NCube/papyrus huggingface dataset:
Eye disease and mobility limitations in older adults

Objective: To examine the extent of mobility limitations in patients with age-related macular degeneration (AMD), glaucoma, or Fuchs corneal dystrophy as compared to a control group of older adults with good vision. Design: Cross-sectional hospital-based study Participants: 253 people (61 with AMD, 45 with Fuchs, 79 with glaucoma, and 68 controls) Methods: Patients were recruited from the ophthalmology clinic of Maisonneuve- Rosemont Hospital (Montreal, Canada) from September 2009 until October 2010. Patients with AMD and Fuchs had to have visual acuity in the better eye of worse than 20/40 while patients with glaucoma had to have visual field deficit in their worse eye of at least -4dB. Control patients who had normal visual acuity and visual field were recruited from the same clinic. Questionnaire (life space and falls) and performance-based (one-legged balance test, timed Up and Go (TUG) test) mobility data were collected, visual acuity, contrast sensitivity, and visual field were assessed, and the medical record was reviewed. Linear and logistic regression were used. Main Outcome Measures: Life space, balance, timed Up and Go, falls Results: The three eye diseases were associated with different patterns of mobility limitations. Patients with glaucoma had the most types of mobility limitations as they had reduced life space, had worse TUG scores, and were more likely to have poor balance than the control group (p < 0.05). Compared to controls, patients with AMD or Fuchs corneal dystrophy had reduced life space (p < 0.05). Falls were not related to eye disease in this study.Conclusions: Our results suggest that eye diseases, especially glaucoma, restrain the mobility of older people. It is important to further explore the impact of eye disease on mobility in this population in order to develop interventions that would help affected older adults maintain their independence.

Keyphrases: life space, eye disease, mobility
Le motif du "domaine" : espace d'une subjectivité dans Les vies frontalières et Rabatteurs d'étoiles de Rachel Leclerc

This masters thesis’s objective is to reveal the poetic subject’s unique way of occupying space in Rachel Leclerc’s Les vies frontalières and Rabatteurs d’étoiles by analysing the “domain’s” motif, recurrent in the two poetical pieces. Clarifying the meaning of this specific motif will be accomplished through the identification of its different underlying structures and by defining how its development is closely linked to that of the poetic subjectivity in Leclerc’s work. The three first chapters of the present thesis intend to shed light on the importance of the “horizon’s structure”, term barrowed from Michel Collot’s works, to highlight the distinctive manner in which the poetic subject appreciates spatiality, temporality and his own subjectivity. As for the fourth chapter, it expands on what can be called the “road structure” that crosscuts and completes the horizon’s structure. The junction of these two lines creates the domain’s space and its T form supports the poetic undertaking in its full spectrum.

Keyphrases: Rachel Leclerc, Contemporary poetry, Quebec poetry, Rachel Leclerc, Space, Time, Poetic subjectivity
Rôles des protéines Staufen 1 et 2 dans la plasticité synaptique des cellules pyramidales hippocampiques

Learning and memory are complex processes that are not completly understood at the cellular and molecular levels. It is however accepted that persistent modifications of synaptic connections, like synaptic plasticity, could be responsible for the encoding of new memories. Whereas long-term potentiation (LTP) is classically defined as a persistent and stable enhancement of synaptic connections, long-term depression (LTD) is a reduction in the efficacy of neuronal synapses.   Numerous studies have identified some of the mechanisms of this phenomenon, in particular, the induction and expression mechanisms, as well as the changes in dendritic spine morphology. The most abundant type of synapse in the hippocampus is the excitatory glutamatergic synapse made on dendritic spines; the presence of the translational machinery in dendrites near spines strongly supports the concept of local mRNA translation. Moreover, those mRNA are transported in dendrites to activated synapses by RNA binding-proteins (RBP). Staufen proteins (Stau1 and Stau2) function in transport, localization and translational regulation of mRNA are now established. However, their precise roles in synaptic plasticity are still unknown.   Thus, this Ph.D. thesis evaluates the importance of Staufen proteins in mRNA transport and regulation in synaptic plasticity. We have identified specific functions for each isoform; while Stau1 is implicated in late-LTP, Stau2 is required for mGluR-LTD. This specificity is also relevant for dendritic spine morphogenesis since Stau1 is involved in mature dendritic spine maintenance while Stau2 participates in dendritic spine morphogenesis at a developmental stage. Moreover, our studies have indicated that Stau1 involvement in spine morphogenesis is dependent on ongoing NMDA receptor-mediated plasticity. Finally, our results suggest that Stau2 is implicated in a particular form of synaptic plasticity through transport and regulation of specific mRNA granules required for mGluR-LTD such as Map1b.  Our work uncovers specific roles of Stau1 and Stau2 in regulation of synaptic plasticity. These studies help to better understand mechanisms involving mRNA regulation by Staufen in long-term synaptic plasticity and memory.    ENGLISH KEY WORDS: Staufen, hippocampus, synaptic plasticity, RNA granules, translation, dendritic spines

Keyphrases: Staufen, Staufen, synaptic plasticity, hippocampus, RNA granules, translation, dendritic spine
Identification des peptides du complexe majeur d’histocompatibilité de classe I par spectrométrie de masse

Adaptive immunity and discrimination between self and nonself in jawed vertebrates relies on the presentation of peptides by the major histocompatibility (MHC) class I receptors. Foreign or self peptide antigens presented by the MHC molecules are probed by CD8 T-cell lymphocyte for proper immune response. The repertoire of MHC I peptides collectively referred to as the immunopeptidome is generated through the proteasomal degradation of endogenous proteins and plays an important role in the regulation of cellular immunity. The composition of the immunopeptidome is cell specific and can harbor important hallmark of human diseases including cancer. Antigenic peptides can also be used in immunotherapy to mount an appropriate immune response against cancer cells displaying these peptides. Mass spectrometry is a tool of choice for the identification, sequencing and characterization of these peptides. However, the amino acid composition, the low abundance and diversity of these peptides make their detection and sequencing more challenging. We developed a software, called StatPeaks, that calculates statistics relative to the fragmentation of peptides. Using this software, we demonstrate that under collision induced dissociation (CID) MHC class I peptides fragment in a very different fashion than tryptic peptides, commonly used in proteomics. However, the higher-energy collisional dissociation (HCD) mode available on the LTQ-Orbitrap Velos enhances peptide fragmentation and provides high resolution fragment information that significantly improves the confidence in MHC class I peptide identification. This inherent advantage confers the ability to perform de novo sequencing to identify polymorphic variants that would normally elude conventional database searches. The comparison of de novo peptide sequencing software Lutefisk, pepNovo, pNovo, Vonode and Peaks indicated that the later software enabled higher rates of correct identification for MHC class I peptides. This software was integrated into a data analysis pipeline for the identification minor histocompatibility antigens (MiHAs). A web-based library that stores spectral information of hundreds of synthetic MHC class I peptides was developed in support to the needs of the immunopeptidome discovery program.

Keyphrases: immunopeptidome, antigen, MHC Class I, mass spectrometry, de novo sequencing, single nucleotide polymorphism
A la quête du « bout de papier» : les perceptions des expériences scolaires, des études et diplômes universitaires chez les lycéens guinéens du privé et du public

This paper aims to analyze the perception of university education and university degree among senior high school students from public and private schools in Guinea. Using a qualitative analysis, the research explores the participants’ academic and nonacademic experience. Semi-directed interviews were conducted among 23 pupils from two high schools in the capital Conakry. The targeted schools differ by their statutes (private/public) and the social origin of their students.  As illustrated by the analysis, the academic and nonacademic experiences vary notably depending on the type of high school attended. School trajectories of students from public institutions are more chaotic than those of students in public institutions. The first benefit from a better learning environment—equipment and teachers—and a more favorable familial context than the latter. Outside school, while students in private schools devote their spare time to leisure activities, their public counterparts spend most of their time involved in petty money-earning activities, ‘‘fighting’’ to pay their school fees.  In addition, the data show that both private and public schools’ students perceive the pursuit of their studies beyond senior high school as a logical continuation of their academic journey. The university attracts and ‘‘fascinates’’ students, notably for the «piece of paper» it grants.  The university degree remains a distinctive mark, a symbol of prestige and, especially among public schools’ pupils, a guarantee of employability. Finally, for girls in private schools, higher education is perceived as a way for future independence, even if they do not disconnect their schooling future from their marital plans.

Keyphrases: High school students, University diploma, Private school, Social perceptions, Academic experience, Guinea, Public school, Getting by
Déterminants individuels et contextuels de la mortalité des enfants de moins de cinq ans en Afrique au sud du Sahara : analyse comparative des enquêtes démographiques et de santé

Child health remains a priority area for health policy in sub-Saharan Africa. Disparities in child mortality between and within countries have persisted and widened considerably during the last few decades. While researchers have devoted considerable attention to the impact of individual-level factors on child mortality, less is known about how community characteristics and institutions affect health outcomes for children, even though they have a prominent role in theoretical models. The aim of this thesis is to identify individual and contextual effects of child mortality by using data from the latest round of Demographic Health Surveys for all countries in sub-Saharan Africa. Two sets of questions are addressed in this research.  First, we evaluate the impact of contextual factors on the risk of dying before age 5 net of the effect of individual factors. The results indicate that some attributes of the community influence the mortality risks of children, over and above the intermediate factors included in this investigation. For instance, in half of the countries under study a 1% increase in the proportion of children fully immunized in the community is associated with a decrease of 17-79% in the odds of dying before age 5. The proportion of women in the community completing secondary school also significantly increases child survival. This effect is, in some countries, in addition to the positive individual-level effect of the child’s own mother being educated. Net of individual and household characteristics, higher community-level ethnic homogeneity is associated with decreased odds of dying before age 5 in some countries. Overall, the results of this study therefore suggest that the challenge to reduce under-five mortality goes beyond addressing individual factors, and requires a better understanding of contextual factors.   Second, the study exploits recent national survey data for nine countries in sub-Saharan Africa to investigate the association of LBW and mortality not only in infancy but also during childhood, using a standardized methodology to adjust missing birth weight data from household surveys while accounting for unobserved family-level factors (genetic or behavioral) that may modify the relationship between birth weight and under-five-years mortality. We find evidence of the impact of birth weight on the risk of dying not only in infancy but also during childhood, which remains strong and significant in all countries even after controlling for potential confounding factors. The main policy implication of our findings is that reducing the incidence of LBW may be an important prevention strategy to combating child mortality in sub-Saharan Africa countries.

Keyphrases: Child mortality, Low birth weight, Individual-level effects, Community-level effects, Sub-Saharan Africa, Survival analysis, Multilevel modeling, Demographic and health surveys
La perception du risque terroriste et de ses conséquences sur la gestion de la sécurité dans le système de transport en commun de Montréal

The research presented in this thesis aims to understand the impact of perceptions on the production and management of security in the Montreal transit system. Fifteen research interviews were conducted with police officers from the Metro Unit to identify the key elements involved in the perception of risk. The police officers are called to work in an environment where, on the one hand, there has never been any terrorist attacks, but on the other, remains a potential target according to experts, governments and popular culture. Our results show that the police officers develop a perception of risk specific to their tasks. In general, they have a pragmatic attitude which allows them to quickly sort situations and decide which ones need their attention. In addition, the police officers adopt justification and protection strategies that allow them to minimize their perception of risk. Participants insist that these strategies are necessary to enable them to perform their daily tasks. Thus, in order to escape falling into a paranoid state, the police officers avoid thinking about the terrorist threat, preferring to focus their attention on the crimes on which they believe to have an actual power. However, vigilance is still required. Although the police officers did not perceive the risk in the same way as administrators, the presence of the Metro Unit remains an important part of the production of security in the Montreal transit system.

Keyphrases: Perceptions, Tranport municipal, Terrorism, Critical infrastructure, Perceptions, Social amplification of risk, Municipal transport
Étude pharmacogénomique sur l’utilisation de la warfarine en pratique clinique réelle

Background: Although numerous genotype-based warfarin dosing algorithms have been published, there is little data comparing the predictive ability of these algorithms in real clinical practice.  Objectives: Our goal was to evaluate the performance of pharmacogenetic algorithms in an unselected patient population initiating warfarin treatment for atrial fibrillation or valve disease in a real-world clinical setting. The principal objective of the analysis was to determine if Gage’s, Michaud’s, and IWPC algorithms could predict the dose achieving the therapeutic International normalized ratio (INR).  Methods: Data from a retrospective cohort study of 605 patients initiating warfarin therapy at the Montreal Heart Institute was used. We compared the dose predicted by the algorithms to the dose achieving the therapeutic INR. Pearson’s correlation coefficient and mean absolute error (MAE) were used to evaluate the predictive accuracy of the algorithms. Clinical accuracy of the predictions was assessed by computing the proportion of patients in which the predicted dose was under-estimated, ideally estimated, or overestimated. Finally, we used multiple linear regression analysis to evaluate the accuracy of a predictive model obtained by adding additional covariables in predicting therapeutic warfarin doses. Results: The proportion of variation explained (adjusted R2) was the highest for Gage’s algorithm (R2 = 44 %) and the mean absolute error was the smallest for the predictions made by Gage’s algorithm (MAE = 1.41 ± 0.06). Moreover, when we compared the proportion of patients whose predicted doses are within ± 20 % of the observed stable dose, Gage’s algorithm also performed the best overall.  Conclusion: The algorithm published by Gage et al. in 2008 is the most accurate pharmacogenetically based equation in predicting therapeutic warfarin dose in our study population.

Keyphrases: VKORC1, Warfarin, Pharmacogenetics, Algorithms
Les facteurs influençant l’utilisation des mesures d’isolement et de contentions en milieu psychiatrique intrahospitalier

Psychiatric staff can have both positive and negative attitudes towards inpatient aggression. Different attitudes towards aggression can have a substantial influence on how such behaviour is dealt with on psychiatric wards. In this manner, seclusion and restraint are frequently used measures for managing violent behaviour. However, their use raises several concerns. Method: Over three hundred staff members were recruited from eight psychiatric hospitals in the province of Quebec. First of all, an examination was conducted from the staff perspective of the organizational and staff factors that may be associated with increased recourse to seclusion and restraint in psychiatric wards. Simultaneously, factorial analysis of the French version of two scales used to measure staff attitude towards institutional violence and aggression (MOAS and POAS) was completed. Results: The final multivariate model showed that the following factors independently predict to greater use of seclusion and restraint: the type of hospital ward; greater expression of anger and aggression among staff members; perceptions of the frequency of incidents of physical aggression against the self; and the perception of insufficient protection measures in the workplace. Factor analyses revealed a four factor structure for the MOAS and a three factor structure for the 12-item POAS, which is similar to what is found in recent scientific literature in North American and European countries. Conclusion: These findings underscore the importance of evaluating a variety of factors, including perceptions of safety and violence, when exploring the management of aggression and violence on psychiatric wards and the reasons seclusion and restraint measures are used. These findings represent the first stage of a research program of the multidisciplinary group to whom the author is associated, aimed at reducing recourse to seclusion and restraint in Quebec psychiatric services.

Keyphrases: Modified Overt Aggression Scale (MOAS), Perception of Aggression Scale (POAS), Violence, Organization, Staff attitude, Psychiatric ward, Seclusion and restraint predictor
Contribution de l'hypoxie à la cicatrisation cutanée anormale chez le cheval : méthodes physiques d'évaluation

Cutaneous wound healing in horse limbs is often perturbed by the development of exuberant granulation tissue while body wounds tend to repair uneventfully. A delay in healing is usually observed in horse limb wounds, which tend to develop exuberant granulation tissue and excessive scarring. The events leading to exuberant granulation tissue formation in horses are not fully elucidated. Tissue hypoxia has been proposed as a major contributing factor as it appears to contribute to the development of similar abnormal skin scarring in human.   The objective of this study was to investigate skin blood flow and tissue oxygen availability in normal / abnormal healing of full-thickness wounds created on the horse limb and body, using infrared thermography and near infrared reflectance spectroscopy. Six healthy, 3- to 4-year-old mares were used for the experiment. Three full-thickness cutaneous wounds were surgically created on the dorso-lateral surface of each metacarpal area (limb wounds) and on the lateral thoracic wall (body wounds). One randomly chosen distal forelimb was then left to heal by second intention without bandage, while the contralateral limb was bandaged postoperatively to induce the formation of exuberant granulation tissue and lead to excessive scarring. Thermal and spectroscopic data were collected from both anatomic sites (limb without bandage, bandaged limb, thoracic wall) at specific times following wounding.   Mean changes in skin blood flow and tissue oxygen availability at specific wound sites over time were compared by use of repeated measures ANOVA with anatomical location and wound management as within-subject factors. A priori contrasts, submitted to Bonferroni sequential correction, were then used to compare pre-selected individual means. The statistical analysis revealed that there were significant differences in skin blood flow and tissue oxygen availability within wounds. Skin blood flow and tissue oxygen availability were significantly increased within body over limb wounds (P<0.05). Skin blood flow was significantly increased within unbandaged limb over bandaged limb wounds (P<0.05). We have recently reported a greater occlusion of microvessels in limb wounds in horses. We report here that skin blood flow and tissue oxygen availability are significantly inferior in limb wounds in horses, especially when exuberant granulation develops. Taken together, these results suggest that equine limb wounds may suffer from altered vascular perfusion and tissue hypoxia, which could favor abnormal skin healing and exuberant granulation tissue development.

Keyphrases: perfusion, skin healing, wound, oxygen, horse, spectroscopy, thermography, exuberant granulation tissue