NCube/papyrus huggingface dataset:
Characterising (pre-)mrnp organisation at different stages of gene regulation using single-molecule microscopy

mRNAs act as the central molecules in gene regulation, helping convert the genetic information stored in the DNA to functional proteins. As a single-stranded polymer, hundreds to thousands of nucleotides in length, mRNAs can form extensive secondary and tertiary structures and, together with proteins, are packaged into assemblies called messenger ribonucleoproteins (mRNPs). The 3D organisation of (pre-)mRNPs influences many aspects of what happens to them, including regulating their processing, export and translation in the cytoplasm. Despite their significance, our understanding of the structural organisation of (pre-)mRNPs in vivo is minimal, as is our comprehension of the principles that govern it.  During my PhD, I have developed an RNA-centric view on (pre-)mRNP organisation. For this, I have established an approach combining single-molecule RNA in situ hybridisation (smFISH) with structured illumination microscopy (SIM) and used it to study mRNP organisation in the nucleus and cytoplasm. Our results suggest that (pre-)mRNP organisation is altered at various stages during its lifetime. We show that (pre-)mRNP packaging starts co-transcriptionally, with introns organised into compact conformations. This organisation is altered during the course of transcription as the polymerase travels along the gene, finally assembling an intron with the ends in proximity in a spliceosome dependent manner, suggesting that co-transcriptional intron organisation could be critical in determining its excision. Once released, mRNPs have a compact linear organisation in the nucleoplasm and possibly a rod-like conformation. mRNP organisation in the cytoplasm is influenced by its translational status. While translation opens up mRNPs, separating the ends of the mRNA, translation inhibition and release of ribosomes, or recruitment to stress granules result in mRNPs having a highly compact structure. Interestingly, we rarely find mRNAs with the 5’ and 3’ ends in proximity, suggesting that closed-looped translation is not a universal state for all translating mRNAs. Together, our results provide a unique and essential view of mRNP organisation in cells and reveal important insight into the role of mRNP conformation in regulating translation and mRNP processing.

Keyphrases: mRNP, pre-mRNP, mRNP organization, single molecule microscopy, closed-loop model, smFISH, mRNP architecture, mRNA structure, 5’-3’ communication, mRNA translation, mRNA splicing, RNA compaction, RNA imaging, super-resolution microscopy, U1-Pol II tethering, intron looping
Renforcement de la sécurité à travers les réseaux programmables

The original design of Internet did not take into consideration security aspects of the network; the priority was to facilitate the process of communication. Therefore, many of the protocols that are part of the Internet infrastructure expose a set of vulnerabilities that can be exploited by attackers to carry out a set of attacks. Distributed Denial-of-Service (DDoS) represents a big threat and one of the most devastating and destructive attacks plaguing network operators and Internet service providers (ISPs) in a stealthy way. Software defined networks (SDN), an emerging technology, promise to solve the limitations of the conventional network architecture by decoupling the control plane from the data plane. On one hand, the separation of the control plane from the data plane allows for more control over the network and brings new capabilities to deal with DDoS attacks. On the other hand, this separation introduces new challenges regarding the security of the control plane. This thesis aims to deal with various types of attacks including DDoS attacks while protecting the resources of the control plane. In this thesis, we contribute to the mitigation of both intra-domain and inter-domain DDoS attacks, and to the reinforcement of security aspects in SDN.

Keyphrases: Blockchains, Software-defined networking (Computer network technology), Wide area networks (Computer networks), Penetration testing (Computer security), Supervised learning (Machine learning), Blockchains
La métaphore vacante : concurrence des images entre 1929 et 1936 : photographie, surréalisme, revue, publicité

This thesis in visual history revisits Surrealist photography from interwar Paris in order to demonstrate the role of periodicals and advertising as agents (dispositifs) of photographic production and dissemination between 1929 and 1936. During a period which I refer to as the “second birth of photography,” I identify a previously overlooked relationship between the dissemination strategies used for photography in periodicals produced in the Surrealist context and the logics of the spectacle that governed the intensified circulation of images through print media. To explore this relationship, I draw upon the concept of competition (concurrence), which I elaborate by way of a pragmatic and energetic approach inspired by theories of the “iconic turn” (such as W. J. T. Mitchell’s), by Jean-François Lyotard’s idea of the dispositif, and by intermedial studies of the kind practiced by the Centre de Recherches sur l’Intermédialité (arts, lettres, techniques).  Adopting the tenets of microhistory, this thesis is structured around a series of case studies involving varied configurations between photography, Surrealism, the periodical and advertising. I offer close readings of the Surrealist periodical Le Surréalisme au service de la révolution (1930–1933), the first publication years of Minotaure (1933–1935), as well as the Électricité portfolio (1931), an advertising commission completed by Man Ray, and the advertising projects for Pétrole Hahn (1933–1935) produced by the Kéfer-Dora Maar studio. My analysis of this carefully chosen body of works sheds new light on the medial relations shaping the vitality of photographic images in the context of an intense visual proliferation. By proposing new conceptual tools to interpret visual sequences and image circulation, the thesis contributes to current conversations in visual studies regarding periodicals and the dissemination of photographs. The history of Surrealist photography I offer, with its novel concern for the energetics of images, also demonstrates the value of continuing to re-evaluate historical avant-gardes in the light of methodological innovations.

Keyphrases: Photography, Surréalisme, Surrealism, Advertising, Periodical, Intermédialité, Intermediality, Iconic turn, Visual history, Dispositif, Man Ray
Les effets du processus de parrainage sur les dynamiques conjugales et les parcours de vie

This thesis focuses on the effects of the sponsorship process on marital dynamics and life courses. Based on a qualitative and interdisciplinary research approach, 20 participants, 7 men and 13 women, who had a sponsorship experience as a sponsor or a sponsored spouse, were interviewed. In this thesis, we explore the effects on conjugal dynamics in two key moments: 1) from the beginning of the sponsorship application process to obtaining the permanent residence visa, and 2) during the sponsorship undertaking of three years. We also document the experiences of a marital separation that occurs during the sponsorship undertaking. The vertical and cross-sectional analysis method used in this thesis made it possible for us to report on the diversity of pathways by articulating the experience of the sponsorship process, in particular with migration trajectory, marital composition, gender and ethnicity. If, at first glance, it seemed obvious that sponsorship creates inequality in couples by positioning the sponsored person under the financial responsibility of his or her sponsor, it turned out that the analysis of conjugal dynamics was more complex. Finally, in the light of the results of the study, we propose a typology of typical pathways that reflects both the diversity of pathways and levels of influence that the sponsorship process can produce on conjugal dynamics.

Keyphrases: Immigration, Conjugal relationship, Sponsorship, Marriage migration, Life course
Overcoming conversion therapy : a qualitative investigation of experiences of survivors

Sexual orientation and gender identity and expression change efforts (SOGIECE)—often referred to as conversion therapy—are practices that aim to change, deny, or suppress transgender and non-heteronormative sexual orientations, gender expressions and gender identities. SOGIECE are ineffective and associated with negative psychosocial consequences. This qualitative study follows an interpretative description design to explore how individuals who have experienced SOGIECE recover from these practices. We conducted in-depth interviews with 20 Canadian adult participants with experiences of SOGIECE. Using thematic analysis of the data, three overarching themes were derived pertaining to participants’ recovery from SOGIECE: 1) rebuilding social support and finding strength in lesbian, gay, bisexual, transgender, queer, and Two-Spirit (LGBTQ2S+) and LGBTQ2S+-affirming communities; 2) overcoming SOGIECE through affirming therapy and healthcare support; and 3) managing SOGIECE instigators. Based on these findings, we offer recommendations to facilitate the recovery process of people who experience SOGIECE.

Keyphrases: LGBTQ2S+ people, Sexual orientation, Gender identity, Conversion therapy, Mental health
Étude de l’effet neuro-protecteur de polyphénols issus de la Pomme-Grenade ainsi que de leurs dérivés métaboliques

Nowadays, a myriad of beneficial effects is attributed to dietary polyphenols. Most of these claims are based on in vitro studies, some in vivo studies, and almost never on clinical trials. It is increasingly realized that the interest of polyphenols does not only lie in their antioxidant power but also in their ability to target multiple molecular pathways such as inflammation. In addition, many studies are beginning to take into account the bioavailability of polyphenols in the body and their interaction with the gut microbiota. That's why in addition to two polyphenols from Pomegranate, we looked at two of their metabolic derivatives. Almost no study has examined the effect of these molecules in the context of neurodegenerative diseases. To do this, we tested punicalagin, ellagic acid, urolithin A and urolithin B on C. elegans models of ALS and Huntington's disease that had motor phenotypes, neurodegeneration and inflammation. Furthermore, we used a mouse model that underwent an axotomy of the optic nerve to confirm the neuroprotective power of urolithin A. Our results showed that these compounds in different proportions were able to reduce the neuronal toxicity of proteins. related to ALS and HD and thus decrease the levels of paralysis and neuro-degeneration of our C. elegans models. In parallel, we observed that this neuroprotection was done through a reduction of the inflammation and for urolithin A an improvement of the morphology of mitochondria via mitophagy. Lastly, we found that urolithin A was able to promote neuronal survival in mice as a result of optic nerve injury. To conclude, this study by its in vivo approach to multiple neuro-degenerative diseases reinforces existing evidence of the beneficial effect of pomegranate consumption and encourages the pharmacological use of urolithin A.

Keyphrases: Neuro-degenerative diseases, Pomegranate, Polyphenols, Metabolic derivatives, Neuroprotection
Développement d’un modèle conceptuel pour la pratique d’activités de pagaie adaptées pour des personnes utilisant un fauteuil roulant comme principal mode de locomotion

Individuals with physical impairments and related disabilities who use a wheelchair as their primary mode of locomotion (WCUsers) face challenges in their daily lives that interfere with meaningful recreational and leisure participation. This accelerates the development or exacerbation of physical health and psychological well-being difficulties, thus creating a vicious cycle of inactivity. Emerging evidence suggests that adapted physical activity (APA) allows WCUsers to mitigate, even overcome, these difficulties. Nowadays, though broad ranges of adapted sports are available, adapted paddling activities have received limited attention. Identifying and modeling the factors influencing their practice remains crucial to further promote adapted paddling activities. This study aimed to develop a novel conceptual model of factors influencing the practice of adapted paddling activities using a four-phase process: 1) the systematized search of the literature and a synthesis of currently-available conceptual models in APA practice, 2) the conceptualization of a preliminary model for the practice of adapted paddling activities, 3) the validation of its construct and content by three APA experts and two independent scientific experts to co-create the final model (i.e., Montreal Model of Adapted Paddling Activities – M2APA) and 4) the testing of the applicability of the M2APA with three WCUsers who previously practiced adapted paddle boarding. Based on these findings, the M2APA offers a comprehensive model allowing one to map key personal and environmental factors needing consideration for the practice of adapted paddling activities. Moreover, the M2APA provides insights to promote participation into adapted paddling activities and, ultimately, strengthen social inclusion of WCusers.

Keyphrases: Adapted physical activity, Disability, Framework, Health promotion, Impairment, Occupational therapy, Paddling, Physical therapy, Rehabilitation, Wheelchair
De la conception prospective et innovante dans les organisations municipales québécoises : vers une régénération des routines en urbanisme ?

Ecological and digital transitions, along with concerns over social inequalities, signal the advent of complex new challenges for contemporary cities. These changes raise the issue of the dynamic capability of urban planners: more specifically, their ability to review their tools and planning routines in urban projects in order to explore the potential of new paradigms of collective action and foster innovative transition paths for cities. European companies, especially in public transportation, have responded to this challenge, with convincing results, by developing tools based on innovative design theories. One of these methodological tools, the Definition-Knowledge-Concept-Proposition (DKCP) process, was used to generate a new range of planning options for three urban districts in Montreal, Canada. The traditional planner’s routine generally focuses on a single activity in the process, the formulation of propositions (Phase P), by slightly adapting former projects to the local context and rules. However, the future urban planners’ routine should include new capabilities for managing upstream stages of projects in the form of a succession of DKCP phases. The need to tackle the complex challenges of the 21st century city opens the way to a new professional identity: the “innovative urban planner”.

Keyphrases: Urban futures, Strategic foresight, Routines, Rule-based design, Innovative design
Classification angiographique d’anévrismes cérébraux traités par voie chirurgicale ou endovasculaire : revue systématique et étude d’accord inter & intra-observateur

INTRODUCTION Intracranial aneurysms are a medical condition associated with serious morbidity and mortality when ruptured. They are mainly treated with surgical clipping or endovascular coiling, and randomized clinical trials comparing both treatments often use angiographic results as a surrogate outcome of treatment success. The development of a standardized, reliable method to report angiographic results, applicable to both treatments using any angiographic modality (Conventional [CA], Computed tomography [CTA], or magnetic resonance [MRA] angiography) is needed. We sought to systematically review existing methods of classifying treated aneurysms and to assess the inter-/intra-rater reliability of a new angiographic grading scale, as well as its clinical relevance.  METHODS We conducted two separate systematic reviews in 5 databases to collect post-clipping and post-coiling grading scales, along with their reliability when reported. The CA of 60 cases of clipped (n=30) and coiled (n=30) aneurysms were independently evaluated by 19 raters of various backgrounds and experiences using a new 3-grade scale. Raters were also asked how they would manage each case (delayed, close follow-up, or retreatment). Fifteen raters performed a 2nd evaluation of the same cases (in a permuted order) at least one month apart. The same methodology was used to study the reliability of the scale when 60 noninvasive angiography cases of clipped (30 CTA) or coiled (30 MRA) aneurysms were evaluated by 24 raters. Inter and intra-rater agreements were assessed using Krippendorff’s Alpha statistics (aK), and the relationship between occlusion grade and clinical management using Cramer’s V test.  RESULTS The systematic reviews found 70 grading scales (44 post-clipping, 26 post-coiling) with significant heterogeneity in terms of reliability (kappa values from 0.12 to 1.00), raters, and patients. Overall inter-rater agreement for the grading scale was substantial for CA results (aK=0.76; 0.67–0.83) as well as for noninvasive results (aK=0.63; 0.55–0.70); regardless of background, experience, or treatment used. A strong relationship was found between angiographic grades and management decisions (V=0.80±0.12 for CA; V=0.77±0.14 for CTA/MRA [p<0.001]).  CONCLUSION A standardized 3-grade scale was found to be a reliable and clinically meaningful tool to compare the results of clipping and coiling of aneurysms using any angiographic modality. It could be used as a valid tool to adjudicate results of comparative randomized trials, and to standardize the reporting of aneurysm treatments.

Keyphrases: clipping chirurgical, Intracranial aneurysm, interrater reliability, surgical clipping, endovascular coiling, grading scale, catheter angiography, computed tomography angiography, magnetic resonance angiography
Foliar spectra accurately distinguish the invasive common reed from co-occurring plant species throughout a growing season

Invasive plant species are one of the main drivers of biodiversity change in terrestrial ecosystems. Accurate detection of exotic species is critical to monitor on-going invasions and early detection of incipient invasions is necessary to prevent further spread. At present, surveillance methods of biological invasions allow to track the spread of invaders across geographic ranges, but less attention has been given to invasive species monitoring across time. Remote sensing platforms, capable of providing detailed information on foliar trait variations across time and space, are uniquely positioned for monitoring invasive plants in real time. Temporal changes in foliar traits are expressed in a species spectral profile through specific absorption features related to variation in photosynthetic pigments and chemical constituents driven by phenology. Thus, variations in a plant’s spectral response can be used to improve the identification of individual species. One of Canada’s most problematic invaders is the common reed, Phragmites australis (Cav.) Trin. ex Steudel subspecies australis, whose spread threatens biodiversity in wetland ecosystems in North America. Determining the time of year when the invader is spectrally and functionally more distinct from other plants in the community would be central to better management of common reed. To do so, we collected a time-series of foliar traits and high-resolution leaf spectral data over the course of a growing season at Boucherville, Quebec, Canada, to determine the spectral separability of the invader from co-occurring species and how its detection varies over time. Our results revealed that leaf-level spectroscopy distinguished Phragmites and co-occurring species with > 95% accuracy throughout the growing season – a promising result for the future remote detection of invasive plant species.

Keyphrases: Leaf spectroscopy, Invasive plant species, Phragmites, Phenology, Wetlands
Covariates of turnover intentions of teleworking call center agents in Québec during the COVID-19 pandemic

Teleworkers from multiple call centers in Québec provided questionnaire data about their various job demands (measured by organizational stressors, mental load, and emotional load), job resources (measured by independence in the work, participation, and relationship with supervisors) as well as for outcome measures of job satisfaction, organizational commitment, and turnover intentions. Hypotheses structured by the JD-R model were tested using correlational methods. As predicted, job resources were significantly related to both job satisfaction and organizational commitment perceived by the sample. Job demands predicted job satisfaction, but they did not relate to organizational commitment. The theoretical and practical implications of these results were discussed.

Keyphrases: teleworkers, call centers, turnover intentions, job satisfaction, organizational commitment
Electrophysiological markers for hostile attribution bias among individuals with anxiety

Background: Anxiety disorders constitute the most prevalent subgroup of mental health conditions. While anxious individuals are more widely known as being socially withdrawn and shy, recent research highlights a rather non-prototypical image, one that is aggressive. The main goal of this event-related brain potentials (ERPs) study is to augment our knowledge of the neurophysiological responding of hostile attribution biases of anxious individuals to ambiguous situations. Methods: Using pre-collected data from a sample of 68 undergraduate and community-based adult participants, this study aims to explore the N400 deflection utilising Gagnon et al.’s (2016) Hostile Expectancy Violation Paradigm with anxious individuals, and whether the N400 deflection persists after controlling for aggression. Results: A more negative amplitude was observed in response to a critical word that mismatched rather than matched with the character’s expected hostile intention. Regression analyses revealed that anxiety scores negatively predicted the N400 following the mismatched expected hostile intention while controlling for reactive aggression suggesting that the violation of hostile expectancy about the intention behind an ambiguous provocative behavior is more pronounced among anxious participants. Conversely, in the hostile condition, the overall model was significant, although anxiety scores did not account for the overall effect, reactive aggression did. Conclusion: This study provides preliminary evidence that anxiety symptoms are uniquely related to hostile attribution bias independent of reactive aggression. Future research should aim to replicate these findings with a clinically diagnosed sample of individuals with anxiety disorders.

Keyphrases: Anxiety, Aggression, Hostile Attribution Bias, N400, Hostile Expectancy Violation Paradigm, Electrophysiology