NCube/papyrus huggingface dataset:
Caractérisation génétique d’une forme d’ataxie tardive

Ataxias are a heterogeneous group of neurodegenerative diseases and are characterized by a lack of voluntary movements. My Master's project was on a late-onset ataxia (LOCA), after 50 years of age. The main clinical features are: cerebellar atrophy on MRI (88%), dysarthria (81%), frontal lobe atrophy (50%) and nystagmus (52%). Disease segregation in the family is suggestive of a recessive transmission.  In order to identify the causal gene of LOCA, we have recruited 38 patients affected by a late-onset ataxia, originated from SLSJ, Eastern townships or other region in Quebec. A first genome scan was done with microsatellite markers on an informative family. Parametric linkage analysis suggested linkage on chromosome 13 (4.4Mb). Haplotype sharing analysis on 17 families reduced the candidate interval to 1.6Mb, but this haplotype was found to be frequent in the French-Canadian population.  A second genome scan with SNPs markers allowed us to performed homozygozity mapping and look for founder mutations in subgroup of patients. Many strategies were performed, including regional clustering. No candidate loci were identified with confidence. We decided to combine the genotyping analysis results with exome sequencing to uncover the causative gene. The analysis on six affected individuals allowed us to obtain a rare variants list with four putative genes. More analysis is needed to identify the gene responsible for LOCA.

Keyphrases: Ataxia, neurodegenerative, exome sequencing, homozygosity mapping
Les patrons d’expression de gènes : ont-ils évolué avec la complexité des organismes?

Regulating transcription is one of the most fundamental cellular processes and the first step of a long cascade of processes leading to protein expression. Altering transcriptional output often has major effects on cellular homeostasis and is associated with many disease phenotypes, such as cancer. Understanding the fundamental rules governing transcription regulation is therefore instrumental in understanding cellular function as well as in finding disease treatments. Transcription of a gene can occur through two fundamental different modes: “continuous” or “bursting”. Continuous transcription is defined as stochastic process where a promoter is always in its “on” state and each initiation event is independent of the previous. Bursting transcription occurs when a promoter is activated for a short time and multiple mRNAs are produced during the “on” state, followed by long periods of transcription inactivity. It leads to greater variability in an isogenic population, as expression is often bimodal as a sub-population does not express a given gene. Bursting expression is frequently observed in higher eukaryotes, while a continuous pattern seems to be common in lower eukaryotes. The goal of this project is to study how gene expression patterns evolved. We investigate whether Poisson-like transcription is a property of lower eukaryotes and whether transcription patterns have changed when organisms and genomes evolved into more complex systems. Using smFISH, we have systematically determined expression patterns of four evolutionarily conserved genes; mdn1+, PRP8/spp42+, pol1+ and cdc13+, previously shown to be continuously expressed in the yeast S. cerevisiae. Expression was studied in the yeast S. pombe, as an example for another lower eukaryote as well as in human cell-lines. We observe that expression patterns are organism-and-gene specific suggesting that expression patterns have evolved to fulfill gene specific functions.

Keyphrases: transcription, burst, bursting, gene expression, expression pattern
Étude de l’effet d'agents potentiellement perturbateurs de la structure des biofilms sur la diffusion des macromolécules dans les biofilms de Streptococcus mutans :
cas de l’EDTA et de l’aspirine

The aim of this study was to investigate the role of biofilm structure disrupting potential agents in the biofilm permeability to macromolecules.  The effect of ethylenediamine tetraacetic (EDTA) and acetylsalicylic acid (aspirin), two potential disrupting agents, on the diffusion of poly (ethylene glycol) (PEG) and dextran in Streptococcus mutans biofilms was investigated. Attenuated total reflection (ATR) infrared spectroscopy was used to measure the global diffusion coefficients, while the local diffusion coefficients were measured using fluorescence correlation spectroscopy (FCS). On one hand, the results showed that EDTA, at a concentration of 7.5 (w/v) %, increased PEG penetrability and global diffusion coefficient in biofilms.  No effect was noticed for the local diffusion coefficient of fluorescent dextran molecules. This difference was associated with, amongst others, the scale of the measurements and the different nature of the diffusing species. On the other hand, aspirin had no effect on the S. mutans biofilm permeability for PEG. The enhanced penetration of PEG in the presence of EDTA was correlated with bacterial cell viability. The bactericidal effect of penicillin G (PenG) alone and in combination with EDTA, was assessed for the biofilms. The results showed that antibiotic effect of PenG was improved by a factor of 3 when the antibiotic was used in combination with EDTA compared to the same antibiotic used alone. Moreover images obtained by epifluorescence microscopy and laser scanning confocal microscopy indicated that the bacteria in the core of the microcolonies were more affected by PenG when the milieu contained EDTA. These results revealed that the use of disrupting agents of biofilm structure is a promising approach to eradicate biofilms showing resistance to classical antimicrobial agent treatments. More studies should be done to investigate the effect of others potentials disrupting agents on the biofilm permeability to macromolecules.

Keyphrases: EDTA, Streptococcus mutans biofilm, Aspirin
Utilisation de représentations de mots pour l’étiquetage de rôles sémantiques suivant FrameNet

According to Frame Semantics (Fillmore 1976), word meanings are best understood considering the semantic frame they play a role in, for the frame is what gives them context. FrameNet is a lexical database that defines about 1000 semantic frames, along with the roles to be filled by arguments to the predicate calling the frame in a sentence. Our task is to automatically label argument roles, given their position, the frame, and the predicate (sometimes refered to as semantic role labelling). For this task, I make use of distributed word representations, in order to improve generalisation over the few training exemples available for each frame. A maximum entropy classifier using common features of the arguments is used as a strong baseline to be improved upon.

Keyphrases: FrameNet, natural language processing, supervised learning, semantic role labelling, word representations
Expérience subjective et différences individuelles dans l'intégration d'informations visuelle et kinesthésique

Subjective  experience  is  built  after  the  fact  by  integrating  different  sources  of information that interact with each other at different moments (before, during and after the movement). In order to create subjective experience of agency and control, the characteristics of the movement are interpreted by a Bayesian model. To determine the  impact  of  the  interaction  between  the  parameters  that  enter  in  that  Bayesian attribution model and to investigate possible disparities in the formation of subjective experience  of  movement  between  individuals,  a  series  of  90  pulses  of  single-pulse transcranial magnetic stimulation (TMS) followed by four questions on the subjective experience relative to the movement was conducted on 20 normal subjects. Objective data about the movement was gathered using electromyography (EMG) and motion capture.  Individual  regression  models  have  been  conducted  to  determine  the proportion  of  the  subjective  judgements  that  varied  accordingly  to  the  objective parameters of the movement; this proportion varied greatly between participants. The present  study  proposes  that  there  is  an  individual  capacity  to  form  subjective judgements  that  adequately  represent  the  reality,  as  suggested  by  coherence between   different   accuracy   measures   and   different   variables   measuring   the subjective experience.

Keyphrases: Transcranial magnetic stimulation, Subjective experience, Control, Agency, Attribution model, Movement
La mise en scène du savoir-faire musical au cinéma

This research aims at making an inventory and an analysis of the narrative, rhetorical and formal processes, in which three movies are presenting the musical know-how, and especially the teaching-learning situation between a music professor and his student. These three films are: Tous les matins du monde, directed by Alain Corneau (1991); Bird, by Clint Eastwood (1988) and All That Jazz, by Bob Fosse (1979). Eventually, this inventory and this analysis will allow us to identify a prevailing thematic: in these movies, and even in Cinema in general, it seems like music and musical education are portrayed under social and psychological features that are characteristics. There is, one hand, the possession of the other, the submission, the sacrifice and the perpetual dissatisfaction. But on the other hand, there are many gratifications to which education for body mind and spirit is a guarantee. Our hypothesis is that certain cinematographic expression modes — related to variations of framing styles, angle and reverse shots and so on—, and certain film narrative modes might be explaining this ability that Cinema has to show the emotional and social threat that weighs on the musical professor and on his student. These very same processes, thematic and hypothesis will be examined in a feature length script that will focus on the ability of questioning theses topics using the poetical composition.

Keyphrases: Cinema, Music, Apprenticeship, Teaching-learning relationships, Ethics
Caractérisation structurale et fonctionnelle des interactions impliquant TFIIH et les domaines de transactivation viraux

The general transcription factor IIH (TFIIH) plays crucial roles in both transcription and DNA repair. Tfb1/p62 (yeast and human), one of the ten/eleven subunits of TFIIH, has been shown to interact with several important transcription (p53, NFκB, TFIIEα) and repair factors (Rad2/XPG and Rad4/XPC) (1). Most of the interactions with Tfb1/p62 require the Pleckstrin homology (PH) domain located at the amino-terminal end of the protein (2, 3). This PH domain in particular forms complexes with highly acidic domains from target proteins involved in both transcriptional activation and DNA repair. Recent studies has shown that the Tfb1/p62 subunit of TFIIH is also targeted by a number of viral proteins including the Herpes Simplex virus (HSV) protein VP16, the Human papillomavirus (HPV) protein HPV E1 and the Epstein-Barr virus (EBV) protein EBNA-2 (4, 5). These viral proteins interact with the Tfb1/p62 subunit via acidic domain which suggests that they are forming similar interactions as the one observed with human transcription and repair factors. This thesis provides a structural and functional characterization of the complex formed by the viral proteins EBNA2 and the human protein Tfb1/p62 subunit of TFIIH. The analysis is done using isothermal titration calorimetry (ITC), nuclear magnetic resonance (NMR) spectroscopy and a yeast activation assay. This study brings a greater understanding of proteins implicated in diseases such as the Burkitt’s lymphoma directly linked to an EBV infection (review in (6)) and shows a viable target for antiviral drug.

Keyphrases: virus d’Epstein-Barr (EBV), Epstein-Barr virus (EBV), Epstein-Barr nuclear antigen 2 (EBNA2), general transcription factor IIH (TFIIH), protein-protein interaction, isothermal titration calorimetry (ITC), nuclear magnetic resonance (NMR)
La gouvernance autochtone en milieu urbain: le cas de Montréal

In recent years, Aboriginals have obtained from the Canadian State recognition of certain inherent rights, including the right to self-determination and the right to self-government. However, when implementing Aboriginal governance initiatives, the various levels of government have operated on the assumption that Aboriginal groups all have a land base on which they can achieve their objectives, such as First Nations, Inuit and Métis home communities. These models are inadequate for the majority of Aboriginals who live in urban areas and who form a diverse and extremely mobile population without a land base. In order to reconcile the exercise of self-government and urbanity, new theoretical models of governance were developed to provide for better political representation of urban Aboriginals. By taking into account the issue of identifying who holds the right to self-determination, the nature of powers to be exercised and the area over which they would be exercised, we will attempt to determine in this thesis which Aboriginal governance model is best suited for Montreal’s Aboriginal population.

Keyphrases: Aboriginal people, Urban aboriginal, Right to self-determination, Self-government, Aboriginal governance, Personality of laws, Nation with land base, Urban reserve, Community of interest
L'évolution de la conception personnelle de la discipline infirmière d'étudiants en soins infirmiers

Few studies describe the nursing students’ personal conceptual framework of the discipline nor its evolution though it influence their pratice and their continuation in the educational program (Fawcett, 2002; Pepin et al., 2010; Spouse, 2000). The goal of this research was to explore the evolution of nursing students’ personal conceptual framework during their nursing educational program. This paper presents a exploratory qualitative study inspired by a theoretical framework linking the radical constructivism (Glasersfeld, 1994) and the center of interest of the discipline (Pepin et al., 2010). Individual interviews were conducted with first, third and fifth semester nursing students (n=11). The data were analysed by analytic questioning (Paillé & Mucchielli, 2010). The participants describe « human » nursing as a precondition of the « nursing activities ». They describe the person has unique having abilities. The nurse guide the person to be able to accomplish his activities and to take care of himself to maintain mental and physical health. The hospital environment is not meeting the ideal conditions set by the participants. Throughout their educational program, the comprehension of the central concepts of nursing seems to get more complex and mature. The participants identify the experience gained through clinical placements as the main factor of influence on their personal conceptual framework. Finally, this research provides new knowledge to the nursing teachers facilitating the learning of the nursing theory and orient the construction of a useful personal framework for the future practice of the nursing students.

Keyphrases: Nursing students, personnal conceptual framework, evolution, constructivism, focus of the discipline, nursing education
La communauté des consultants en marketing territorial et la diffusion internationale des politiques de branding des villes

Cities of all sizes compete today with places and organizations located on all continents to attract investors, tourists, businesses, workers, students and future residents. To cope with this global competition, the use of territorial marketing and branding approaches and strategies by municipal authorities in their approach to planning and urban management is becoming more common. This thesis looks at a political component of city branding that is relatively unexplored. It exposes the enthusiasm for the adoption of such policies in a growing number of cities and explores the possible influence the community of city marketing consultants exerts in the transfer of such practices. Since it is a new approach, this research is primarily exploratory. It presents a portrait of the community of actors involved in this area of activity and explores some of the elements that may be used to illustrate their influence on the international transfer of such policies and practices.

Keyphrases: marketing territorial, Cities, territorial marketing, city branding, policy transfer, policy communities
L'expérience de femmes atteintes de sclérodermie et vivant avec une limitation fonctionnelle : une étude phénoménologique

Scleroderma is a disease unknown by the general population, as well as by health professionals. Such ignorance is partly due to the fact that it is a rare disease and receives little attention from researchers, funding agencies and pharmaceutical companies. Thus, presently, there are few studies that have been conducted to explore women’s experience of being diagnosed with scleroderma undergoing functional limitation. This study aimed to describe and understand the meaning of the experience of women living with scleroderma and functional limitation. The student-researcher used Watson’s philosophy of human caring, as nursing perspective (1988, 1999, 2005, 2006a, 2008). Giorgi’s (1997) qualitative phenomenological method was selected to analyse the interviews. Six women agreed to participate to the study by sharing their experiences during an individual interview. The data analysis identified three themes: Urgency to live, Decline of autonomy as a source of suffering and Continuous reappropriation of self. The results help understand the experiences of women with scleroderma and living with a disability. The uncertainty related to scleroderma development for these women greatly contributes to the urgency to live a normal life before it is too late. The results highlight adaptive strategies they choose to do, while living moments of distress accompanied by hope. This psychological and emotional distress is tainted by restrictive consequences of the symptoms and alteration of body image. In everyday life, these women adapt to a new self-renewal with the evolution of the disease, scleroderma.

Keyphrases: women, chronic illness, degenerative disease, functional limitation, sleroderma, lived experience, phenomenology, human caring philosophy
Des bio-objets pour la bioéthique. Compte rendu de Bio-Objects: Life in the 21st Century

The collective work Bio-Objects: Life in the 21st Century, edited by Niki Vermeulen, Saka Tamminen and Andrew Webster analyzes new forms of life arising from the biosciences in terms of their bio-objectification. Firmly anchored in the field of science and technology studies, this collection invites us to follow bio-objects through the way they challenge the boundaries of the living and their associated social, legal and ethical issues.

Keyphrases: biotechnologies, biosciences, bio-objectification, bioethics, sociology, science and technology studies, anthropology, biotechnology, life sciences, bio-politics
Isolated greater tuberosity fractures of the proximal humerus : validation and clinical implications for a new radiologic measurement method and classification

Isolated fractures of the Greater Tuberosity (GT) of the proximal humerus are rare and a challenge to study. Three main problems arise: 1: Though 5mm+ superior GT displacement is often a surgical indication, measurement errors on radiographs may surpass 10mm. 2: The Neer and AO classifications describe only one type of GT fracture (large fragment, vertical fracture line). Two other fracture types have been described: an avulsion-type (small fragment), and a very lateral Hill-Sachs-type. 3: There are no studies on the treatment or prognosis of GT fractures according to fracture morphology.  Article 1 introduces and tests a simple method to measure superior GT displacement (the GT ratio) using standard radiographs; this correlates very well with computed tomography (CT). Article 2 presents the Morphologic classification for GT fractures. It describes three fracture types (Avulsion, Split, Depression) and has good to excellent reliability. The ultrasonographic, radiologic, and clinical results of 54 patients (average follow-up 2.5 years) with isolated GT fractures are then described. Patients <50 years had higher rates of rotator cuff tears and displaced (≥ 5mm) GT fractures were associated with supraspinatus atrophy. Both full rotator cuff tears and supraspinatus atrophy resulted in poor outcomes.  The impact of fracture morphology on prognosis was not significant. However, age, sex, and associated glenohumeral dislocation differed by fracture type and this may reflect their pathophysiology. A more thorough evaluation of the prognosis and treatment of GT fractures by morphologic type would require a prospective multicenter study.

Keyphrases: Grosse tuberosite, Fracture, Deplacement, Classification, Proximal humerus, Greater tuberosity, Fracture, Displacement, Radiographs, Classification, Ultrasound, Rotator cuff, Clinical outcome, Treatment
Le téléenseignement avec la vidéoconférence et le développement professionnel d’enseignants du collégial

Many colleges have their technical programs at risk due to demographic decline and the exodus of young people. This situation is directly related to the offer of formation: 46.1% had to leave their area because the chosen curriculum was not available. It is in Gaspésie-Îles-de-la-Madeleine that the biggest drop customers could happen, a decrease of over 40 % compared to the observions at fall 2008 (Bezy, 2011). This finding also raises a lot of questions about the professional development of teachers. An innovative project is carried out in this region and could help change the situation. Indeed, the Cégep de la Gaspésie et des  Iles has established a distance learning initiative in two programs (accounting techniques and management, nursing care). This research is based on a sample of 6 teachers and aims to describe the challenges and obstacles faced by those, in the change process, and the benefits and perceived benefits of the practice of distance education. Also,  the  changes in individuals videoconferencing teaching practices according to different levels of adoption of technology. To measure these different aspects of their practice, the CBAM model (Hall & Hord, 2006) was used and the interconnected model of professional development (Clarke,2002). The results were obtained by questionnaires (SoC and TAM) and interviews (LoU and detailled interview on major topics  of the study), they can provide a detailed overview of the role of these teachers while meeting the research objectives individual and group profiles portrait presented to identify characteristics of professional development in the context of this innovation. The results show great similarities between the cases in the sample (6 teachers) and it also show’s taht the most importants issues for these teachers are classroom management and technical and pedagogical challenges that distance learning requires.

Keyphrases: Innovation, CBAM, Innovation, Videoconferencing, Distance formation, Professional development, CBAM