NCube/papyrus huggingface dataset:
Fonction de CFTR dans les processus de réparation de l’épithélium des voies aériennes et développement de nouvelles stratégies thérapeutiques en fibrose kystique

The Cystic fibrosis (CF) pathology is caused by mutations of the gene coding for the CFTR channel. The most common mutation is the deletion of Phe508 (∆F508) causing protein misfolding and degradation. Thus, the absence of CFTR channel causes the dysfunction of ion and fluid transport that impairs mucociliary clearance resulting in mucus thickening and plugging in the airways. These conditions then favor P. aeruginosa bacterial colonisation and inflammation in the airways, which contribute to airway damage and remodeling. Ultrstructural analysis of bronchial sections of lungs collected from CF patients at the time of transplantation showed some area with signs of ongoing epithelial repair. However, a progressive epithelial damage is still observed in CF patients and it appears that the repair process is insufficient to restore epithelial integrity.  The main objective of my work was to study the role of CFTR in the CF repair processes and to explore the impact of CFTR correction on epithelial repair under pathogen-free condition as well as in the presence of infectious products. Our study showed that CF airway epithelium exhibits a repair defect, associated, at least in part, to the absence of a functional CFTR channel. Furthermore, we demonstrated for the first time that CFTR rescue with the CFTR corrector VRT-325 significantly improved the wound-healing capacity of CF epithelial cell monolayers. Then, we showed that the presence of bacterial filtrate, more precisely P. aeruginosa diffusible material (PsaDM), not only alter CFTR function and expression, but also impaired epithelial repair processes. Finally, our results suggested that infection has a deleterious impact on CFTR rescue, and affected the beneficial effect on epithelial repair processes induced by VRT-325.  My work allows to better understand the role of CFTR in the CF epithelial repair mechanisms and to propose new therapeutic strategies to promote epithelial regeneration in CF patients in attempt to stabilize their condition, despite the deleterious impact of infection.

Keyphrases: Infection, CFTR corrector, Epithelial injury, Repair processes
Étude des cellules dendritiques chez les patients qui ont subi une greffe de cellules souches allogéniques

The intensity of the immune response that is generated by the dendritic cells (DCs) has established these cells as central mediators in the activation of T lymphocytes. The vulnerability of leukemic cells present in chronic myeloid leukemia is mostly attributable to the ability of the leukemic stems cell to differentiate themselves into potent DCs. The latter are then able to present peptides which come from endogenous origin and from leukemic stem cells to the T lymphocytes. In this thesis, we demonstrate that, before allogeneic stem cell transplant, the majority of patients afflicted by CML have a considerable lack of DCs in their peripheral blood as well as in their bone marrow. The low levels of circulating DCs result to a great extent from a loss of diversity in the CD34+ leukemic progenitor cells located in the bone marrow. Moreover, these CD34+ leukemic progenitor cells display a reduced capacity to differentiate themselves into DCs in vitro. Our findings show that having a low level of DCs prior to an allogeneic transplant is associated with a significant decline in survival rates as well as with increased risks of developing life threatening complications. Since the DCs’ reconstitution following an allogeneic bone marrow transplant is missing, our study supports the thesis that pre graft DCs are essential in the Graft versus leukemia effect (GVL).Therefore, our research suggests that tallying DC before proceeding with an allogeneic transplant could act as a prognostic marker to identify LMC patients who present risks of complications after an allogeneic transplant.

Keyphrases: bcr/abl, Chronic myeloid leukemia, dendritic cells, homeostasis, immunotherapy
La collaboration entre l'oncogène E2A-PBX1 et Hoxa9 lors de l'induction de B-ALL implique l'activation de Flt3

The fusion protein E2A-PBX1 induces pediatric B cell leukemia in human. It has strong transactivating properties and can bind to DNA and homeobox (HOX) proteins through conserved domains in the PBX1 portion, suggesting that deregulation of HOX/PBX target genes contribute to leukemogenesis. Previously, we reported oncogenic interactions between Hox genes and E2A-PBX1, which are dependent on cell type as well as on the particular Hox member. A proviral insertional mutagenesis screen provided support for collaboration between Hoxa genes and E2A-PBX1 in B cell leukemogenesis. Whether these interactions occur in B cells and lead to B-ALL, relevant for human disease is still not clear. Here we report that Hoxa9 confers a proliferative advantage to E2A-PBX1 B cells. Transplantation experiments with E2APBX1/Hoxa9 positive B cells isolated from bone marrow (BM) chimeras showed that Hoxa9 interacts with E2A-PBX1 contributing to the oncogenic transformation of B cells, but is unable to transform B cells alone. Q-RT-PCR analysis demonstrated a strong repression of B cell specific genes in leukemias co-overexpressing Hoxa9 and E2A-PBX1 in addition to Flt3 activation, indicating inhibition of B cell differentiation in combination with enhanced proliferation. Overexpression of Hoxa9 in E2A-PBX1 mouse leukemic B cells also resulted in a growth advantage in vitro, likely mediated by the enhanced expression of Flt3 and Pdgfδ. In conclusion we show for the first time that Hoxa9 collaborates with E2A-PBX1 in the oncogenic transformation of B cells in a mouse model that involves Flt3 signaling, which is potentially relevant to human disease.

Keyphrases: E2A-PBX1, Hoxa9, B-ALL, Flt3, Leukemia, Mouse model, Hox genes
Exploration of implicit theories in the formation of expert opinion in portuguese criminal law

This dissertation examines different aspects involved in the formation of psychologists’ expert opinion in the Portuguese criminal justice system, more precisely, as this opinion is reflected in assessment reports. The present dissertation is comprised of three qualitative studies, the first sought to provide a general portrait of a sample of 106 forensic psychological reports as to their overall quality as measured in terms of relevance and coherence. Results show that the formal markers of quality are present in the sample analysed, a certain number of weaknesses have been observed, notably concerning the internal coherence of the reports as well as the relevance of the information reported on. The second study explored the opinions of 17 Portuguese judges and state prosecutors concerning the use they make of this type of forensic report. It appears that they consider these reports to be useful and very credible, specially so when they have been produced under the auspices of the National Institute of Legal Medicine and Forensic Sciences, which is the state forensic institution. Furthermore, it appears that judges and prosecutors were particularly interested in data that allowed for a personalised portrait of the assessee. The third study sought to better comprehend the conceptual bases on which psychologists construct their reports. To this end, an exploratory study was undertaken with a sample of key-actors; the analysis of their interviews shows that they define their judicial mandate as well as the basic concepts that are associated to this mandate in different ways. A theoretical framework provided by an implicit theories model was used to help understand these results.

Keyphrases: Expert Opinion, Forensic Psychological Report, Forensic Psychology, Criminal Law, Qualitative Methodology, Decision-making, Implicit Theories, Forensic Institution, Méthodologie qualitative
Du tracé manuel à la ligne en mouvement : mutations esthétiques et sémiotiques dans la calligraphie latine contemporaine

Contemporary Latin calligraphy, a discipline that has existed in its current form for little more than a century, differs enormously from previous forms of Western handwriting. Since it first appeared at the end of the 19th century, its purpose and application have also changed significantly. Our goal is to understand how these changes have come about. What factors have influenced the series of mutations that contemporary Latin calligraphy – this newly reinvented form of visual expression of the Latin alphabet – has undergone? Through the analysis of specific contemporary works and of some singular traits within these works, this archaeological study will subject Latin calligraphy to analysis from both a semiotic and an esthetic point of view.

Keyphrases: Alphabet, Main, Outil, Image, Alphabet, Cinema, Stroke, Line, Motion, Writing, Calligraphy, Hand, Tool, Image
Modification des propriétés optiques de nanofils à base de GaN par plasma N2/O2

A cylindrical electrostatic Langmuir probe was used to characterize the flowing afterglow of a N2-O2 surface wave plasma. The spatial distribution of the number density of positive and electrons as well as the EEDF were measured. A maximum of the number density of electrons in the mid 1013 m-3 was obtained in the center of the early afterglow, while it decreased at 1011 m-3 early in the late afterglow, thus indicating non-macroscopically neutral media all along the flowing afterglow. It is characterized by an EEDF close to a Maxwellian with an electron temperature of 0.5±0.1 eV, while it increased at 1.1±0.2 eV in the early afterglow due to the contribution of important vibration-electron collisions. After addition of small amounts of O2 in the main N2 microwave discharge, the charged particles densities and electron temperature first strongly increased then decreased with increasing O2 concentration. A change in the charged population in the afterglow by the creation of NO+ to the detriment of the N2+ ions is responsible of this phenomenon. This N2 flowing afterglow was later used for plasma-induced modification of pure GaN nanowires and InGaN/GaN dot-in-a-wire heterostructures and characterized by PL. While the band edge emission from GaN nanowires and the GaN matrix of the InGaN/GaN nanowires strongly decreased due to the creation of non-radiative recombination centers in the near-surface region, the emission from the InGaN inclusions strongly increased. PL excitation measurements show that this increase cannot be explained by a plasma-induced shift of the GaN absorption edge. Instead a dynamical annealing process induced by the desexcitation of N2 metastables following their collision with the nanowire surface and the passivation of surface defects such as nitrogen vacancies by the highly reactive nitrogen atoms in the afterglow are responsible of the increase of the PL intensity. The addition of O2 gives the same results as the pure N2 treatment, but a redshift of the emission band related to the InGaN inclusions is also observed, suggesting an important contribution of the oxygen species.

Keyphrases: plasma micro-onde, interactions plasma-surface, flowing afterglow, microwave plasma, Langmuir probe, emission spectroscopy, nitride semiconductors, nanowires, plasma-surface interactions
Le problème de Coulomb-Dunkl dans le plan

This master's thesis, composed of an article in collaboration with Luc Vinet and Vincent X. Genest, is the result of a work done on superintegrable quantum systems defined by Hamiltonians of the Dunkl kind. More specifically, the aim of this paper is to analyse the Coulomb-Dunkl problem in the plane which is a generalization of the quantum system of hydrogen involving operators of reflection on the variables x and y. The model is defined by a potential in 1/r. First, we notice that the Hamiltonian is separable in polar coordinates and the wave functions are written in terms of products of generalized Laguerre polynomials and Dunkl harmonics on the circle. The algebra generated by the symmetry operators has also allowed us to confirm the maximally superintegrable character of the Coulomb-Dunkl problem. We also write explicitly the representations of the same algebra. We finally found the energy spectrum algebraically.

Keyphrases: Superintegrability, Coulomb problem, Dunkl operator, Symmetry algebra, Representation
Classification et relations entre les traits fonctionnels des crustacés zooplanctoniques : de l’organisme à l’écosystème

Ecologists have long recognized that organisms are sustained by the flux, storage and turnover of ecosystem energy, which fuels biological metabolism, and material, used to construct biomass. Over the past three decades, the importance of individual organisms in regulating ecosystem processes, such as consumer-driven nutrient cycling, has been increasingly recognized. Occupying a central position in aquatic food webs, zooplankton are known to influence other trophic levels and exert a strong influence on energy fluxes or material processing in ecosystems. Several species’ characteristics have been pointed out as being good indicators, or predictors, of the effect of zooplankton on their environment, including individual body size, corporal stoichiometry and specific physiological rates. Most of these characteristics can also be termed “functional traits”. While the use of traits has recently gained popularity amongst aquatic community ecologists, few have applied this approach to concretely link zooplankton community structure to ecosystem processes. In the present study, we compiled data from a wide variety of literature to construct a database of crustacean zooplankton species and their traits contributing directly or indirectly to C, N or P ecosystem fluxes. Our literature search yielded over 9000 empirical observations on 287 different species and thereby allowed identification of knowledge gaps in the literature. We explored trait relationships amongst taxonomic units and between marine and freshwater habitats. Of all cross-correlations tested among 16 zooplankton traits, 35 were significant, with most traits being related to body mass. Our synthesis revealed significantly different patterns between freshwater and marine zooplankton respiration and allometry (body mass vs. length). We propose a novel trait classification scheme according to both organismal and ecosystem functions. Our goal is to provide a database for zooplankton functional traits, tools to link organisms to ecosystem processes, and to promote a search for general patterns and trade-offs amongst traits.

Keyphrases: Allometry, Biogeochemical cycles, Body size, Ecosystem functioning, Functional traits, Metabolism, Nutrient recycling, Zooplankton
Is social phobia characterized by a distinct interpersonal pattern?

Traditionally, the construct of social phobia has been viewed intra-personally, as a disorder of anxiety. In recent years, an alternative interpersonal account of the concept has been proposed, whereby social phobia is characterized as an overall self-protective pattern of specific fearfully self-protective patterns of interpersonal behaviour. The main objective of this dissertation was to test hypotheses drawn from this interpersonal approach. Two studies, presented in the form of research articles, were devised to examine whether specific self-protective interpersonal patterns of powerlessness and submissiveness are characteristic of the overall socially phobic pattern. The studies also examined whether self-protectiveness is interrelated with anxiousness. The first study compared the interpersonal patterns, assessed using an Interpersonal Circumplex measure, of 132 socially phobic individuals to those of 85 single sexually dysfunctional and 105 normal control participants. The relationship between self-protective patterns and social anxiety, general distress, and social functioning were also examined in the socially phobic group. The second study examined the evolution of self-protectiveness, as well as social anxiety, general distress, and social functioning, in 85 socially phobic individuals at four time-points: Prior to being treated by an interpersonal approach, post-treatment, as well as at a six-month and one-year follow-up. Remitted and non-remitted participants at the one-year follow-up were also compared. Results support the hypothesis that social phobia is characterized by self-protective patterns of powerlessness and submissiveness. Specifically, these interpersonal patterns were found to characterize the socially phobic group to a larger extent than either of the two contrast groups. They were also shown to improve meaningfully after treatment, especially in participants who achieved remission one year later.In addition, a relationship between the self-protective patterns and increased levels of social anxiety and subjective distress was found in the socially phobic group. Results also showed an improvement in anxiety, general distress, and social functioning consistent with the shrinking in self-protectiveness after treatment. In conclusion, the findings are consistent with predictions drawn from an interpersonal approach and provide support for this alternative conceptualization of social phobia.

Keyphrases: Social phobia, Interpersonal approach, Self-protective pattern, Powerlessness, Submissiveness, Interpersonal Circumplex
Réorganisation neurofonctionnelle permettant le maintien des habiletés d’évocation lexicale lors du vieillissement

The maintenance of optimal cognitive performance in aging has been associated with adaptive changes in cerebral activation patterns for various abilities that tend to decline with age. Yet, few studies have investigated this neurofunctional reorganization based on communication abilities, particularly with regard to the expressive side of language.  Considering that a number of language components usually remain well preserved in older adults, it is, however, necessary to further explore the underlying cerebral mechanisms to better understand the determinants of successful cognitive aging.  The objective of this thesis is to examine in detail the effects of aging on activation patterns and functional interactions among neural substrates contributing to expressive communication abilities. Two functional neuroimaging studies, using distinct methodological approaches, have been conducted by means of an innovative mixed design and an overt self-paced semantic and orthographic verbal fluency task, performed by well-educated young and older adults.  Specifically focusing of cerebral activation patterns associated with high levels of verbal fluency performance, the first study shows that the relative preservation of lexical speech production abilities in aging is characterized by marginal neurofunctional changes in high-performing older adults. Yet, the second study indicates that functional interactions between cortical areas contributing to speech productions significantly decrease with age, without, however, having an impact at the behavioral level. In addition, this effect of aging on the functional integration of the network engaged during semantic and orthographic verbal fluency was found to be exacerbated by task demands, which is expressed by local functional connectivity disruptions.  In sum, this thesis demonstrates that a neurofunctional reorganization to maintain lexical speech production abilities in aging is unnecessary in well-educated and high-performing older adults, despite an age-related decrease in functional networks integration. These results may reflect a loss of neural efficiency with age, although insufficient to have behavioral outcomes in individuals who benefited from protective factors known to promote successful aging, which is discussed in light of the concept of cognitive reserve.

Keyphrases: functional magnetic resonance imaging, neurofunctional reorganization, normal aging, expressive language, communication abilities, lexical speech productions, verbal fluency, functional connectivity, language networks
Activité cérébrale reliée à la rétention des sons en mémoire à court-terme auditive

The capacity to retain auditory information for a short period of time is fundamental for a variety of cognitive operations. Sounds, in particular, often do not reveal their meaning before being integrated in their temporal context; the retention of tones that are no longer present in the environment is thus necessary for understanding the significance of auditory information. Retaining tones ultimately leads to a successful interaction with the environment. The goal of this thesis was to study brain activity related to the retention of tones, thereby providing a better understanding of low-level mechanisms related to auditory short-term memory. Three empirical studies have been conducted, each of them focusing on a different aspect of the retention of tones. The first article investigated electrophysiological correlates of the retention of tones differing in timbre using the event-related potential technique. The electrophysiological results revealed a fronto-central component that varied with memory load. In the second article, the oscillatory pattern of electric brain activity was explored using electroencephalography. The results revealed that alpha band amplitudes were modulated by memory load during retention. Furthermore, a dissociation of oscillatory activity between the retention of tones and the comparison of test tones against retained tone representations was observed. This study also revealed distinct but interrelated processes taking place at the same time by showing specific amplitude modulations in the alpha and beta bands. The third article focused more on brain areas underpinning the retention of tones. Brain activity was measured with magnetoencephalography and subsequent source localisations were performed. The results suggested the implication of a network of temporal, frontal, and parietal brain areas which was more pronounced in the right hemisphere than in the left hemisphere. The results of the empirical studies emphasized the sensory aspect of auditory short-term memory. In addition, they revealed similarities between the retention of tones differing in fundamental sound characteristics such as timbre and pitch. Considered as a whole, the studies of this thesis contributed to the identification of neural processing underlying the retention of tones by studying electromagnetic brain activity and the implication of corresponding brain areas on a fine temporal scale.

Keyphrases: Audition, Timbre, Audition, Short-term memory, Working memory, Pitch, Timbre, Electroencephalography, Magnetoencephalography, Event-related potenials, Brain oscillations, Source localisations
Recherche et caractérisation de systèmes binaires dont l'une des composantes est de faible masse

We report the discovery of 14 new low-mass binary systems containing mid-M to mid-L dwarf companions with a separation larger than 250 AU. These systems were ﬁrst identiﬁed by searching for common proper motion sources in the vicinity of known high proper motion stars, based on a cross-correlation of wide area near-infrared surveys (2MASS, SDSS, and SIMP). An astrometric follow-up, for common proper motion conﬁrmation, was made with SIMON and/or CPAPIR at the Observatoire du Mont-Mégantic (OMM) and Cerro Tololo Inter-American Observatory (CTIO) telescopes for most of the candidates identiﬁed. A spectroscopic follow-up was also made with GMOS or GNIRS at Gemini to determine their spectral types. Statistical arguments are provided to show that all of the systems we report here are very likely to be truly bound. One of the new systems we discovered has a brown dwarf companion: 2M1259+1001 (L4.5). The study of the new systems we have discovered will be useful to help us better understand how very low mass stars and brown dwarfs form.

Keyphrases: Astrophysic, Brown dwarf, Binary system, Low-mass star