NCube/papyrus huggingface dataset:
Le processus de construction identitaire chez les personnes atteintes de troubles mentaux

Recent research has identified the important role of work in a person’s identity.  Given that most people who suffer from mental health disorders find themselves unemployed, the lack of exposure to the work environment has a significant effect on the process of their identity construction.  This thesis explores the process of identity reconstruction and resulting identity of people having suffering life altering mental health problems who are then prevented from returning to work.  Using Dubar as a starting point, we built an analytical model applicable to our research and then applied that model to 28 subject and 6 counsellor interviews.  The interviews, qualitative data issued previously from research conducted from 1995 to 1997, were analyzed using NVIVO and then classified according to the requirements of the model.  The model consists of four quadrants resulting from the interaction of the identities developed from self perception and from the perception of others.  Our results show the reconstruction of identity of people with mental health difficulties is problematic.  The first and largest category consists of people who aspire to lead a normal life including regular work.  Their counsellors find them unable to work.  Our second group, find themselves in agreement with their counsellors.  They feel unable to contribute normally to society because they are mentally sick.  Our third category has one participant.  This is a person who does not have aspirations for a normal life but their counsellor felt they were capable of working and interacting normally with society.

Keyphrases: Aspirations, Mental illness, Identity reconstruction, Welfare, Aspirations, Recognition
Théorèmes de point fixe et principe variationnel d'Ekeland

The Banach contraction principle, which certifies that a contraction of a complete metric space into itself has a fixed point, is for sure the most famous of all fixed point theorems. However, in many case, the contraction we consider is only defined on a subset of a complete metric space. Of course, to certify that such a contraction has a fixed point, we need to add some restrictions. The Caristi theorem, which certifies the existence of a fixed point of a function of a complete metric space into itself satisfying a particular condition on d(x,f(x)), was later generalized to multivalued functions. By introducing different types of inwardness assumptions, we will be able to state some fixed point theorems for multivalued functions defined on a subset of a metric space. This is related to the recent work of French and Polish mathematicians. We were able to generalize some theorems to Fréchet spaces and gauge spaces such as the Caristi theorems and the Ekeland variational principle. We were also able to generalize some fixed point theorems for functions that are only defined on a subset of a Fréchet space or a gauge space. To do so, we used new types of contractions; contractions on Fréchet spaces introduced by Cain and Nashed [CaNa] in 1971 and generalized contractions on gauge spaces introduced by Frigon [Fr] in 2000.

Keyphrases: Contraction, Fixed point theorem, Caristi theorem, Ekeland variational principle, Contraction, Inward function, Multivalued function, Fréchet space, Gauge space
Biocompatibilité des microcapsules d'alginate : purification d'alginate, réaction immunitaire de l'hôte et protection du receveur

Islet of Langerhans inmmunoisolation is proposed as a way to avoid the use of immunosuppressive drugs after transplantation. Microcapsules, the immuno-isolating device, are composed of alginate and poly-L-lysine and the protection of the graft is granted by a semi-permeable membrane. This membrane allows small molecules to freely diffuse within the microcapsule, such as nutrients, glucose and insulin while protecting the graft against the host immune system. Biocompatibility is one of the challenges that must be addressed before the successful clinical application of this device. Microcapsules biocompatibility is related, first, to the biocompatibility of alginate, the polymer used to made microcapsules and second, to the in vivo stability of these microcapsules. In facts, it is well know that the use of an unpurified alginate containing many foreign contaminants to make microcapsules induce the host reaction against microcapsule (HRM). Moreover, damaged or broken microcapsules can allow the dissemination of cells from the encapsulated graft, activating the host immune system. We believe that a better understanding of the initiation processes of the HRM in terms of alginate purification efficacy to remove contamination as well as an improve microcapsule stability will increase microcapsules biocompatibility. Results reported in this thesis suggest that foreign proteins found in alginate are playing a key role in the initiation of HRM and that the reduction of these foreign proteins, by the improvement of alginate purification processes, improves microcapsules biocompatibility. In order to increase microcapsules stability, we also described and characterized an innovative type of microcapsules which involve covalent bonds. These covalently cross-linked microcapsules were found to by highly resistant and stable. The novel fabrication process of these microcapsules was not harmful for the encapsulated cell survival and was also found to confine the graft inside the microcapsules. This characteristic enables us to increase microcapsules biocompatibility by the protection of the host from the encapsulated cells.

Keyphrases: Microencapsulation, Réticulation covalente, Type I Diabetes, Islet Transplantation, Microencapsulation, Alginate purification, Foreign Body Reaction, Covalent cross-link, Cell therapy
Excommunication : la puissance de la création langagière contemporaine

This thesis broaches the value of contemporary literature as power (puissance) of language creation. Given that humanism becomes obsolete with the end of the printing press media dominance, and given that contemporary capitalism assigns an economical and recreational role to culture, “literature” is left without any “final criterion” to think its non-economical power. In other words, which intermedial effects of language creation through book form survives humanism while withstanding recreational communication? In the process, the practice of creative writing and its idea are set under a new paradigm. The first chapter explores the relationships between humanism and the printing press based on a concept of fungibility, and it introduces a set of key concepts. The second chapter presents another set of concepts (including vertical gesture), this time in order to think language in terms of ruling power (pouvoir) and virtual power (puissance). Chapter three broaches the idea of “civilizational capitalism” in intermedial terms. Saturation, separation and windowing are considered according to a game/play ethic. Chapter four is about plasticity. Finally, chapters five and six follow two examples—examples of virtual power, those of contemporary French writer Valère Novarina (Lumières du corps) and American novelist David Foster Wallace (Infinite Jest). The theoretical corpus is composed of elements taken, on the one hand, from Walter Benjamin’s and Giorgio Agamben’s works (regarding messianic materialism), and on the other hand, from Gilles Deleuze’s works. Some ideas are also influenced by Michel Foucault’s and Ludwig Wittgenstein’s works.

Keyphrases: Wallace [David Foster], Deleuze [Gilles], Agamben [Giorgio], Humanism, Humanities, Capitalismn, Plasticity, Literature, Creative writing, Creation
Une étude des conceptions de l’opinion publique chez les chroniqueurs politiques et éditorialistes québécois

The notion of public opinion is central to political action and media coverage of politics, in western democracies. It usually refers to the sum of all citizens’ individual attitudes, and to survey results. Yet, the limitations of public opinion thus conceptualized appears ever more clearly to scholars, calling into question its value as an input to the political process. In order to better understand the role of public opinion in the political process in Quebec, we have been seeking to understand how some important political actors — elite francophone political columnists and editorialists — view public opinion. By interviewing those journalists, we gathered their “lay theories”, i.e. the way they understand public opinion and its place in the democratic process. We found out that these pundits distinguish different types of public opinion, which are of unequal value to them. They are mostly interested in “latent public opinion”, a concept that includes dimensions of intensity and transformation potential of opinion. They believe surveys are somewhat useful, but incomplete tools for assessing public opinion. Therefore, they turn to other means of knowing it: conversations, and a certain “public opinion sense”. According to them, the media can have an influence on public opinion, but above all it can have an influence on public deliberation and on the way politicians view public opinion. Respondents also believe they can contribute, by their journalistic work, to the construction of a more considered public opinion — which is in tune with their ideal of participatory democracy.

Keyphrases: Public opinion, Latent opinion, Polls, Media, Journalists, Pundits, Columnists, Editorialists, Public policy, Quebec
Non-negative matrix decomposition approaches to frequency domain analysis of music audio signals

We study the application of unsupervised matrix decomposition algorithms such as Non-negative Matrix Factorization (NMF) to frequency domain representations of music audio signals. These algorithms, driven by a given reconstruction error function, learn a set of basis functions and a set of corresponding coefficients that approximate the input signal. We compare the use of three reconstruction error functions when NMF is applied to monophonic and harmonized musical scales: least squares, Kullback-Leibler divergence, and a recently introduced “phase-aware” divergence measure. Novel supervised methods for interpreting the resulting decompositions are presented and compared to previously used methods that rely on domain knowledge. Finally, the ability of the learned basis functions to generalize across musical parameter values including note amplitude, note duration and instrument type, are analyzed. To do so, we introduce two basis function labeling algorithms that outperform the previous labeling approach in the majority of our tests, instrument type with monophonic audio being the only notable exception.

Keyphrases: Unsupervised machine learning, Semi-supervised machine learning, Non-negative matrix factorization, Sparse coding, Music information retrieval, Pitch detection
Extraction, purification et caractérisation
d’isoformes d’hexokinase
du tubercule de pomme de terre (Solanum tuberosum)

Hexokinase (HK) catalyzes the first step of hexose metabolism by phosphorylating hexose to generate the corresponding hexose phosphate thereby allowing hexose entrance in glycolysis. Even though glucose is the main substrate, HK can also phosphorylate a broad spectrum of hexoses. Despite its importance this enzyme has never been purified to homogeneity in a native form. The aim of this work was therefore to purify this enzyme from Solanum tuberosum tubers and subsequently characterize its kinetic properties. Before I started this work, another group had already separated and partially purified 3 HK isoform from S. tuberosum. An extraction protocol was available but improvement was necessary since the extracted HK had little stability. By adding some protease inhibitors and by modifying the concentration of certain components in the extraction buffer we were able to obtain an extract with a HK activity stable for at least 72 h after extraction by preventing degradation. With this buffer and chromatography on butyl sepharose it was possible to separate 4 HK isoforms from S. tuberosum. After 5 more chromatographic steps, one HK isoform was purified to homogeneity (HK1). This enzyme was characterized and sequenced by MS/MS. We were able to associate this protein sequence with the gene product of StHK1 from S. tuberosum. With a specific activity of 10.2 U/mg of protein, this is the HK with the highest specific activity ever reported from a plant tissue. All the information gathered while purifying HK1 was used to undertake the purification of a second isoform (HK3). We were able to obtain preliminary results on its kinetic properties.

Keyphrases: Hexokinase, Hexokinase, Potato tuber, Protein purification, Protein characterization
In silico analysis of mitochondrial proteins

The important role of mitochondria in the eukaryotic cell has long been appreciated, but their exact composition and the biological processes taking place in mitochondria are not yet fully understood. The two main factors that slow down the progress in this field are inefficient recognition and imprecise annotation of mitochondrial proteins.  Therefore, we developed a new computational tool, YimLoc, which effectively predicts mitochondrial proteins from genomic sequences. This tool integrates the strengths of existing predictors and yields higher performance than any individual predictor. We applied YimLoc to ~60 fungal genomes in order to address the controversy about the localization of beta oxidation in these organisms. Our results show that in contrast to previous studies, most fungal groups do possess mitochondrial beta oxidation. This work also revealed the diversity of beta oxidation in fungi, which correlates with their utilization of fatty acids as energy and carbon sources. Further, we conducted an investigation of the key component of the mitochondrial beta oxidation pathway, the acyl-CoA dehydrogenase (ACAD). We combined subcellular localization prediction with subfamily classification and phylogenetic inference of ACAD enzymes from 250 species covering all three domains of life. Our study suggests that ACAD genes are an ancient family with innovative evolutionary strategies to generate a large enzyme toolset for utilizing most diverse fatty acids and amino acids. Finally, to enable the prediction of mitochondrial proteins from data beyond genome sequences, we designed the tool TESTLoc that uses expressed sequence tags (ESTs) as input. TESTLoc performs significantly better than known tools.  In addition to providing two new tools for subcellular localization designed for different data, our studies demonstrate the power of combining subcellular localization prediction with other in silico analyses to gain insights into the function of mitochondrial proteins. Most importantly, this work proposes clear hypotheses that are easily testable, with great potential for advancing our knowledge of mitochondrial metabolism.

Keyphrases: Mitochondria, Subcellular localization prediction, Machine learning, Beta oxidation, Fatty acid degradation, Amino acid degradation, Acyl-CoA dehydrogenase, Evolution, Evolution, Expressed sequence tags
Cerebral edema and acute liver failure : pathophysiological mechanisms and new therapeutic approaches

Hepatic encephalopathy (HE) contains a spectrum of neuropsychiatric abnormalities observed in patients with liver disease. A quick worsening of consciousness and increasingly growing cerebral edema, high intracranial pressure, which leads to cerebral herniation and death, are characteristics of acute liver failure (ALF). Multiple factors are found responsible for the development of HE, whereas, over 100 years, hyperammonia is considered the most crucial factor in defining the pathogenesis of HE in ALF, which can increase to millimolar concentrations in the brain at the coma stages of HE.  The present thesis comprises 4 articles, which demonstrates new pathogenic mechanisms involved in the development of HE and cerebral edema in ALF, and elucidates part of the therapeutic mechanism of hypothermia and minocycline in the prevention of HE and cerebral edema during ALF. The major findings are listed below:   (1) Experimental ALF leads to the increase in brain production of proinflammatory cytokines (IL-6, IL-1, TNF-α), and provides the first direct evidence that central inflammatory mechanisms play a role in the pathogenesis of the encephalopathy and brain edema in ALF (chapter 2.1 - article 1; chapter 2.1 - article 2).  (2) Activation of cerebral microglia, measured by OX-42, OX-6, predicts the presence of severe encephalopathy (coma) and brain edema in rats with ischemic ALF, which accompanies the increased production of brain proinflammatory cytokines (chapter 2.1 - article 1; chapter 2.2 - article 2).  (3) Oxidative/nitrosative stress participates in the pathogenesis of brain edema and its complications in experimental ALF animals with ischemic liver failure. The increases in cerebral NOS isoform expression caused by ALF were sufficient to cause increased NO production in the brain (chapter 2.3 - article 3; chapter 2.4 - article 4).  (4) Anti-inflammatory treatment, such as hypothermia or antibiotics, may be beneficial in patients with ALF (chapter 2.1 - article 1; chapter 2.2 - article 2).  (5) The beneficial effect of both hypothermia and minocycline on the neurological complications of experimental ALF is mediated, at least in part, by reduction of brain-derived oxidative/nitrosative stress (chapter 2.3 - article 3; chapter 2.4 - article 4).

Keyphrases: Acute liver failure, Hepatic encephalopathy
Caractérisation d’un nouveau récepteur à octopamine exprimé chez la palourde 
Spisula solidissima

A cDNA encoding for an octopamine receptor named Spi-OAR was cloned and sequenced from the surf clam Spisula solidissima oocytes. An analysis of its predicted amino acid sequence showed a high degree of similarity with β-adrenergic and octopamine receptors. This receptor qualifies as a novel receptor closely related to the proposed class of insect octopamine « β-adrenergic–like » receptors coupled to Gs protein. This cDNA was introduced into an expression vector (pCEP4), with an added N-terminal FLAG tag sequence, and transfected in host cells (HEK 293). Immunofluorescence studies showed expression of the receptor with a proper localization to the plasma membrane. Measurements of cAMP in transfected cells revealed that addition of octopamine, and to a lower extent, tyramine induced a rise in cAMP while dopamine, serotonine and histamine had no effect. Overexpression of Spi-OAR in mammalian cells induced slight constitutive increase of cAMP. An RT-PCR analysis with specific oligonucleotides revealed the presence of the receptor mRNA not only in oocytes but also in whole gonads, heart, adductor muscle, gills and ganglia suggesting that this receptor is likely ubiquitously expressed. Expression of Spi-OAR was also detected at different embryonic stages. Despite the demonstrated expression of Spi-OAR in oocytes, octopamine had no effect on meiotic reinitiation. Further studies will examine the function of Spi-OAR.

Keyphrases: Octopamine, RCPG, Mollusque, Calcium, GPCR, Surf clam Spisula solidissima, Mollusc, Oocyte, cAMP, Calcium
L’épistémologie de Marcel Proust dans
À la recherche du temps perdu : littérature et savoirs en 1900 : une pensée de l’imprévisible

The comprehensive novelistic survey presented by À la recherche du temps perdu is worth a research to be taken literally and establishes the knowledgeable subject as a scholar-researcher against his object of knowledge. Proust makes of “knowledge” the condition of talent and engages his hero in an exploration that presents itself as a priority for being a quest for knowledge.  The present essay follows in the wake of Epistemocritique, a discipline that studies the inscription of knowledge in the literary text in general, with a specific focus on knowledge related to science. Our aim is to bring forward the epistemic position that characterizes the narrator of À la recherche du temps perdu as he acquires various forms of knowledge in the course of his observations.  The narrator’s cognitive path is examined with regard to the four main pillars of his quest, which we redefine in terms of paradigms: the paradigm of exploration, which defines an “epistemology of the observer”; the paradigm of communication, which defines an “epistemology of the social being”; the paradigm of Introspection which prepares for the elaboration of an “epistemology of the internal character”; and finally, the paradigm of vocation, which combines the answers to most of the questions that have marked the narrator’s cognitive path. This last paradigm presents itself as an “epistemology of creation”, an “epistemology of reality”, and an “epistemology of chance”. For, in spite of an approach that appears to be subject to cultural interventions, the quest by Proust’s main character appears as a thought of the unpredictable. Although strongly determined by the cognitive quest of the protagonist, it nevertheless remains irreducible to this sole quest.   In conclusion, we emphasize the status reserved to science and to positive knowledge from the perspective of the discovery of vocation, but also in view of the elaboration of a theory of literary creation: does Proust consider these two areas of knowledge as irreconcilable, with one having an evident priority over the other, or, to the contrary, does he considers them as equal factors in knowledge and artistic creation?

Keyphrases: Epistemocritique, Literature and Science, Experimental psychology, Unconscious, Conventionalism, Crisis of Physics, Pierre Janet, Pierre Janet
AURA : a hybrid approach to identify framework evolution

Software frameworks and libraries are indispensable to today's software systems. As they evolve, it is often time-consuming for developers to keep their code up-to-date.   Approaches have been proposed to facilitate this. Usually, these approaches cannot automatically identify change rules for one-replaced-by-many and many-replaced-by-one methods, and they trade off recall for higher precision using one or more experimentally-evaluated thresholds.   We introduce AURA (AUtomatic change Rule Assistant), a novel hybrid approach that combines call dependency and text similarity analyses to overcome these limitations. We implement it in a Java system and compare it on five frameworks with three previous approaches by Dagenais and Robillard, M. Kim et al., and Schäfer et al. The comparison shows that, on average, the recall of AURA is 53.07% higher while its precision is similar (0.10% lower).

Keyphrases: Software evolution, Empirical study