenase activity is consequently inhibited.       To better understand this phenomenon, in this Master’s thesis point mutations were created by site-directed mutagenesis at specific conserved residues of the AmtB protein, namely, D338, G367, H193 and W237, in order to examine their role in ammonium transport, formation of an AmtB-GlnK complex, and the regulation of nitrogenase (Switch-off/ADP-ribosylation).  Plasmid-borne mutant alleles were transferred to a ∆AmtB strain of R. capsulatus, and the resultant strains were subjected to a series of tests.  These demonstrated the importance and necessity of certain residues, such as G367, in the regulation of nitrogenase and ammonium transport, in contrast to residue D338, which seems to have no direct role in the regulation of nitrogenase activity. These results suggest further hypotheses about the roles of specific amino acids of AmtB in its functions as a sensor and transporter for ammonium.

Keyphrases: Nitrogen fixation, ADP-ribosylation, ADP- ribosylation, Nitrogenase, Site-directed mutagenesis, AmtB protein, PII proteins, Transport d`ammonium, Ammonium transporter
Algorithmes de recommandation musicale

This thesis is composed of three papers which unite under the general theme of large-scale music recommendation. The first paper presents a recommendation technique that works by collecting text descriptions of items and using this textual aura to compute the similarity between them using techniques drawn from information retrieval. We show how this representation can be used to explain the similarities between items using terms from the textual aura and further how it can be used to steer the recommender. Because our system is content-based, it is not victim of the usual problems associated with collaborative filtering recommenders like the cold start problem. The second paper presents a machine learning model which automatically applies tags to music. The model uses features extracted from the audio files and was trained on a very large data set constructed with social data from the online community Last.fm. The third paper presents an approach to generating steerable playlists. We first demonstrate a method for learning song transition probabilities from audio features extracted from songs played in professional radio station playlists. We then show that by using this learnt similarity function as a prior, we are able to generate steerable playlists by choosing the next song to play not simply based on that prior, but on a tag cloud that the user is able to manipulate to express the high-level characteristics of the music he wishes to listen to.

Keyphrases: Similarité musicale, Machine learning, Music recommendation, Music similarity, Automatic tagging of music, Playlist generation, Signal processing
Analyse par apprentissage automatique des réponses fMRI du cortex auditif à des 
modulations spectro-temporelles

The application of linear machine learning classifiers to the analysis of brain imaging data (fMRI) has led to several interesting breakthroughs in recent years. These classiﬁers combine the responses of the voxels to detect and categorize different brain states. They allow a more agnostic analysis than conventional fMRI analysis that systematically treats weak and distributed patterns as unwanted noise. In this project, we use such classifiers to validate an hypothesis concerning the encoding of sounds in the human brain. More precisely, we attempt to locate neurons tuned to spectral and temporal modulations in sound. We use fMRI recordings of brain responses of subjects listening to 49 different spectro-temporal modulations. The analysis of fMRI data through linear classifiers is not yet a standard procedure in this field. Thus, an important objective of this project, in the long term, is the development of new machine learning algorithms specialized for neuroimaging data. For these reasons, an important part of the experiments is dedicated to studying the behaviour of the classifiers. We are mainly interested in 3 standard linear classifiers, namely the support vectors machine algorithm (linear), the logistic regression algorithm (regularized) and the naïve bayesian gaussian model (shared variances).

Keyphrases: Linear classifier, Neuroimagerie, Neuroimaging, Modulation spectro-temporelle, Spectro-temporal modulation, Auditory cortex, fMRI, fMRI, Naïve bayesian gaussian model, Support vectors machine, Logistic regression
Les effets du lien social et du niveau de défense des ressources sur l’utilisation des tactiques producteur et chapardeur par les diamants mandarins

Many species foraging in groups show behaviours in agreement with the producer-scrounger (PS) game. Originally, the PS game did not consider many elements likely to be found within feeding groups. However, recent studies suggest that some factors, namely resource defendability and social attachment, could indeed influence the predictions of the PS game. Thus, to investigate the effects of resource defendability and social bonds, we exposed flocks of zebra finches (Taeniopygia guttata), a monogamous species, to four different treatments intended to vary: (1) group size and, (2) degree of attachment among birds in a group. For the first time, we show that resource defendability has a true impact on the use of the two foraging tactics in the PS game. As a matter of fact, contrary to what is predicted in the original PS game, we found that the frequency of scrounger tactic did not increase with group size when tested in an economically defendable feeding context. On the other hand, even though pair bonding changed the individual scrounging and aggressive behaviours of the birds, we found no significant influence of this factor on the tactic use. Although the result was not significant, we found that scrounging was more frequent between social pairs than between experimental pairs, but individuals initiated aggressions towards their social partner with a lesser intensity. Thus, our results are promising and they call for many more studies on the effects of social bonds and resource defendability in gregarious species.

Keyphrases: Group size, Pair bonding, Producer-Scrounger game, Resource defendability, Social bonds, Zebra finch
Révision taxonomique de la famille des Harrimaniidae (Hemichordata: Enteropneusta) incluant les descriptions de sept espèces de la côte Est du Pacifique

This comparative study is a revision of the family Harrimaniidae based on morphological characters of described and undescribed species from the collections of William E. Ritter, Theodore H. Bullock and Kandula P. Rao, gathered in the 20th century. The new descriptions bring the total number of genera to nine by the addition of Horstia n. gen., Mesoglossus n. gen., Ritteria n. gen and Saxipendium, a genus previously assigned to the monospecific family Saxipendidae The number of species is increased to 34, resulting from the description of five new species from the eastern Pacific: Horstia kincaidi, Mesoglossus intermedius, Mesoglossus macginitiei, Protoglossus mackiei and Ritteria ambigua. The description of a sixth species,  Stereobalanus willeyi Ritter et Davis, 1904 (nomen nudum) is presented here for the first time and a brief description of Saxipendium coronatum is also presented. Four species previously assigned to the genus Saccoglossus are transfered to the genus Mesoglossus: M. bournei, M. caraibicus, M. gurneyi, and M. pygmaeus, while Saccoglossus borealis is transfered to the genus Harrimania. A phylogenetic hypothesis on the Harrimaniidae  is postulated presenting the possible evolution of morphological characters within the group. Finally, notes on the wide but spotty distribution of several species suggest that the Enteropneusta may have once had a wider distribution that has since become fragmented.

Keyphrases: taxonomy, systematic revision, morphology, Enteropneusta, Hemichordata, Harrimaniidae, zoogeography
Impacts de la fertilisation phosphatée sur la biodiversité microbienne de sols agricoles

Phosphorus fertilization is a widespread practice in North American agriculture. Although it is generally efficient to increase yields, its use can also induce some environmental contaminations. Several management practices are considered in order to decrease this problem. Among these possibilities there is the challenging one of manipulating microbial flora, which is well known for its implication in many processes related to soil fertility. We have demonstrated in field trials that both the form of fertilizer added to soil and the applied P amounts impact microbial distribution in plots. A first experiment performed on alfalfa monocultures in semi-arid prairie conditions demonstrated that samples coming from plots that had received different doses of P fertilizer presented significant differences on their bacterial and fungal communities. AMF population remained stable between treatments. A second experiment was conducted over three growing season of an intensive maize/soybean rotation cropping system. It aimed to determine the effect of different organic and mineral fertilizers containing equal P amount on bacterial and fungal populations. It was demonstrated that these communities varied according to the fertilizer type applied. Changes are independent from the grown crop. However, microbial populations have undergone greater variation within each growing season. DGGE approach allowed to observe changes occurring in soil microbial diversity but have only permit to identify a small proportion of organisms. A second experiment in the latter study was performed on the same site and focused on arbuscular mycorrhizal fungi (AMF) as they are organisms living in a mutualistic symbiosis with most land plants and increasing host nutrition and resistance to stresses. It led to the identification and comparison of the different AMF found in maize and soybean soil and root samples. In opposition to what was observed with bacteria and fungi previously, AMF presented a very stable diversity between the different treatments. However, some ribotypes were significantly more present in soil or roots during each growing season. Finally, our whole project demonstrated that P fertilization affected microbial community structure on studied sites. Nevertheless, in each experiment, sampling time also played a substantial role in the organism distribution. Many soil parameters were also monitored and presented a seasonal variation. The sum of possible interactions between these parameters, which in some cases varied according to treatment, would thus have more impact on microbial diversity that the sole fertilization.

Keyphrases: Agriculture, Champignons mycorrhiziens, DGGE, Microbial diversity, Mycorhizal fungi
Algorithmes pour la réconciliation d’un arbre de gènes avec un arbre d’espèces

A reconciliation between a gene tree and a species tree depicts an evolutionary scenario of the homologous genes in terms of gene duplications and gene losses. To infer such a reconciliation given a gene tree and a species tree, parsimony is generally used according to the number of gene duplications and/or losses. The combinatorial models of reconciliation are based on probabilistic or combinatorial criteria. The first paper defines a simple and more general combinatorial model of reconciliation which clearly identifies duplication and loss events and does not only induce the most parsimonious reconciliation. An architecture of all possible reconciliations is developed together with efficient algorithms (that is counting, randomization, and exploration) to study combinatorial properties of the space of all reconciliations or only the most parsimonious ones. Based on the classical birth-death process, an algorithm that computes the likelihood of a reconciliation has recently been proposed. The second paper uses this algorithm together with the combinatorial tools described above to compute efficiently, either exactly or approximately, the posterior probability of the reconciliations located in the considered subspace. Based on realistic gene duplication and loss rates and on real/simulated datasets of fungal gene families, our results suggest that the probability mass of the whole space of reconciliations is mostly located around the most parsimonious ones. In the context of posterior probability approximation, our approach is a valuable alternative to a MCMC method and can competes against a sophisticated, efficient, and exact computation of the probability of a given reconciliation. The Gene Tree Parsimony (GTP) problem is to infer a species tree that minimizes the number of duplications and/or losses over a set of gene family trees. Based on a new approch that explores the whole species tree space for the considered taxa and an efficient computation of the reconciliation cost, the third paper describes a Branch-and- Bound algorithm that solves exactly the GTP problem. When the considered number of taxa is too large, our algorithm can naturally take into account predefined relationships between sets of taxa. We test our algorithm on a dataset of eukaryotic gene families spanning 29 taxa.

Keyphrases: Gene family, Gene duplication, Gene loss, Homology, Comparative genomics, Species tree, Gene tree, Coevolution, Probability, Reconciliation, Parsimony, Evolution, Phylogenetic
Altérations métaboliques et nature des acides gras : implication dans la différenciation des cellules régénératives du tissu adipeux

The secretion of a large number of bioactive mediators by adipose tissue in abdominal obesity promotes metabolic diseases such as glucose intolerance, insulin resistance and type 2 diabetes. Cardiovascular complications, in particular atherosclerosis, are the leading causes of mortality in patients with type 2 diabetes. It has been shown that the stromal vascular fraction of adipose tissue comprised adipose-derived regenerative cells (ADRC) and that these cells possess progenitor cells characteristics. Effects of glucose intolerance and type 2 diabetes on adipocytes are well documented. However, consequences of these pathologies on ADRC behaviors are not well understood. Particularly, the impact of these metabolic alterations on the adipogenic and endothelial differentiation potential of ADRC has not been investigated.  Aim of this project was to evaluate, in a murine model, the effect of these metabolic alterations on the balance of the in vitro ADRC differentiation into adipocytes or endothelial cells. Glucose intolerance and type 2 diabetes were induced in mice by the intake of two high-fat diets enriched in vegetal (VD) or animal (AD) fat. The impact of the fat origin on the ADRC differentiation was then evaluated. To do this, the development of cellular culture conditions of ADRC was necessary and an important part of this work. Our results suggest that DMSO is an efficient cryoprotective agent that conserves the viability and progenitor properties of ADRC following their freezing. Moreover, among tested scaffolds for the culture of ADRC, collagen is the best matrix to maintain progenitor characteristics and this matrix enriched the cellular population in progenitor cells. The cellular density of non-adipose cells fraction in the adipose tissue was significantly more elevated for VD mice than for the control group. The in vitro evaluation of adipogenic differentiation demonstrated an increase in the differentiation potential for ADRC from VD group compared to AD and control groups. In addition, the endothelial differentiation was abrogated for ADRC from VD group, compared to a delayed one for AD. These results suggest that the adipogenic and endothelial differentiation potential of ADRC and, consequently, the balance between emerging mature cells, are affected by the metabolic status of mice together with the nature of fatty acids. These results highlight, for the first time, the importance to evaluate the ADRC behavior in function to the metabolic status of donor, a parameter that could have an important impact in the use of autologous ADRC in cell-based therapy for the repair of injured vascular tissues in diabetic patients.

Keyphrases: Adipocytes, Adipose-derived regenerative cells, Type 2 diabetes, Adipocytes, Endothelial cells, Vascular cellular therapy
Les conditions liées à l’intégration de l’approche écologique dans la programmation de prévention-promotion offerte à la clientèle aînée par des CSSS du Québec : une étude de cas

This multiple case study investigates conditions that influence the integration of an ecological approach in disease prevention and health promotion (DPHP) programs offered to older adults by local health organizations in Quebec. Scheirer’s implementation model guided the study in five CSSS that were selected to portray differing degrees of ecological character in their DPHP programs. Data collection proceeded through content analysis of thirty-eight semi-structured interviews conducted with professionals and managers as well as document analysis. Professional, organizational and environmental factors were explored. Results indicate that the ecological character of programs is influenced by organizational norms, competing priorities, team structure, external partnerships, preconceived ideas regarding DPHP for older adults as well as professional interest and training. These results suggest avenues for action to optimize the impact of services offered to an ageing population through disease prevention and health promotion programs.

Keyphrases: Health promotion, Prevention, Ecological approach, Older adults, Public health organizations
Remodelage neuronal de la cicatrice cardiaque suite à un infarctus du myocarde

GENERAL ABSTRACT Following myocardial infarction, scar formation represents an adaptive response required to heal the damaged myocardium and prevent cardiac rupture. Infarct healing requires the coordinated action of scar myofibroblasts, angiogenic cells, sympathetic fibres and nestin positive cardiac neural stem cells. A perturbation of one or more of the aforementioned events could lead to inadequate scar healing and further worsening of ventricular function. A better understanding of the cellular events and the underlying mechanisms involved in scar formation is of a primordial importance. The focus of the following studies consists of elucidating the role of the sympathetic system and cardiac neural stem cells during scar healing and their potential interaction. We tested the hypothesis that nestin positive neural stem cells are endogenous to the heart, contribute to angiogenesis and sympathetic innervation of the infarcted myocardium following ischemic injury.  Nestin positive cardiac neural stem cells are found in a number of species including the infarcted human heart. Nestin positive cardiac neural stem cells represent a resident population in the heart, are derived from the neural crest and detected intercalated between nestin negative cardiac myocytes. Following their isolation from the infarcted rat heart, neural stem cells proliferate as a neurosphere and under appropriate in vitro conditions differentiate to a neurofilament-M immunoreactive neuron. Following myocardial infarction, nestin mRNA levels are significantly elevated in the viable left ventricle and infarct region. Our data further suggests that the increased expression of nestin in the infarct region reflects in part the migration of these neural stem cells from the viable myocardium. During cardiac wound healing, neural stem cells may represent a novel substrate for de novo blood vessel formation and further contribute to sympathetic fibre growth and innervation of the infarct region.  Lastly, we demonstrate that scar formation and healing is associated with sympathetic fibre sprouting of the peri-infarct/infarct region. In addition, sympathetic fibres in the infarct region were detected in close proximity to small calibre blood vessels. These latter data indirectly suggest that innervating sympathetic fibres may play a role in angiogenesis during cardiac wound healing. Following the administration of the corticosteroid dexamethasone inadequate scar healing was observed and associated with a significant reduction of neurofilament-M immunoreactive fibres in the peri-infarct/infarct region. The loss of sympathetic fibre sprouting in the scar may be related to a dexamethasone-mediated suppression of myofibroblast growth and the concomitant reduction of nerve growth factor mRNA expression.

Keyphrases: Coeur, Neurofilament, Heart, Myocardial infarction, Neural stem cell, Nestin, Neurofilament, Sympathetic fibre, Angiogenesis, Fibrosis, Neural crest, Myofibroblast
Calibration de systèmes de caméras et projecteurs dans des applications de création multimédia

This thesis focuses on computer vision applications for technological art projects. Camera and projector calibration is discussed in the context of tracking applications and 3D reconstruction in visual arts and performance art.  The thesis is based on two collaborations with québécois artists Daniel Danis and Nicolas Reeves. Projective geometry and classical camera calibration techniques, such as planar calibration and calibration from epipolar geometry, are detailed to introduce the techniques implemented in both artistic projects. The project realized in collaboration with Nicolas Reeves consists of calibrating a pan-tilt camera-projector system in order to adapt videos to be projected in real time on mobile cubic screens. To fulfil the project, we used classical camera calibration techniques combined with our proposed camera pose calibration technique for pan-tilt systems. This technique uses elliptic planes, generated by the observation of a point in the scene while the camera is panning, to compute the camera pose in relation to the rotation centre of the pan-tilt system. The project developed in collaboration with Daniel Danis is based on multi-camera calibration. For this studio theatre project, we developed a multi-camera calibration algorithm to be used with a wiimote network. The technique based on epipolar geometry allows 3D reconstruction of a trajectory in a large environment at a low cost.  The results obtained from the camera calibration techniques implemented are presented alongside their application in real public performance contexts.

Keyphrases: Projection adaptative, Pan-tilt camera calibration, Multi-camera system, Camera-projector system, Mobile screens, Adaptative projection, 3D reconstruction, Technological art