NCube/papyrus huggingface dataset:
Études structurales d’interactions protéine/protéine impliquées dans l’érythropoïèse

Hematopoietic development is regulated through a combinatorial interplay between lineage-specific activators and the general transcription machinery that enables cell-specific patterns of gene expression. This thesis reports structural and functional studies of interactions involving the transcativation domains (TAD) of activators proteins and their role in hematopoietic development. Interactions between the TAD of activators and their partners play an important role in the transcriptional regulation of all genes including those regulating hematopoiesis. The first section reports the identification and characterization of a novel interaction between the erythroid transcription factor GATA-1 and the tumor suppressor protein p53. Using a combination of isothermal titration calorimetry (ITC), NMR spectroscopy and in vivo studies, we identified and characterized the direct interaction between these two important transcription factors in an attempt to determine the role of this interaction in erythroid development. Based on our results, the TAD of p53 directly interacts with the DNA-binding domain of GATA-1 in a cell-type specific manner. Through this interaction, GATA-1 inhibits activation of select p53-regulated genes and we postulate that the inhibition of p53-dependent apoptotic pathways is essential for survival of erythroid precursor cells. In the second section, we report on the interactions between two acidic TADs and the general transcription factor IIH (TFIIH). The structure of the complexes formed by the Tfb1/p62 subunit of TFIIH (Tfb1PH/p62PH) and the acidic TAD of Herpes Simplex viral protein 16 (VP16) and the Erythroid Krüppel-like factor (EKLF) were determined by NMR spectroscopy. The structure of the Tfb1PH/VP16 complex demonstrated that a viral TAD has the ability to mimic the actions of the TAD from the human p53 with Tfb1PH/p62PH. The TADs of both VP16 and p53 adopt a 9-residue α-helix in complex with Tfb1PH/p62PH. Interestingly, the NMR structure of the EKLF/Tfb1PH complex demonstrated that despite sharing a common binding site with p53 and VP16 on Tfb1PH, the EKLF/Tfb1PH binding interface is distinctly different from the binding interfaces we previously observed with p53/Tfb1PH and VP16/Tfb1PH complexes. Surprisingly, EKLF adopted a similar binding mechanism as the general transcription factor TFIIEα in interaction with p62PH as both interact in an extended conformation. Moreover, based on our structural data, we have identified Trp73 as a key residue within the TAD of EKLF that is required for the formation of the EKLF/Tfb1PH complex. Mutations of Trp73 disrupted the binding to Tfb1PH/p62PH and significantly reduced the transcriptional activity of EKLF in red blood cells.

Keyphrases: GATA-1, EKLF, p53, VP16, Transcription, Domaine transactivation, General transcription factor, Nucelar magnetic resonance spectroscopy
Spectro-imagerie optique à faible flux et comparaison de la cinématique Ha et HI d'un échantillon de galaxies proches

A new EMCCD (Electron multiplying Charge Coupled Device) controller is presented. It allows the EMCCD to be used for photon counting by drastically taking down its dominating source of noise : the clock induced charges. A new EMCCD camera was built using this controller. It has been characterized in laboratory and tested at the observatoire du mont Mégantic. When compared to the previous generation of photon counting cameras based on intensifier tubes, this new camera renders the observation of the galaxies kinematics with an integral field spectrometer with a Fabry-Perot interferometer in Ha light much faster, and allows fainter galaxies to be observed. The integration time required to reach a given signal-to-noise ratio is about 4 times less than with the intensifier tubes. Many applications could benefit of such a camera: fast, faint flux photometry, high spectral and temporal resolution spectroscopy, earth-based diffraction limited imagery (lucky imaging), etc. Technically, the camera is dominated by the shot noise for flux higher than 0.002 photon/pixel/image.  The 21 cm emission line of the neutral hydrogen (HI) is often used to map the galaxies kinematics. The extent of the distribution of the neutral hydrogen in galaxies, which goes well beyond the optical disk, is one of the reasons this line is used so often. However, the spatial resolution of such observations is limited when compared to their optical equivalents. When comparing the HI data to higher resolution ones, some differences were simply attributed to the beam smearing of the HI caused by its lower resolution. The THINGS (The HI Nearby Galaxy Survey) project observed many galaxies of the SINGS (Spitzer Infrared Nearby Galaxies Survey) project. The kinematics of THINGS will be compared to the kinematic data of the galaxies obtained in Ha light. The comparison will try to determine whether the sole beam smearing is responsible of the differences observed. The results shows that intrinsic dissimilarities between the kinematical tracers used are responsible of some of the observed disagreements. The understanding of theses differences is of a high importance as the dark matter distribution, inferred from the rotation of the galaxies, is a test to some cosmological models.

Keyphrases: EMCCD, Galaxies, SINGS, Astronomical instrumentation, Photon counting, EMCCD, Clock  Induced Charges, Galaxies, Kinematics, Dark matter, Fabry-Perot interferometry, 3D spectroscopy, SINGS
Identification et caractérisation de gènes différemment exprimés dans les tubules proximaux de reins diabétiques et impliqués dans le développement de la néphropathie diabétique

Diabetic nephropathy is a disease characterized by a nephrotic syndrome and glomerulosclerosis. It is related to capillaries angiopathy caused by diabetes. It is one of the main sources of end stage renal disease in America. Tubular anomalies such as apoptosis or tubular detachment from glomeruli are known to be efficient markers for the progression of this disease. Thus, it has been proposed during the work related to this thesis to study the different molecular mechanisms linked with proximal tubules apoptosis, particularly those related with reactive oxygen species (ROS). A previously stated hypothesis made by our laboratory stated that one of the initial sources of the development of tubular damages may be regulated by the production of ROS by NADPH oxidases. Thus, one of the first series of experiments carried during this thesis was done on an animal model of type 2 diabetes, the db/db mouse. Following the characterization of different renal pathologies and their reduction in the proximal tubules by the antioxidant enzyme catalase, experiment with genetics expression microarrays were carried. Using this tool and bioinformatics analysis, it was possible to profile different genes linked to pathways involved by diabetes and the catalase enzyme. Thus, it was possible to carry further studies on these genes linked to apoptosis and overexpressed in the proximal tubules of diabetic mice. One of the pro apoptotic genes characterized in this thesis was the Bmf gene, a member of the family of Bcl-2 regulator, involved in apoptosis related to the release of cytochrome c from the mitochondria. Thus, it was determined that this gene is overexpressed in the proximal tubules of diabetic mice, and that it was also upregulated by in vitro models of diabetes. This enabled our team to conclude that Bmf must play an important role in the regulation of apoptosis and atrophy of the proximal tubules. Another study carried during this thesis was linked with the use of a transgenic animal model to better define the role played by damages related to oxidative stress in the progression of renal pathologies related to renin-angiotensin system activation. The results obtained by this study stated that overexpression of the antioxidant enzyme catalase managed to reduce the different kidney pathologies observed in the transgenic model, which let us conclude that reactive oxygen species have an important role to play in the development of hypertension and kidney damages.

Keyphrases: Rein, Hypertension, ROS, Kidney, Renin-angiotensin system, Diabetic nephropathy, Hypertension, ROS, Microarrays, Transgenic mice
Rétro-ingénierie des diagrammes de séquence 
par visualisation interactive

We propose a semi-automated approach for the reverse engineering of UML sequence diagrams. Our approach starts with a set of execution traces that are automatically aligned to determine the common behavior. Sequence diagrams are then extracted with the help of an interactive visualization, which allows navigating though execution traces and performing extraction operations. We provide a concrete illustration of our approach with a case study, and show in particular that the resulting diagrams are more meaningful and more compact than those extracted by automated approaches.

Keyphrases: reverse engineering, sequence diagram, execution trace, interactive visualization
Sélection des risques de morbidité et de mortalité en Afrique subsaharienne aux fins d’une tarification en assurance-vie

Abstract: Progress in medical research has prolonged life expectancy, improved patient quality of life; these changes translate in such domain as life insurance underwriting. The principle of underwriting in life insurance is based on the comparison of the probability of death of an individual candidate for an insurance policy to the probability of death of a reference population closed to the candidate. A review and analysis then becomes an of the medical literature become an indispensable tool for risk selection. Life insurance has been present in sub-Saharan Africa for approximately two hundred years, but up to date the insurers do not have specific underwriting tools which are adapted to the African context. This work is the first one in our knowledge to explore risk selection for Life insurance in Africa. Its purpose is to elaborate underwriting tools which will take into account specific aspects of mortality and morbidity in sub-Saharan Africa. First, we made a literature review of all available medical publications on different health problems; then, in a second step, we sorted out the risk factors for both morbidity and mortality, in order to suggest algorithms for underwriting risk selection. It appeared rapidly that mortality studies, and mainly long-term follow-ups, are scarce in sub-Saharan Africa. When they exist, they are of short duration, and enrol a limited number of patients. This makes our analysis and extrapolation of risk difficult for underwriting purposes. However identification of morbidity and mortality factors is important to allow some basic underwriting. The black African has a mortality and morbidity profile which are appreciably different from the one of a Caucasian subject. Consequently it will be important to adapt the underwriting tools used for underwriting life insurance in sub- Saharan Africa. Sub-Saharan Africa needs more than ever solid epidemiological data, and health policies implementation for the development of risk selection in insurance medicine. These changes mean the implementation of a coordinated public health network, a reliable demographic monitoring system and a continuous follow-up of the population’s migration. To reach such objectives, the collaboration with developed countries which are already very advanced in these fields will be very useful.

Keyphrases: Africa, Sub-Sahara, Selection, Risk, Morbidity, Mortality, Underwriting
Paradis crépusculaire ; suivi de Impostures : examen d’une démarche créatrice

The first part of this M.A. Thesis, “Paradis crépusculaire”, is a novel.  The narrator and main character is a young lady hunted by suicidal thoughts.  She describes her own psychological development starting with the meeting of a man and with the beginning of their relationship.  Love awakes her suicidal temptations and brings her in a universe of fear and madness.  The story takes roots in the daily lives of both characters.   The second part, “ Impostures : Examen d’une démarche créatrice ”, is an essay about my own writing experience.  My personal thoughts on literary creation, especially about the production of a novel, are linked with different theories of literature.  This essay elaborates on a feeling of imposture that has haunted me threw all my writing process.

Keyphrases: Imposture, Suicide, Literary creation, Novel, Writing, Imposture, Suicide, Love
La complémentarité et la place de différents types de savoirs dans l'intervention
psychosociale en réadaptation physique

Social workers practicing in the physical rehabilitation field work with different types of knowledge, but only a few studies looked into the relationship between them. The present research project aims at understanding the place these social workers allow different types of knowledge in their practice. We distinguish theoretical knowledge, produced scientifically, practice knowledge, built from action and experience, and existential knowledge, like beliefs and values. The information collected qualitatively from eight semi-directed interviews with these social workers was codified and analyzed horizontally and vertically. This demonstrates that all types of knowledge have a place in practice and are equal and complementary. They fulfill different functions either addressed to specific actors, and moments in intervention, or to many of them at once. This project produced both practical and theoretical knowledge that have an impact on practice and research, but that leave some unresolved questions to get back to in the future.

Keyphrases: Intuition, Practice wisdom, Types of knowledge, Tacit knowledge, Intuition, Knowledge production, Sources of knowledge, Reflective practice, Social work, Rehabilitation, Physical handicap
Les produits dérivés des marchés européens du
carbone

During the last decade, the European Union has regulated emissions of Greenhouse Gases on its own territory. Consequently, a European Carbon Market (EU ETS) is currently emerging where CO2 emission certificates (EUA and CER) and derivatives are traded on Exchanges. The objectif of this research is to evaluate and compare different models to represent the emission certificates' price and to price derivatives of the carbon markets.

Keyphrases: Tarification, EU ETS, EUA, CER, Carbon Markets, Derivatives, Asset Pricing, Emission Certificates
La herencia de la época de oro en el cine mexicano de los años noventa : La ley de Herodes y Danzón

This thesis studies the traces of the so-called “golden age” of Mexican cinema in films produced in the nineties. In Mexico, the upsurge of cinematic production between 1935 and 1955 established the principal norms and genres of a national cinema. The cinema of this era, critically acclaimed and widely diffused through television and video, continues to influence contemporary filmmaking. Focusing our analysis on two films, María Novaro’s Danzón (1991) and Luis Estrada’s La ley de Herodes (1999), we study how films from the nineties at once render homage to golden age cinema and use it to comment upon new trends in Mexican politics and cultural production.  The continued diffusion of golden age cinema allows us to partially explain its influence on Mexican filmmakers working in the nineties. The nineties’ historical context, strongly marked by neoliberalism and globalization, allows us to propose further hypotheses as to why contemporary filmmakers have recuperated elements of “national-popular” cinema. We believe that this context explains both the homage and the criticisms that today’s films direct towards the cinema of the golden age. Our analysis of the dialogue between the films produced in these two periods borrows from theories of filmic intertextuality.

Keyphrases: Danzón, María Novaro, La ley de Herodes, Luis Estrada, Mélodrame, Mexican cinema, Golden age, National-popular culture, Neoliberalism, Globalization, Melodrama, Intertextuality
Étude des facteurs de perturbation de chambres d’ionisation sous conditions non standard

During the past decade, technological developments in radiation therapy have considerably transformed treatment techniques. Novel nonstandard beams improve target dose conformity, but increase the complexity of dosimetry procedures. As recent studies demonstrated the invalidity of these protocols to nonstandard beams, a new protocol applicable to nonstandard beam reference dosimetry is in preparation by the IAEA-AAPM. The first goal of the study is to characterize the factors responsible for non-unity corrections in nonstandard beam dosimetry, and provide conceptual solutions to minimize the magnitude of the corrections. The second goal is to provide methods to estimate uncertainties accurately in nonstandard beam dosimetry, and estimate uncertainty levels achievable in typical clinical situations. Results of this study show that reporting dose to the sensitive volume of the chamber filled with water reduces the correction factor approximately by half under high gradients. A theoretical expression of correction factor is obtained for ideal nonstandard reference fields. In radiochromic film dosimetry, levels of uncertainty of the order of 0.3% are achieved with strict procedures and show great potential for nonstandard beam measurements. Results also suggest that experimental uncertainties in nonstandard beam are an important issue to consider both during daily QA routine and reference dosimetry, and could be a limiting factor in the new generation of protocols.

Keyphrases: Medical physics, Nonstandard dosimetry, Monte Carlo method, Radiochromic film, Experimental uncertainties
"Les mille tableaux du réel" : analyse de la perception dans La terre est ici d'Élise Turcotte

This M.A. thesis concerns the collection of poems La terre est ici of the poet Élise Turcotte. It studies the modalities by which the perception of the poetic subjects displaces the notion of « landscape » in the work of Turcotte.  The first chapter, in studying enunciation, tries to understand how the subjectivities of La terre est ici invest the language and build the reality that surrounds them to create a singular perception. The second chapter analyzes the creation of this unique visual space which deploys itself around the notion of « detail », whereas the third and last chapter questions the vision engendering an « art de faire » which aims towards direction and movement. The study of this stage as a way to convoke the subjects in the language introduces the idea of the space as a practised place. Thus, the multiple perceptions of the subjects compose a « landscape », understood in a visual sense and as possibility of action.

Keyphrases: Élise Turcotte, La terre est ici, Perception, Quebec poetry, landscape, poetry
Cognition sociale et traitement du contexte dans la schizophrénie : effets des stéréotypes

Individuals with schizophrenia (SZ) have a deficit in social cognition including mental state attribution, social perception and emotional perception. The results of a study by Hardy-Baylé et al. (2003) suggest that their inability to infer intentions and beliefs to others may result from their inability to use contextual information. Studies (Ivanko & Pexman, 2003; Pexman & Olineck, 2002b) showed that several factors such as level of incongruity between context and speaker’s utterance, vocal inflections and character’s features can influence the comprehension of an ironic intent among healthy (HT) subjects. The aim of this study is to manipulate contextual information to determine if stereotypes (type of speaker’s occupation) are social factors that cue comprehension of speaker’s intention (theory of mind; ToM) and social perception in schizophrenia. Thirty SZ patients and thirty HT participants were recruited for this study. Participants were tested on working memory and irony comprehension. Each story had been manipulated with two conditions of speaker’s occupation: occupation that cues ironic intent (e.g. actor), and occupation that does not cue ironic intent (e.g. priest). The results showed that SZ patients have an impaired ToM and are not sensitive to stereotypes as CT participants. However, the results revealed that SZ participants do not have a deficit in social perception.

Keyphrases: social cognition, stereotypes, schizophrenia, context processing, theory of mind, social perception, irony
L’asphyxie en médecine légale : une étude rétrospective de six ans sur les suffocations non-chimiques au Québec

Suffocation is a general term that encompasses several forms of asphyxia generated by a deprivation of oxygen. It includes different subtypes such as environmental suffocation/ entrapment, choking, smothering and traumatic/ positional asphyxia. In the forensic literature, suffocation has been the object of several papers, but mainly case reports or cases series. Studies of subsets of suffocation deaths, limited to a specific scenery or category, have also been reported, such as suffocation in motor vehicle collisions. Nonetheless, there are still several areas of forensic pathology mainly based on tradition, with textbook explaining and describing common knowledge that is not supported by modern research data: suffocation makes no exception. The present project is intended to contribute to evidence-based data on non-chemical suffocation deaths. It comprises a 6-year retrospective study of all non-chemical suffocation cases in the forensic victim population of Quebec. As far as we know, this is the first paper to ever portray a systematic study of non-chemical suffocation deaths in forensic setting. In general, the results are concordant with the textbook literature, therefore supporting common knowledge related to manner of death in non-chemical suffocation. However, discrepancies have been underscored in smothering. Furthermore, the classification of asphyxia and the definitions of subtypes, such as suffocation, are far from being uniform, varying widely from one textbook to another and from one paper to the next. Unfortunately, similar research designs can lead to totally different results depending on the definitions used. Closely comparable cases are classified differently by equally competent forensic pathologists. Therefore, the present project highlights the discrepancies between textbook classifications and tries to draw mainstream definitions, in order to propose a more unified classification of asphyxial deaths.

Keyphrases: Suffocation, Strangulation, Forensic sciences, Asphyxia, Suffocation, Smothering, Choking, Traumatic asphyxia, Positional asphyxia, Environmental suffocation, Strangulation, Chemical asphyxia