NCube/papyrus huggingface dataset:
The Association Between Food Security and Diet Quality Among First Nations Living On-Reserve in Canada

Background: First Nations (FN) experience high levels of food insecurity that greatly exceed those of the non-aboriginal population. Associated with this burden are alarming rates of obesity and nutrition-related chronic disease. Little is known about food insecurity’s relationship to diet quality outcomes for FN living on-reserve. Objective: This study explores the associations between household food insecurity (FI) and poor diet quality for FN adults living on-reserve in 5 Canadian regions (south of the 60th parallel).  Methods: Dietary recall data from the First Nation Food Nutrition and Environment Study (FNFNES), a cross-sectional study, were analyzed using two diet quality indices: a Canadian Healthy Eating Index (HEI) and NOVA, which assesses diet by level of food processing. Regression analyses explored socio-demographic correlates of FI and diet quality. HEI total and component scores and the caloric contribution of NOVA groups and subgroups were compared between food security levels.  Results: FI prevalence was high (35.7%), notably in households with children (40.4%), those where all members are unemployed (45.4%), and those receiving social assistance (55.5%). Sex, age group, and education level were also correlated with FI. The mean total HEI score was low (49.0  12.65). Total HEI mean scores were associated with sex, age group, region, social assistance, traditional food consumption, any household TF activity, and education. They were also significantly higher for people from food secure households compared to FI (49.7 vs. 48.1, respectively), though not after adjusting for socio-demographic variables. After adjustments, FI remained significantly associated with higher intakes of processed culinary ingredients (sugars and plant oils), lower intakes of homemade dishes, and less fruit and vegetable consumption. Conclusions: This study found a small, but significant, relationship between food insecurity and diet quality. Findings also emphasized the need to address income, social assistance benefits and access to traditional foods to improve food security and nutritional outcomes for First Nations.

Keyphrases: HEI, NOVA, Autochtones, Food security, Food insecurity, Diet quality, Food processing, Aboriginal, First Nations
Étude d’impact : analyse des données de fréquence alimentaire, d’activité physique et d’image corporelle chez des enfants d’âge scolaire au Burkina Faso

A study conducted in Ouagadougou, Burkina Faso, in 2009 and 2014 assessed the behavior of school-aged children. The aim of this study was to evaluate the impact of an intervention in schools on dietary habits, physical activity, and attitudes and perceptions towards body image. The nutritional intervention, called the “Nutrition-Friendly Schools Initiative” (NFSI) initiated by the World Health Organization in 2006 to prevent the double nutritional burden, was launched in six intervention schools in Ouagadougou. A baseline study in 2009 collected dietary and socio-demographic data from the six intervention schools as well as from six control schools that were comparable in terms of socioeconomic status (private/public) and geographic location (urban/peri-urban), prior to the initiation of the NFSI. Grade 5 students completed a questionnaire on the frequency of consumption of "healthy" foods (fruits, vegetables, meat, fish, legumes) and "superfluous" foods (cakes, biscuits, sweets, ice cream, soda), determinants of eating behavior,  body image perception, and physical activity. Similar data were collected in 2014, five years after the initiation of NFSI, among 709 schoolchildren (54,3% girls) in the same 12 schools. The average age of the schoolchildren was 11,6  1,3 years. The analyses revealed an effect of the intervention on the consumption of "healthy" foods but not of "superfluous" foods. In intervention schools, schoolchildren ate "healthy" foods more frequently than in control schools. Schoolchildren who participated in the NFSI showed greater satisfaction with their body image in 2014 than in 2009 (p = 0.030), compared with students in control schools (p = 0.974). Between 2009 and 2014, sports practice increased in both groups of schools, with a higher frequency of practice in intervention schools than in control schools. However, the practice of sport was already higher in intervention schools in 2009, before the establishment of the NFSI. In intervention schools, there was a decrease in the use of active transportation and a higher tendency to watch television and use the computer during the week compared to control schools. This study found improvements in diet, sport practice and satisfaction with body image in schoolchildren. However, the results also showed an increase in sedentary behavior among students. After five years of NFSI activity, it is difficult to establish causal links between the intervention and changes in students’ eating behavior and lifestyle. Thus, future longitudinal school-based studies would be required to assess the impact of the NFSI on student behavior.  Keywords: Food consumption, body image perception, physical activity, sedentary lifestyle, impact, intervention, school age children, Ouagadougou, Burkina Faso, Africa.

Keyphrases: Impact, Intervention, Ouagadougou, Burkina Faso, Food consumption, Body image perception, Physical activity, Sedentary lifestyle, School age children, Africa
An approach to improved microbial eukaryotic genome annotation

New sequencing technologies have considerably accelerated the rate at which genomic data is being generated. One ongoing challenge is the accurate structural annotation of those novel genomes once sequenced and assembled, in particular if the organism does not have close relatives with well-annotated genomes. Whole-transcriptome sequencing (RNA-Seq) and assembly—both of which share similarities to whole-genome sequencing and assembly, respectively—have been shown to dramatically increase the accuracy of gene annotation. Read coverage, inferred splice junctions and assembled transcripts can provide valuable information about gene structure. Several annotation pipelines have been developed to automate structural annotation by incorporating information from RNA-Seq, as well as protein sequence similarity data, with the goal of reaching the accuracy of an expert curator. Annotation pipelines follow a similar workflow. The first step is to identify repetitive regions to prevent misinformed sequence alignments and gene predictions. The next step is to construct a database of evidence from experimental data such as RNA-Seq mapping and assembly, and protein sequence alignments, which are used to inform the generalised Hidden Markov Models of gene prediction software. The final step is to consolidate sequence alignments and gene predictions into a high-confidence consensus set. Thus, automated pipelines are complex, and therefore susceptible to incomplete and erroneous use of information, which can poison gene predictions and consensus model building. Here, we present an improved approach to microbial eukaryotic genome annotation. Its conception was based on identifying and mitigating potential sources of error and bias that are present in available pipelines. Our approach has two main aspects. The first is to create a more complete and diverse set of extrinsic evidence to better inform gene predictions. The second is to use extrinsic evidence in tandem with predictions such that the influence of their respective biases in the consensus gene models is reduced. We benchmarked our new tool against three known pipelines, showing significant gains in gene, transcript, exon and intron sensitivity and specificity in the genome annotation of microbial eukaryotes.

Keyphrases: Annotation Structurale, Saccharomyces, Neurospora, Ustilago, Plasmodium, Nuclear Genome, Structural Annotation, Microbial Eukaryote, Protists, Fungi
Étude du rôle de la phosphatase DUSP1 dans la régulation de la réponse immunitaire innée autonome dans les cellules épithéliales pulmonaires lors de l'infection par le virus respiratoire syncytial et le virus Sendai

Introduction: One of the major causes of death worldwide are the lower respiratory infections, particularly those caused by viruses like the respiratory syncytial virus (RSV). To defend the host, cells produce an autonomous antiviral response that is mostly dependent on type I/III interferons to limit viral replication. They also secrete proinflammatory cytokines/chemokines to orchestrate the immune response. In order to avoid tissue damage caused by an excessive cytokine production, these responses have to be strictly regulated. Key activators of the host's defense against respiratory viruses are activated by multiple phosphorylation events, making phosphatases important negative regulators.  Results: In this Master's thesis, we study the dual-specificity phosphatase 1 (DUSP1) and its implication in the negative regulation of the host's response induced by RSV and Sendai virus (SeV). We found that DUSP1 is induced in early RSV and SeV infections in A549 cells and is subjected to proteasomal degradation. We also show that DUSP1 negatively regulates the activation of JNK and p38 MAPKs during SeV and RSV infections. Interestingly, we found that AP-1 activation and subsequent cytokine production were not modulated by DUSP1, potentially due to the protection provided by the JIP1-JNK interaction. Finally, we show for the first time that DUSP1 promotes apoptosis and suppresses cell migration.  Conclusion and relevance: Our data suggest that DUSP1 acts as a negative regulator of tissue repair mechanisms during RSV and SeV infection, making it an interesting potential therapeutic target.

Keyphrases: DUSP1, JIP1, JNK, p38, migration, cytokines, Pneumovirus, Apoptosis, Respiratory Syncytial Virus
Caractérisation structurale et biophysique de l’impact de l’acétylation de SUMO1 sur son interaction dépendante de la phosphorylation avec PML

PML-Nuclear Bodies (PML-NBs) formation and dynamics is regulated by an extensive network of post-translational modifications (PTMs), which includes SUMOylation of PMLNB- resident proteins, phosphorylation of SIMs (SUMO-Interacting Motifs) and acetylation of SUMO proteins. Recent studies suggest that acetylation of SUMO proteins regulates PML-NB function, but the precise role of acetylation is still not clear. Using Isothermal Titration Calorimetry (ITC) and X-ray crystallography studies, we have investigated the impact of SUMO1 acetylation on its interaction with the phospho SIMs of PML and Daxx. Interestingly, neutralizing the positive charges of K37, K39, K45 or K46 by either acetylation or glutamine substitution significantly decreases the binding affinity towards phospho-mimetic PML-SIMs as measured by ITC, but the decreases are more dramatic with the K39 and K46 variants than with the K37 and K45 variants. In the crystal structures of the phospho-SIMs of PML and Daxx in complex with K46Ac, there are dramatic disruptions of interactions at the binding interfaces, but the changes that occur at the interface appear to be distinct for the SIM involved. The other acetylated variants in complex with the phospho-SIM of PML displayed a more global effect of charge re-organization at the binding interface. Together, our results provide an atomic level description of how SUMO1 acetylation can modulate its interaction with different phospho-SIMs, indicating that there is considerable plasticity in SUMO/SIM interactions and this plasticity could be altered by different types of PTMs in order to regulate distinct cellular functions.

Keyphrases: SUMO, PML, SUMOylation, X-ray crystallography, ITC, PML-NBs, SIM, tumor suppressor, phospho-sérines, phosphoserines, X-ray crystallography, Isothermal Titration Calorimetry (ITC), PML-Nuclear Bodies (PML-NBs), SUMO-Interacting Motif (SIM), Tumour suppressor, Phosphoserines
H3K27M/I mutations promote context-dependent transformation in acute myeloid leukemia with RUNX1 alterations

Neomorphic missense mutations affecting crucial lysine residues in histone H3 genes have been shown to be initiating mutation in a variety of solid tumors. Despite the high prevalence of H3K27M mutations in pediatric glioblastoma proceeded by the loss of global H3K27me2/3, these mutations have not been studied in human hematological cancers. Using the H3.3K27M/I transgenes we studied the effects of the loss of H3K27me2/3 on normal and transformed hematopoietic cells. We identified oncogenic histone H3K27M/I mutations in human acute myeloid leukemia (AML) that led to a significant reduction of H3K27me2/3. The mutation profiles of H3K27M/I patients revealed that these lesions invariably co-occurred with RUNX1 alterations. Expression of H3.3K27M/I in an AML1-ETO9a driven mouse model resulted in accelerated in vitro proliferation and in vivo disease latency. The expression of H3.3K27M in human CD34+ umbilical cord blood cells led to a selective expansion of a primitive hematopoietic progenitor population, but was insufficient to drive leukemogenesis on its own. This demonstrates a collaboration between RUNX1 and loss of H3K27me2/3. In the context of RUNX1 alterations in AML, hypo-H3K27me3 accelerates disease progression. We conclude that H3K27me2/3 has a leukemia suppressive function in RUNX1 mutant and translocated AML. Our findings have the potential to inform the development of a targeted therapeutic strategy for the treatment of RUNX1mut AML patients.

Keyphrases: Hematopoietic Stem Cells, Acute Myeloid Leukemia, H3.3 K27M/I, Oncohistones, RUNX1, Leucegene
Qualité de l'allaitement chez le nourrisson diagnostiqué avec une ankyloglossie suite à une frénotomie linguale

Objectives. To assess breastfeeding efficacy and mother’s nipple pain over time after lingual frenotomy in infants diagnosed with ankyloglossia. The secondary objective is to assess the impact of timing of the procedure and type of frenum on the outcomes. Methods. Healthy infants under 3 months of age diagnosed with ankyloglossia and difficult breastfeeding were recruited for this cohort study at the Montreal Children’s Hospital. Age of infant and type of ankyloglossia according to Coryllos classification were noted and frenotomy was done if indicated. Breasfeeding efficacy using the Infant Breastfeeding Assessment Tool (IBAT) and nipple pain using Numerical Pain Rating Scale (NRS) were recorded at baseline, 7 days and 1 month post-frenotomy. A 6-month telephone follow-up was used to assess length of breastfeeding.  Results. Seventy infants diagnosed with ankyloglossia were included in this study and received a frenotomy. Sixty-one percent were males and the average age at time of the frenotomy was 17 days.  Ankyloglossia of type 2 (41%) was the most common, followed by type 3 (38%), type 1 (17%) and type 4 (4%). In all types, IBAT and NRS scores improved significantly between baseline and 7 days (p<.001) and between 7 days and 1 month (p<.001). Fifty-five percent of infants were 14 days or less. Infant age at the time of frenotomy and frenum type were not significantly correlated to breastfeeding scores or pain rating. Conclusions. A significant improvement of IBAT and mothers's NRS in infants presenting with ankyloglossia and breastfeeding difficulties were observed after frenotomy, regardless of the timing of the procedure and type of frenum. Ankyloglossia should always be examined in infants with breastfeeding difficulties, and frenotomy may be considered by healthcare providers.  Keywords : Tongue-tie, ankyloglossia, frenotomy, frenuloplasty, breastfeeding problem

Keyphrases: Tongue-tie, Ankyloglossia, Frenotomy, Frenuloplasty, Breastfeeding problem
Le syndicalisme au Québec, enjeux de représentation des membres d’origines ethnoculturelles diverses

This Master’s paper focuses on the various issues surrounding ethnocultural minorities’ participation and representation in Quebec trade unions. The aim of this research is to better understand the determining factors that underlie the implication of ethnocultural minority members within trade unions, as well as to assess the impact of these determinants on the level of inclusion within these organizations. This analysis of trade union inclusiveness and of their associated practices taken in relation to the participation of minority group members was inspired by Poutignat’s typology of trade union practices aimed toward diversity.  In this research, a two-phase approach was adopted. At first, with the objective of filling a major statistical gap regarding ethnic minority representation, the researcher gathered descriptive statistical analysis in order to establish the current state of affairs. Subsequently, twelve semi-directed interviews were conducted with members, representatives and employees of a Quebec-based trade union, this with the intention of identifying the inner workings of minority group member participation within trade unions.  Firstly, our analysis has shown that immigrants are underrepresented within trade unions. The individuals that are most strongly affected are those who have been living in Quebec for less than 10 years, independently of sex, scholarship and employment sector. The Haitian community is the only group in which these statistical findings do not apply. People from this community are not characterized by an underrepresentation in unions, although, conversely, their unionization rate is higher than the reference group i.e. people of French and English Canadian descent. Secondly, three key findings have emerged from the interviews that were conducted. On one hand, people belonging to an ethnic minority are confronted with specific issues that are less likely to affect individuals from the majority ethnic group. On the other hand, three types of determinants appear to have an impact on the participation of people from an ethnic minority group : micro (individual), meso (workplace), and macro (trade union center). Finally, the results of this research suggest that the presence of a significant ethnic minority group and the activism that certain minority group representatives may display are the two main factors that determine the adoption of an inclusive stance by a trade union.

Keyphrases: Discrimination, Unionism, Representation, Discrimination, Minority groups, Ethnocultural minorities
Essai sur la radicalité : les violences faites contre soi

This thesis aims to understand political radicalism through the study of self violence. I worked with three ideal types of violence : the mystical, the ascetic and the charismatic one. In order to analyze these types of political violence, I developed the idea of « way of being in the world » which refers to a particular set of mind, a way of understanding the world and shaping it. The notion gathers, among other things, a political imaginary, a scale of values, a specific cosmogony and a set of choices and acts, which can be violent or not. To elaborate this point and to link it with the concept of self violence, I selected three cases : Mohammed Atta embodies the mystical violence, Bobby Sands and Catherine de Sienne illustrate the ascetic violence and the PKK pictures the charismatic violence.

Keyphrases: Immolation, Violence, Radicalism, Bombing attack, Hunger strike, Ideal type
L’adaptation des travailleurs sociaux en contexte de réorganisation du réseau de la santé et des services sociaux

This thesis explores how social workers in Quebec adapt to organizational change. Mainly it aims to understand the adaptation experiences of the professionals within the health and social services network during the reform, in which was caused by Bill 10 (Act to modify the organization and governance of the health and social services network, in particular by abolishing the regional agencies) (Assemblée nationale du Québec, 2015). Through a qualitative perspective, twelve social workers of the health and social services network of the region of Montreal, participated in a semi-structured interview. Schlossberg's mutli-dimensional model (2011), the 4 S's (situation, self, support and strategies) has been used as conceptual framework. This model allows us to understand the adaptation of the person in process of change. Furthermore, this study helps us to understand the importance of change management in process of adaptation because the impacts can be significant at the personal, professional and organizational levels.

Keyphrases: Adaptation, CISSS, CIUSSS, Transition, Schlossberg, Barrette's reform, Bill 10, Health and social services network, Organizational change, Social work
Bonheur et politique : une étude comparée des provinces canadiennes

This paper builds on happiness studies, and strives to explain the disparities of life satisfaction levels between Canadians. Since 1985, the well-being level expressed by Quebecers has risen considerably more than in other Canadian provinces. Political factors partly explain these provincial gaps, as well as the growth observed in Quebec. Left-wing politics positively affect the overall pursuit of happiness. The reach of the welfare state, the degree of economic regulations and the strength of labour unions movements explain, to some extent, the gap between life satisfaction levels amongst the Canadian federation. The Quebec model, distinct from the rest of Canada, has dealt rather well with the shifts of the previous decades.

Keyphrases: Satisfaction with life, Happiness, Subjective well-being, Canadian politic, Quebec politic, Social policies, Welfare state, Union
Recherche de quarks vectoriels produits par l'échange de gluons lourds dans le cadre de modèles de Higgs composite avec le détecteur ATLAS

Being the missing piece of the Standard Model (SM) for decades, the Higgs boson was finally observed by the ATLAS experiment in 2012. Despite this discovery, it is justified to think that the SM is an effective theory at low energy scale, and one of the physics goal of the ATLAS experiment is to understand the origin of the electroweak symmetry breaking which the SM fails to explain. The technical and logistic challenges necessary for such a discovery makes the ATLAS detector one of the most sophisticated apparatus in the world. As a multipurpose detector, the ATLAS detector is built to investigate physics Beyond the SM and discover new particles. Composite Higgs models (CHM) are extensions to the SM that shed light on some problems left open, such as the mass hierarchy problem. Composite Higgs models also predict the existence of new particles such as vector-like quarks (VLQs). As one the simplest extension to the SM particle content VLQs are actively search for at the LHC.  This thesis presents the results obtained in the search for the single production of VLQs $\BH$ of charge $-1/3$ through the exchange of a heavy gluon $G^*$. Based on a simplified minimal CHM, the search is performed for the process $pp \to G^* \to \BH\bar b/\bar B_\text{H}b \to H\bbbar \to \bbbar\bbbar$. The dataset corresponds to 19.5~$\fb$ of $pp$ collisions at a centre-of-mass energy of $\sqrt s = 8$~TeV. No significant excess of events with respect to SM predictions is observed. Therefore upper limits on the cross section times branching ratio are set. Using a specific benchmark model, a lower limit of 2.0~TeV on the $G^*$ mass is obtained when $\mg = 2\mb$.

Keyphrases: LHC, ATLAS, VLQ, 8 TeV, Composite Higgs, Mass hierarchy problem, Vector-like quarks, Heavy gluon, Single production