NCube/papyrus huggingface dataset:
Étude anatomique de la relation entre les neurones exprimant l’hormone de relâche des gonadotrophines et le nerf terminal lors du développement postnatal de l’opossum (Monodelphis domestica)

While quite immature at birth, the opossum is nevertheless able to crawl from the urogenital opening to a mother's nipple to which it attaches to pursue its development. Sensory information are required to guide the newborn to the nipple and induce attachment. Olfaction is one of the sensory modalities often proposed. However, recent physiological experiments in the laboratory using in vitro preparations suggest that the olfactory system is too immature to influence the newborn behaviors. Furthermore, an immunohistochemical study using a marker of axonal maturity (neurofilament 200kDa, NF200) has shown that the prosencephalon is nearly devoid of mature fibers except for a thin fascicle running from the olfactory bulbs to more caudal areas of the brain. Olfaction is thus unlikely to guide the locomotion of the newborn, but the presence of this fascicle is intriguing and its development is studied in the present thesis. This fascicle is described from the day of birth to the end of the second postnatal week, when NF200 labeling is no more visible in this region. It is also shown that this fascicle superpose with fibers expressing GnRH1, a neurohormone characterizing hypothalamic neurons in the adult. The results indicate that this fascicle is the terminal nerve, and might serve as a pioneer pathway to GnRH1 fibers cells. Until P15, the olfactory cortex was devoid of NF200 projections, supporting that the olfactory systems is too immature to influence the behavior of newborn opossums.

Keyphrases: GnRH1, NF200, Terminal nerve, Olfactory system, Opossum
Influence de la structure du paysage sur les communautés de parasitoïdes de la tordeuse des bourgeons de l’épinette

Improving understanding on how spatial structure influences biological processes is essential to build realistic models and information on the spatial scale at which these processes operate is mainly missing in the literature. Spruce budworm-associated parasitoids offer a great opportunity to investigate the importance of scale on space-related processes. The Côte-Nord region of Quebec, Canada, is currently experiencing a SBW outbreak on a vast extent that had been used to study how landscape structure can influence the parasitism rates on SBW and at which spatial scale. To answer these questions, 20 000 SBW larvae were collected in this region and reared individually to calculate parasitism rates. In this thesis, I examined two specific questions pertaining to spatial variation in SBW parasitism. First, I investigated the spatial scale of response of the parasitoid community as a whole to landscape structure (Chapter 1). Second, I explored how the spatial scale of parasitoids’ responses to spatial structure varies as a function of a morphological trait related to flight (i.e., wing load). I explore this relationship between wing load and scale of response using the five most common species of parasitoids (Chapter 2). The results from the first chapter suggest that the community of parasitoids is responding to landscape at a scale corresponding to buffers of 2000-2500 meters radius. At this scale, the most important explanatory variables are landscape heterogeneity and the age of outbreak. Greater heterogeneity was linked to higher level of parasitism rates in SBW larval stages whereas age of outbreak favoured parasitism in pupae. These results indicate that there exist important differences in how parasitoids respond to spatial heterogeneity and that the scale at which they respond may depend on the species. In my second chapter, I hypothesised that variation in the spatial scale of response could be related to varying species dispersal capacities. Parasitism events were therefore divided in three groups according to the wing load of the responsible parasitoid (i.e., light, medium and heavy wing load). This division showed that a greater proportion of variance in parasitism rates could be explained in models based on dispersal-related trait than in a model considering the community as a whole. Moreover, the group with the lightest wing load (and supposedly the greatest dispersal capacity) had the greatest spatial scale of response to landscape as expected. The results presented in this thesis could have implication in forest management to reduced SBW impact but also in other modelling researches where there is a general lack of empirical data to support model building.

Keyphrases: Boreal forest, Dispersal ability, Forest management, Heterogeneity, Landscape heterogeneity, Landscape structure, Parasitism rates, Parasitoids, Pest outbreaks, Spatial scale, Spruce budworm, Wing load
Au-delà de l'appât du gain et des pommes pourries : corruption organisationnelle et conflits d'intérêts à la FTQ

Individuals who are caught participating in organizational corruption are often dismissed as bad apples who forgo ethics to achieve monetary gain. However, research on the subject of organizational corruption has shown that corrupt individuals tend to not view themselves as corrupt. Furthermore, initiation to corrupt practices is achieved through socialization in corrupt organizations. Thus, the corruption of an organization is not carried out by a single individual and cannot be explained as such. Our research is an interpretation of instances of organizational corruption and conflicts of interest identified by the Commission of Inquiry on the Awarding and Management of Public Contracts in the Construction Industry (CEIC) as having occurred at the Quebec Federation of Labour (FTQ). According to a model developed by Anand, Ashforth, and Joshi (2004), corruption is perpetuated in organizations because of two mutually reinforcing processes. First, strategies to rationalize corrupt acts are used by leaders and members of the organization to simultaneously justify and neutralize the feelings of guilt normally associated with a deviant act. Second, socialization strategies are used by corrupt members of the organization to initiate newcomers to these rationalization strategies. If the socialization succeeds, the newcomer will integrate the rationalization strategy into his discourse and the organizational corruption will be perpetuated. The goal driving this research is to demonstrate how methods of analysis that go beyond the traditional “Bad Apple” theory and the profit motive and that focus on the social dimension of corrupt acts can offer a richer and more in-depth understanding of the inner workings of organizational corruption and conflicts of interest.

Keyphrases: Construction, Organizational corruption, Conflicts of interest, Union, Construction, Quebec, Commission of inquiry on the awarding and management of public contracts in the construction industry (CEIC), Quebec federation of labor (FTQ)
Optimisation du traitement numérique de signaux générés dans un cristal de ICs

The goal of this work is to optimize the digital processing of signals generated in the CsI crystal of an electromagnetic calorimeter, in the context of high counting rate experiments like Belle II. The scintillation from the crystal is converted into an electronic signal by a Hamamatsu photopentode with a gain of 150±2 electrons per photoelectron, to then be amplified by a preamplifier. The signal is then shaped by the shaper, a CR-(RC)^4 active filter, before it is digitized by an ADC, to be processed by the DSP. Using reference shapes, the DSP can extract the energy deposited by an incident particle and the time of occurence of it going through the crystal.   To define the reference shapes, we determined that of the three approaches studied, which are experimental average shapes, the analytical function for an active filter and the sum of 3 gaussian functions, the best results were achieved using the last one, both with the pulse generator and the CsI crystal. Also, a conversion formula has been established to convert the measured signals' amplitudes into deposited energy in the crystal, despite a narrow dynamic range.  We also observed average propagation times of the scintillation through the crystal of 47±4 ns and 3,4±0,5 $\mu$s, related to the two accessible excitation states of the CsI atoms, but also to the crystal's geometry, the reflections of photons on its surface and the reaction time of the electronics circuits, which make those scintillation times appear longer.

Keyphrases: ICs, Shaper, DSP, Belle II, Electromagnetic calorimeter, CsI, Digital processing
Évaluation des justifications normatives menant à une condamnation morale de la pornographie selon une éthique minimaliste

Pornography is often morally disapproved ethically, socially, politically and legally. In this research, we will ask ourselves on the normative justifications leading to a moral condemnation of pornography are valid according to a minimalist ethic from Ruwen Ogien. First, we will try to define the concept. Thereby, we will see that it is difficult to establish a clear and objective definition because pornography is often accompanied by moral judgments. This attempt to present a definition is problematic on the moral level, because the standards to qualify pornography is based on subjective judgments. Then, we will clarify the minimalist ethic and the substantial conception of sexual well being of Ruwen Ogien to suggest that the criterion of consent is essential to the ethical level and it cannot be bypassed. Still according to a minimalist ethic, we will see that censorship should be applied minimally limiting to the principle of non nuisance. Sexual objectification that offers modern pornography is often targeted as a moral issue. According to the minimalist ethic, although modern pornography shows women as sex objects, it should not be judged morally. Now, all the justifications leading to moral condemnation are not valid if we rely on the substantial conception of sexual well being, freedom of offence and the principle of non nuisance from Ruwen Ogien.

Keyphrases: Pornography, Post- pornography, Minimalist ethics, Consent, Censorship, Sexual objectification
La webométrie en sciences sociales et humaines : analyse des données d’usage de la plateforme Érudit

This study explores the usage of open access (OA) and delayed OA journals in the social sciences and humanities hosted by the journal platform Érudit. Relying on Érudit’s download data, the goals of the study are: 1) to describe the usage of scholarly articles, 2) to examine download patterns of national and international users, and 3) to analyze the effect of OA policies on journal download rates. The study is based on an analysis of 39,437,659 downloads, which were extracted from 999,367,190 HTTP requests stored in Érudit’s log files between 2010 and 2015. The results show that the majority of users came from Quebec, France and other French-speaking countries, and that most users access articles through Google. Download patterns varied between countries: although articles were most frequently accessed during working hours, US users were more active in the evening, at night and during weekends than Canadian and French users. The study also demonstrates a clear OA advantage, as freely available articles were downloaded more frequently than delayed OA articles affected by an embargo, and downloads per article increased substantially after embargos ended. This effect was less pronounced for Canadian users, who often have access to Érudit journals via institutional subscriptions and are thus not affected by the embargo periods. The results show the positive effect of OA on knowledge dissemination in Canada as well as internationally, and emphasize the importance of national journals in the social sciences and humanities.

Keyphrases: Érudit, bibliometrics, webometrics, usage data, downloads, social sciences and humanities, Quebec
HERG-BRET / Évaluation par la technologie BRET de l'interaction moléculaire avec le canal potassique Kv11.1 responsable d'arythmies ventriculaires médicamenteuses

The Kv11.1 channel is directly involved in cardiotoxic adverse effects since its inhibition is responsible for a prolongation of the QT interval. In 2006, Health Canada established a guideline that constrains drug developers to a preclinical evaluation of QT prolongation risks for new molecules and their metabolites. The gold standard method (patch-clamp) consists in electrophysiology measurements on cultured cardiomyocytes for a brief exposition to the tested compound (<30min). Even though this method is the most reliable, it only allows the identification of molecules that inhibit the channel by preventing ions from traveling through the pore (acute effect).  The HERG-BRET method aims to identify molecules that can interact with Kv11.1 and alter its vesicular transport as a proxy for inhibiting the activity of the channel (chronic effects). This study attemps to determine if a BRET-based cellular localization assay will allow a high throughput screening and a better evaluation of the affinity of pharmaceuticals compounds with hERG, in comparison to alternative methods. In the HERG-BRET model, a fusion protein generated with the gene sequence for hERG and the one for the renilla luciferase (energy donor) is stably expressed in a HEK 293 cell line. The same cell line also stably expresses a green fluorescent protein (energy acceptor) that is anchored at the plasma membrane. The energy transfer that occurs between the donor and the acceptor suggests that hERG is located at the membrane. Variations of BRET ratios following a 16 hours inucabtion with a compound reflects the compound’s effects on Kv11.1’s translocation. Twenty-five compounds that have been previously characterized in the literature were tested: 12 were categorized as pharmacological chaperones, 4 as traffic inhibitors, 1 as an inhibitor that undergoes both effects and 8 remain uncategorized.   The biosensor’s behavior towards the tested compounds suggests that the HERG-BRET method cannot be used alone to assess cardiotoxic liability, but it can bring interesting facts to our attention regarding the nature of the interaction between the hERG subunits of Kv11.1 and a tested compound.

Keyphrases: Kv11.1, hERG, BRET, QT interval prolongation, Inhibition mechanisms, In vitro preclinical evaluation, Patch-clamp
La prise de médicaments antiasthmatiques pendant la grossesse et le risque de diabète gestationnel

Asthma is a chronic respiratory disease that is frequent in pregnancy with a prevalence of 8%. Maternal asthma is known to increase the risk of gestational diabetes (GD), but the evidence is scarce regarding the impact of asthma controller medications on the risk of this pregnancy complication. A research study was developed to evaluate whether the risk of GD is associated with the dose of inhaled corticosteroids (ICS) or the use of long-acting β2-agonists (LABA) in pregnant women with asthma. To achieve our goals, we used a case-control design nested within a cohort of pregnancies from asthmatic women who delivered between 1998 and 2010 reconstructed from the linkage of two administrative databases from the province of Québec (Canada): Maintenance et exploitation des données pour l’étude de la clientèle hospitalière (MED-ECHO) and Régie de l’assurance maladie du Québec (RAMQ). GD was defined as at least one recorded diagnosis of gestational or chronic diabetes or a prescription for an antidiabetic medication filled after week 20 of gestation. Each case was matched to 30 controls according to calendar year and gestational age. Generalized estimating equation models were used to estimate odds ratios  (aOR) and 95% confidence interval (95% CI) of GD adjusted for asthma severity and control and other risk factors of GD. The association between GD and ICS doses was estimated among women unexposed to LABA, while the association with LABA was estimated among women exposed to ICS at the date of the outcome for cases and the date of selection for controls. The cohort included 12 587 pregnancies from asthmatic woman and 1001 cases of GD (8.0%) were identified. The risk of GD showed no trend towards a higher risk with increasing dose of ICS among non-users of LABA with aOR (95% CI) of 0.95 (0.74 to 1.23) for low doses (<251 μg in fluticasone propionate equivalents), 1.14 (0.80 to 1.64) for medium doses (251 to 500 μg), and 1.13 (0.71 to 1.81) for high doses (>500 µg) of ICS. Moreover, the risk did not increase when LABA was added to an ICS (aOR=0.99; 95% CI: 0.69 to 1.44). Our results provide further evidence for the safety of LABA and ICS doses during pregnancy, but more studies are needed to examine the potential association between higher ICS doses and the risk of GD.

Keyphrases: Asthma, Gestational diabetes, Pregnancy, Asthma controller medications
Unfolding RNA 3D structures for secondary structure prediction benchmarking

Ribonucleic acids (RNA) adopt complex three dimensional structures which are stabilized by the formation of base pairs, also known as the secondary (2D) structure. Predicting where and how many of these interactions occur has been the focus of many computational methods called 2D structure prediction algorithms. These methods disregard some interactions, which makes it difficult to know how well a 2D structure represents an RNA structure, especially when large amounts of base pairs are ignored. MC-Unfold was created to remove interactions violating the assumptions used by prediction methods. This process, named unfolding, extends previous planarization and pseudoknot removal methods. To evaluate how well computational methods can predict experimental structures, a set of 321 RNA monomers corresponding to more than 4223 experimental structures was acquired. These structures were mostly determined using nuclear magnetic resonance and X-ray crystallography. MC-Unfold was used to remove interactions the prediction algorithms were not expected to predict. These structures were then compared with the structured predicted. MC-Unfold performed very well on the test set it was given. In less than five minutes, 96% of the 227 structure could be exhaustively unfolded. The few remaining structures are very large and could not be unfolded in reasonable time. MC-Unfold is therefore a practical alternative to the current methods. As for the evaluation of prediction methods, MC-Unfold demonstrated that the computational methods do find experimental structures, especially for small molecules. However, when considering large or pseudoknotted molecules, the results are not so encouraging. As a consequence, 2D structure prediction methods should be used with caution, especially for large structures.

Keyphrases: Tertiary structure, Constraint satisfaction problem
Modules réflexifs de rang 1 sur les variétés nilpotentes

Let G be a simple, connected, simply connected complex linear algebraic group with parabolic subgroup P  G and nilpotent ideal n  p. The proper collapsing map G  x P n  = Gn factors through the normal affine variety N := SpecC [G  x P n] which is called a nilpotent variety. Assuming the collapsing is generically finite, we describe the equivariant divisor class group of N using rank 1 reflexive equivariant C[N]-modules. A representative of each class may be chosen as global sections of a line bundle over G x  P' n' where G x  P' n' =  Gn' is a possibly distinct collapsing that factors through the same nilpotent variety. Assuming either G is of type A or the collapsing comes from specific weighted Dynkin diagrams,we showthat each representative arise from a weight that may be chosen dominant. Moreover, if the module represents a torsion element within the class group, then it is Cohen– Macaulay and we deduce a cohomological vanishing theorem.

Keyphrases: normal nilpotent variety, class group, reflexive module, vanishing theorem, cohomology of line bundles, cotangent bundle of a flag variety
Détection et amélioration de l'état cognitif de l'apprenant

This thesis aims at detecting and enhancing the cognitive state of a learner. This state is measured by the ability to acquire new knowledge and store it in memory. Focusing on three types of environments to enhance reasoning: environment Logic, serious game LewiSpace and intelligent serious game Inertia. Physiological measures (in particular the electroencephalograms) have been taken in order to measure learners’ engagement and mental states. Improving learners’ reasoning is key for successful learning process. In a first part, we present the implementation of logic environment. We present statistics on this environment, with data collected during an experimental study. Three types of data: engagement, workload and distraction, these measures were effective and can predict and classify learner’s performance. In a second part, we describe the LewiSpace game, aimed at teaching Lewis diagrams. We conducted an experimental study and collected data from electroencephalograms, emotions and eye-tracking software. Combined with machine learning algorithms, it is possible to anticipate a learner’s need for help using these data.  In a third part, we finish by presenting some assistance strategies in a virtual reality game called Inertia (to teach Physics). The latter adapts according to two measures extracted from electroencephalograms (frustration and engagement). Based on our study, we were able to enhance the learner’s success rate on game missions, by improving its cognitive state.

Keyphrases: Cognitive environment, Educational game, Virtual reality game, Electroencephalogram, Eye tracker, Electrodermal activity, Emotions, Need of help, Machine learning
Visualisation de données dans le domaine de l’E-recrutement

The large amount of data available nowadays, so-called Big Data, requires a relevant analysis to derive information and get insights for decision making. Data visualization is an effective way to convey this information interactively and synthetically. This work, which is part of BPP Project, a collaboration between the RALI and LBJ, aims to meet this need by implementing a dashboard for visualization of job offers on the web. These offers consist of several sections: title, company, description, etc. Some information contained in the description cannot be extracted directly. Thus, for the extraction of skills from the description of an offer, we use machine learning techniques, especially Conditional Random Fields (CRF) used for sequence labeling. We also tested the ability of those models to find skills in the description of the offer with partial labeled training dataset, as we do not have a complete list of skills required for labeling, and also because new skills appear constantly.

Keyphrases: E-recruitment, Data visualization, Information extraction, Machine learning