NCube/papyrus huggingface dataset:
Un nouveau rôle de la voie Hippo dans la synthèse des gonadotrophines

The pituitary gland is responsible for regulating many physiological processes. Through the secretion of gonadotropins FSH and LH, the pituitary is considered a major regulator of reproduction. These hormones are dimeric glycoproteins composed of a common α subunit (CGA) and unique β subunits (LHβ and FSHβ), which confer biological specificity. The synthesis of FSH and LH at pituitary gonadotrope cells depends mostly on the expression of key genes as Fshb and Lhb. GnRH, produced by the hypothalamus, is the primary regulator, but other factors such as activins, which signal through proteins called SMADs, participate in this regulation. The activity of the SMAD pathway can be altered by crosstalk with the Hippo pathway in several tissues and cell types, but whether the Hippo pathway is involved in regulating gonadotropin synthesis has not been determined. The core Hippo signaling pathway consists of a kinase cascade that regulates the activity of the functionally redundant transcriptional co-regulators YAP and TAZ. To elucidate the roles of YAP/TAZ in gonadotropin synthesis and secretion, we decided to use a conditional gene targeting approach (cKO), which allowed us to promote the depletion of Yap/Taz specifically in the gonadotrope cells. Such conditional deletion resulted in increased circulating levels of FSH and LH in male mice, along with a slight sperm density increase. cKO female mice had augmented circulating LH (but not FSH) levels, which were associated with a hyperfertility phenotype characterized by higher ovulation rates and larger litter sizes. Surprisingly, the loss of YAP/TAZ in gonadotropes did not appear to affect key gonadotropin synthesis-related genes, but both basal and GnRH-induced LH secretion was increased in pituitary cells from cKO mice cultured in vitro. Similar results were obtained using pharmacological inhibition of YAP/TAZ in LβT2 gonadotrope-like cells in vitro. Together, these results indicate that YAP/TAZ suppress gonadotropin release (particularly LH) in gonadotrope cells and reveal a completely novel role of the Hippo pathway in mammalian reproduction.

Keyphrases: YAP, TAZ, Gonadotropins, cKO mice, Fertility
Revue systématique sur les valeurs estimées de paramètres influençant la détection de la tuberculose bovine chez les cervidés d’élevage

Bovine tuberculosis is a zoonotic disease mostly transmitted by inhalation of contaminated material. This disease leads to the economic losses (e.g. condemnation of meat from infected animals at the abattoir) and impede trade since countries can stop importing live cervids from tuberculosis endemic countries. In Canada, the control of bovine tuberculosis started in 1923 in cattle and then was implemented in farmed cervids in 1989. This program is composed of surveillance, response to the outbreaks and movement control of cervids. The capacity of detecting this disease during the surveillance activities depends on the performance of diagnostic methods used at each step of the component of the surveillance system. At the abattoir, the inspection is carried out by visual inspection of organs and carcass and diagnostic tests carried on abnormal tissues by using histopathology, PCR or culture. In live cervids, the detection is carried out through skin or serological testing. The main objective of this project was to provide, through a systematic literature review, the estimates of main parameters that can influence the probability of detecting bovine tuberculosis in the context of surveillance activities in farmed cervids at the abattoir and in live cervids. The probability of presence of macroscopic lesions estimated by studies ranged from 20% to 100% while the estimate of probability of detection of lesions was greater than or equal to 90%. The estimate of sensitivity of diagnostic tests used during bovine tuberculosis surveillance at the abattoir (histopathology, PCR and culture) ranged from 63.6% to 98.6%. In live cervids, studies that investigated the performance of serological tests reported an estimate of sensitivity ranging from low to high (1.4% to 100.0%)  while skin tests were reported to have a sensitivity ranging from 65.0% à 100.0%. Given that the stage of the disease affects the performance of most diagnostic test while that variable was not reported by studies, it was difficult to compare  the performance of the various tests. Bovine tuberculosis prevalence estimated by studies using a cross-sectional or disease control design reported a low prevalence (prevalence at the animal level within a herd). One study carried out in Canada evaluated the risk factors for bovine tuberculosis infection and found that the increase of herd size was associated with an increase of risk of herd positivity to bovine tuberculosis. This information on the performance and limits of bovine tuberculosis diagnostic tests is critical for orienting the choice of appropriate diagnostic method and for a valid evaluation of the surveillance activities

Keyphrases: M. bovis, Surveillance, Bovine tuberculosis, Cervids
IIRC : Incremental Implicitly-Refined Classification

We introduce the "Incremental Implicitly-Refined Classification (IIRC)" setup, an extension to the class incremental learning setup where the incoming batches of classes have two granularity levels. i.e., each sample could have a high-level (coarse) label like "bear" and a low-level (fine) label like "polar bear". Only one label is provided at a time, and the model has to figure out the other label if it has already learned it. This setup is more aligned with real-life scenarios, where a learner usually interacts with the same family of entities multiple times, discovers more granularity about them, while still trying not to forget previous knowledge. Moreover, this setup enables evaluating models for some important lifelong learning challenges that cannot be easily addressed under the existing setups. These challenges can be motivated by the example "if a model was trained on the class bear in one task and on polar bear in another task, will it forget the concept of bear, will it rightfully infer that a polar bear is still a bear? and will it wrongfully associate the label of polar bear to other breeds of bear?". We develop a standardized benchmark that enables evaluating models on the IIRC setup. We evaluate several state-of-the-art lifelong learning algorithms and highlight their strengths and limitations. For example, distillation-based methods perform relatively well but are prone to incorrectly predicting too many labels per image. We hope that the proposed setup, along with the benchmark, would provide a meaningful problem setting to the practitioners.

Keyphrases: Deep Learning, Machine Learning, Lifelong Learning, Continual Learning, Incremental Learning, Computer Vision
L'action furtive : une étude de ses situations de diffusion

Art furtif is an artistic process that consists of integrating art anonymously into urban space, without any explicit signage designating its artistic status. Produced anonymously, in secret and without an audience; furtive actions are integrated into the artistic field through documents of all kinds. These documents are then transmitted through a variety of media. These range from art exhibitions to exhibition catalogues and all of its forms of promotional communications in which the documentation of an artwork is likely to appear: pamphlets, posters, press kit, website set up for the occasion, event pages on social networks, etc. Beyond these modes of transmission, which are linked to a specific event, there are others more independent media such as presentations, conferences, journal articles and publications. Our task is to demonstrate, through the work of Diane Borsato, karen elaine spencer and Steve Giasson, how photographs have made it possible for gestures, interventions, or performances, which seem to have nothing in particular—apart from their desire to go unnoticed—to become known works of art. Our goal is to understand the mediations that have allowed the integration of furtive actions into the artistic field. This study gives a better understanding of their nature and underlying mechanism. Studying mediations will in turn make it possible to identify the function of an artwork documentation within a given medium — as well as the function of the latter — which, all things considered, will provide a better understanding of furtive action and its reception.

Keyphrases: Art furtif, Intervention, Performance, Documentation, Contemporary art, Furtive art, Photography, Social networks
Écophysiologie de l'épinette noire des pessières à mousses et à lichens nordiques

Climate change is likely to affect the growth, development and regeneration of black spruce stands across the boreal forest. Regeneration failures cause gaps in the dense black spruce-feathermoss (BSFM) mosaic increasing the landscape proportion of open lichen-woodland (LW). The aims of the study are to determine whether the contrasting characteristics of BSFM and LW induce different light-saturated maximum photosynthesis (Amax) in black spruce trees across a latitudinal or seasonal gradient. Then the study will attempt to determine if Amax is likely to reflect their physiological capacities based on their maximum carboxylation rate (Vcmax) and maximum electron transport rate (Jmax) derived from CO2 response curves. Vcmax and Jmax are different between BSFM and LW mainly because nutrient acquisition seems different between stand types. Latitude affects values of Vcmax and Jmax, but the effect could be explained by soil and vegetation composition between experimental plots rather than by latitude. Physiological capacities do not match Amax values for stand type and latitude because Amax would be limited by CO2 concentration which does not allow saturation of rubisco. Despite the lack of difference between the Amax of BSFM and LW stands, future increase in CO2 concentration and temperature could induce a gap between their respective photosynthesis rates because of their different physiological capacities.

Keyphrases: Latitude, Ecophysiology, Maximum carboxylation rate, Maximum electron transport rate, Black spruce, Growing season, Black spruce-feathermoss, Lichen woodland
Les représentations de la controverse Roman Polanski dans la presse française (2002-2020)

Roman Polanski is a French-Polish filmmaker who has been considered a fugitive by Interpol since 1978. In 1977, during a trial for rape, the 44-year-old director plead guilty to illegal sexual relations with a 13-year-old girl. Upon his release from prison, fearing that the judge would reverse his decision to release him, Roman Polanski fled the United States to take refuge in France. The director would go on to pursue a successful career in the world of cinema. To date, twelve women have accused him of committing acts of sexual violence. This dissertation is a qualitative analysis carried out using the framing method on the deployment of the discourses of the controversy associated with Roman Polanski in the French press. The analytical frames identified are: rape culture (1), the artist and his work (2), Justice (3) and complacency (4). We collected a sample of 100 press articles published between 2002 and 2020 in three daily French newspapers: Libération, Le Monde and Le Figaro. The analysis is carried out from a theoretical framework derived from feminist studies, more specifically from the perspectives of radical and materialist feminism. The objective of this research is to illustrate and to understand how the rhetoric associated with the Roman Polanski controversy are articulated in the media in France, as well as on a larger scale in French society.

Keyphrases: Roman Polanski, France, discours, rape culture, feminism, media, discourse, power, women's violence, controversy
L'arithmétique de Boèce : le transfert de savoir mathématique grec

Roman author of the 6th century known for his Latin translations of Aristotle’s Greek texts, Boethius has also composed a translation-adaptation of a treatise on arithmetics written by Nicomachus of Gerasa.  The first section of this master’s thesis focuses on characterizing Boethius as a intermediary, transferring Greek knowledge to the Latin West. His relationship with Symmachus is highlighted in order to argue that Boethius had been able to learn Greek and reach such a high level of learning in Rome, without the need to study in the Athenian or Alexandrian schools of his time. The mathematical content of the De institutione arithmetica is the main topic of the second section. After showing how the De arithmetica is related to Boethius’ magnum opus – the Latin translation of the Greek philosophers – the choice of Nicomachus of Gerasa’ Introduction to Arithmetics as the source of Boethius’ treaty on arithmetics is studied. Then, a catalogue raisonné of the mathematical concepts showcased is provided, organized around the notions of quantity constant of itself and relative quantity which retain the opposition between the Same and the Other and stems from the pythagoricians’ fondamental opposition between the Limited and the Unlimited. This masters’ thesis ends with an analysis of the medieval transmission of the De institutione arithmetica and of its influence on medieval mathematics and education through the quadrivium.

Keyphrases: De institutione arithmetica, quadrivium, Boethius, medieval arithmetics, Nicomachus of Gerasa
Redefining the anthology : forms and affordances in digital culture

As the longtime dominant U.S. television business model has been challenged in various ways by industrial and technological changes in recent years, more heterogeneous narrative forms have emerged in addition to original serial structures. The diversity of televisual forms became particularly evident since national, local television landscapes started opening up to foreign markets outside of the U.S., finally embracing a transnational, global perspective and tracing alternative value-chains. The transition to internet-distributed television played a pivotal role in this formal fragmentation and new dynamics of online streaming opened up another path for understanding the flow of television content, which today reflects a highly interconnected, networked media and digital environment. Indeed, the proliferation of video-on-demand services is forcing seriality to adapt to the contemporary mediascape, giving rise to audiovisual products that can be transferred online and present specificities in production, distribution and reception. One of the outcomes of such changes in U.S. television series at the dawn of the twenty-first century is the anthology series divided in different seasons with separate stories, yet linked by tone and style. My research positions itself in such a technological, industrial and cultural context, where television content is increasingly fragmented. Given such a fragmentation, this thesis considers the ways contemporary television content is distributed in the interaction between algorithmic-driven recommendation processes and more traditional editorial practices. The aim of the project is to investigate the way certain narrative structures typical of the anthology form emerge in the context of U.S. television seriality, starting from specific conditions of production, distribution and consumption in the media industry. By focusing on the evolution (temporal, historical dimension) and on the digital circulation (spatial, geographic dimension) of U.S. anthology series, and observing the peculiarities in their production and style, as well as their distributional networks and the consumption patterns they foster, this thesis ultimately insert itself into a larger conversation on digital-cultural studies. The final purpose is to examine the relation between anthological forms, distribution platforms and consumption models, by proposing a comparative approach to the anthology that is at the same time cross-cultural, cross-historical, cross-genre and accounting for both pre- and post-digital practices for cultural content organization.

Keyphrases: Anthology, Digital Culture, Media Studies, Internet Studies, Platform Ecology, Internet
Predictors of HSIL Treatment Failure

Objective: Repeated treatments for high-grade squamous intraepithelial lesions (HSIL), which are necessary in the case of treatment failure, are associated with negative obstetric outcomes, such as an increased risk of neonatal death. We investigated the association between a large number of potential risk factors and HSIL treatment failure in an effort to identify potentially modifiable predictors of treatment failure.   Methods: The source population included 1,548 Canadian women who received a first treatment for HSIL. Treatment failure was defined as the histological diagnosis of HSIL or cancer within the two years following treatment. We conducted a nested case-control study that included all 101 cases of treatment failure and controls that were matched 1:1 on treatment center and date of failure. We used conditional logistic regression to calculate the odds ratios (OR) and 95% confidence intervals (CI) between treatment failure and age, parity, smoking status, number of sexual partners, condom use, method of contraception, margins, number of passes, diagnosis on the treatment specimen, HPV genotype and number of types. We also estimated the association between HPV16 and HPV18 viral loads and variants and HSIL treatment failure.   Results: Having positive vs. negative margins (adjusted OR=4.05, 95% CI 1.57-10.48), being positive for HPV16 and/or HPV18 vs. any other type (adjusted OR=2.69, 95% CI 1.32-5.49), and having a prototype-like variant of HPV16 vs. the prototype (adjusted OR=2.49, 95% CI 1.07-5.83) were predictors of HSIL treatment failure. Older age, more severe lesions, single-type infections and a variation at the 7521 position of the HPV16 genetic sequence may lead to a higher risk of treatment failure but were not statistically significant. Estimates for all other factors were near the null value. The effect of genotype on the risk of treatment failure was not modified by smoking status, nor by margin status.  Conclusion: Only positive margins, HPV16/18 positivity, and having a prototype-like variant of HPV16 were predictors for HSIL treatment failure within two years of treatment. Despite being non-modifiable, the identified predictors are clinically significant in regards to management and follow-up of patients.

Keyphrases: Epidemiology, Risk factors, Squamous intraepithelial lesions of the cervix, Cervical intraepithelial neoplasia, Cervical cancer, Human Papillomavirus, Cervical conization, LEEP, Treatment failure
Association entre les déterminants du style de vie, l'ostéoporose et la lipodystrophie chez les personnes vivant avec le VIH : une analyse transversale de la Cohorte canadienne VIH et vieillissement.

Background: As a consequence of ART, people living with HIV (PLWH) are at higher risk for osteoporosis and lipodystrophy. However, the risk may also be influenced by lifestyle factors, but few studies have explored the association between modifiable lifestyle factors and the risk of osteoporosis or lipodystrophy in the PLWH population.  Objectives: Our primary objective was to evaluate the lifestyle factors in relation to the risks of osteoporosis and lipodystrophy in a PLWH-based cohort.  Methods: We conducted a cross-sectional analysis of data from the Canadian HIV and Aging Cohort Study (CHACS). We included all participants with available bone mineral density T-scores, which were measured by dual-energy X-ray absorptiometry (DXA) scans. Lifestyle risk factors of interest included annual income, education level, alcohol intake, tobacco use, illicit drug use and physical exercise. Other covariates considered were full antiretroviral medication history, medical comorbidities, coinfections, viral load, nadir CD4+ and current CD4+ count. Osteoporosis was defined by a T-score of -2.5 or lower at any of the measured sites. Lipodystrophy was assessed on whole body DXA and defined as a fat mass ratio (the ratio between trunk and lower limbs fat mass) greater than 1.33 for women and 1.96 for men. Baseline prevalence odds ratios (ORs) and 95% confidence intervals (95% CIs) were estimated by multivariate logistic regressions.  Results: We included 547 PLWH (median age 55 years, 88% males) and 97 HIV-uninfected controls (median age 57 years, 64% males). Osteoporosis was present in 13.0% of PLWH (95% CI 10.2 – 15.8%) and 6% of controls (95% CI 1.4 – 11.0%); the OR of osteoporosis for HIV seropositivity was 2.21 (95% CI [0.96 – 6.06]). Lipodystrophy was found in 138 (28.3%, 95% CI 24.3 – 32.3%) of the 487 PLWH for which a fat mass ratio (FMR) was available. None of the lifestyle factors of interest were associated with osteoporosis or lipodystrophy. However, covariates associated with an increased risk of osteoporosis were increasing age, lower body mass index (BMI) and hepatitis C coinfection. Covariates associated with an increased risk of lipodystrophy were older age, hypertension, longer antiretroviral duration, and longer exposure to nucleoside reverse transcriptase inhibitors (NRTIs) and integrase strand inhibitors (INSTIs).  Conclusion: No association was found between any of the lifestyle factors of interest and osteoporosis or lipodystrophy.

Keyphrases: DXA, Tabagisme, TAR, HIV, Osteoporosis, Lipodystrophy, BMD, T-score, Lifestyle risk factors, Socio-economic status, Physical exercise, Alcohol intake, Smoking, ART
La pollution sonore des océans et la règlementation du bruit sous-marin : un enjeu international qui prend tout son ampleur dans l’Arctique canadien

The world oceans are filled with natural sounds, which are being increasingly encroached upon by human sourced noises (anthropogenic noise). This thesis provides an overview of the current state of knowledge on the different sources of underwater noise and their negative effects on marine species, ecosystems and coastal populations. While anthropogenic noise is an environmental stressor similar to other forms of pollution, the management of anthropogenic noise has been neglected by States and by international law. This study highlights how scientific uncertainties and gaps complicate the process of crafting specialized international and domestic instruments to mitigate the impacts of underwater anthropogenic noise. The thesis identifies and analyzes binding and soft law instruments currently in force, internationally and in Canada, to discover whether they can be used to reduce noise pollution in Canadian Arctic waters. The adoption of legal instruments specifically applicable to anthropogenic underwater noise is advocated but with the caveat that it will require concerted inter and intra sectoral cooperation at the national, regional and international levels between legislative, scientific and decision-making circles.

Keyphrases: pollution marine, Arctic, noise pollution, law of the sea, environment, anthropogenic sound, anthropogenic underwater noise, marine environment, international law, marine pollution, environmental protection, marine mammals