NCube/papyrus huggingface dataset:
Évolution moléculaire : un modèle Markov-modulé pour les processus de substitution

Time-continuous Markovian process are widely used to understand the mechanism of nucleotidic acids and proteins evolution along phylogeny. Already existing probabilistic models based on such hypothesis are designed to satisfy the non-homogeneity of functional and environmental constraints acting across those biological sequences. Recently, Markov-modulated models have been introduced to describe site-specific temporal rate variation (heterotachy). Moreover, studies have demonstrated that not only strength but also the nature of the constraint acting on a specific site can vary over time. Here we propose to accommodate this evolutionary reality with a Markov-modulated model for proteins under which sites are authorized to change their amino acids propensities across time. Posterior estimation of the stochastic kernel hidden parameters with Monte Carlo methods is a challenging approach that we partially overcome with parallel computing. Fine-tuning are otherwise planned to accelerate convergence toward the target posterior stationnary distribution. Qualitatively, our model seems to be able to capture temporal heterogeneity from real sequences data sets whose evolutionary history is assumed to be rich in substitutional switch events. Furthermore, evaluation of the model performance suggest that he provides a better fit to the data set than the time-homogeneous equivalent model. Nonetheless, substitutional histories sampled from the posterior distribution are quite noisy and remain difficult to interpret biologically.

Keyphrases: Molecular evolution, Bayesian inference, substitution process, Markov-modulated model
Étude sur les fonctions in vivo des GEFs DOCK chez les mammifères

Dock1 (also known as Dock180) is the prototypical member of the Dock family of Rho GTPase activators (RhoGEFs). Genetic studies in Drosophila and C. elegans have demonstrated that Dock1 orthologues act upstream of the Rac GTPase to activate it during various biological processes. Myoblast city (mbc), Dock1 ortholog in the Drosophila, is an important regulator of myoblast fusion during muscle fiber formation. Moreover, mbc regulates the collective migration of a cluster of border cells downstream of the activation of some tyrosine kinase receptors (RTKs). Migration of border cells is often view as a model for studying the invasive migration of cancer cells during metastasis development. Work done in cell lines also suggests that Dock1 is an important cytoskeletal regulator that controls cell migration. The Dock1/Rac pathway was also shown to act downstream of some RTKs to promote the invasion of glioblastoma cells. Yet, the in vivo functions of Dock1 in mammals are still poorly understood and the identification and characterization of some of these functions is the main objective of my thesis.  Guided by the function of mbc, in Aim #1 we revealed that Dock1 is essential to embryonic development by characterizing a Dock1 knock-out mouse model. A deficiency in myoblast fusion was observed in Dock1-null embryos which led to a reduction in their muscle mass. Furthermore, we uncovered a contribution of the other Dock1-related GEF, Dock5, to myofiber development.  In Aim #2 a correlation between high level of DOCK1 expression and a poor prognosis in HER2+ breast cancer patients was revealed. Amplification or overexpression of the HER2 receptor tyrosine kinase is associated with near 20% of breast cancer cases. The presence of this genetic abnormality correlates with a poor prognosis and the development of metastasis.  Biochemical and in vitro studies led us to identify that DOCK1 interacts with HER2 and is essential to HER2-mediated RAC activation and migration. The use of a HER2 breast cancer mouse model with Dock1 inactivation in the mammary gland led us to identify DOCK1-RAC signaling as novel effectors in HER2-mediated tumor growth and metastasis.  We conclude that the use of Dock1 mouse models allowed us to identify some of the key functions regulated by this gene in vivo. Much like its ortholog mbc, Dock1 is essential to embryonic development and regulates myoblast fusion. Our study also reveals important degree of conservation of the mechanisms that regulate fusion between species. In addition, DOCK1 acts downstream of the HER2 RTK in mammary epithelial cells where it contributes to the progression of breast cancer pathology and the formation of metastasis induced by this oncogene.

Keyphrases: Dock1, Dock180, Dock5, Myoblast fusion, Breast Cancer
Étude sur le rôle des mutations de novo dans l’étiologie génétique de la schizophrénie

Schizophrenia is a severe psychiatric disorder that affects roughly 1% of the general population. It has been clearly demonstrated that the disease possesses a strong genetic component, but thus far, studies have had limited success in identifying key schizophrenia genes. With the advent of new DNA sequencing technologies it is now possible to study a type of genetic variation that has been previously looked over: de novo mutations (new mutations not transmitted by parents) The main aim of the present thesis is to better characterize de novo mutations in schizophrenia. As the role of these variations is not very well known, it was also necessary to study them in a global context in the human population. The first part of our project was to do a comprehensive study of de novo mutations found in the coding section (exome) of patients affected with schizophrenia. We found that the mutation rate was higher than expected. We also observed an aberrant number of nonsense mutations, which suggests a pathogenic profile of mutations. Thus, we strongly suggested that de novo mutations are key players in the genetic mechanism of schizophrenia. The second part of the work builds on the genes bearing mutations identified in the exome sequencing analysis. We sequenced these genes in a larger cohort of cases and controls in order to establish the profile of rare variants for these genes. We were able to conclude that the global mutational profile of the genes identified during de novo mutation studies are indeed pathogenic, which confirms that some of those genes are really involved in the disease and are not sequencing artefacts. Additionally, we were also able to identify some genes that had an aberrant rare variation profile.  The third part of the work aimed to characterize the paternal age effect on the de novo mutation rate. Indeed, in schizophrenia, it has been shown numerous times that paternal age is a risk factor for the disease. Thus, we have chosen to characterize this effect in a cohort of healthy subjects. We were able to observe a high correlation between paternal age and an elevated germline mutation rate. We were also able to confirm the existence of genomic regions that present an elevated number of de novo mutations, supporting the notion of mutational hotspots.  Our results were amongst the first to be published on the scientific area to directly involve de novo mutations in the genetic mechanism of schizophrenia. Those results bring new clues on the biological networks underlying schizophrenia by investigating a genetic variation type long overlooked.

Keyphrases: Schizophrenia, Genetic, De novo mutation, Genetic variation, Parental age effect
Une méthode d'évaluation fiable pour mesurer les caractéristiques psychoacoustiques de l'acouphène

The diagnosis of tinnitus relies on self-report. Psychoacoustic measurements of tinnitus pitch and loudness are essential for assessing and discriminating true claims from false. For this reason, the quantification of tinnitus remains a challenging research goal. We aimed to: (1) assess the precision of a new tinnitus likeness rating procedure with a continuous pitch presentation method, controlling for music training, and (2) test whether tinnitus psychoacoustic measurements have the sensitivity and specificity required to detect people faking tinnitus. Musicians and non-musicians with tinnitus, and simulated malingerers without tinnitus were tested. Most were retested several weeks later. Tinnitus pitch matching was first assessed using the likeness rating method: Pure tones between 0.25 to 16 kHz were presented randomly to participants who had to rate the likeness of each tone to their tinnitus, and to adjust its loudness from 0 to 100 dB SPL. Tinnitus pitch matching was then assessed with a continuous pitch method. Participants had to match the pitch of their tinnitus by moving their finger across a touch sensitive strip, which generated a continuous pure tone from 0.5 to 20 kHz in 1 Hz step. Pitch matching abilities to external tones were assessed using this device. The predominant tinnitus pitch was consistent across the two methods for both musicians and non-musicians, although musicians displayed better external tone pitch matching abilities. Simulated malingerers rated loudness much above the other groups with a high degree of specificity (94.4%) and were unreliable in loudness (not pitch) matching from one session to the other. Retest data showed similar pitch matching responses for both methods for all participants. In conclusion, tinnitus pitch and loudness reliably corresponds to the tinnitus percept and psychoacoustic loudness matches are sensitive and specific to the presence of tinnitus. Furthermore, this novel method should be used along with visual analog scales, which are more correlated to mood and distress.

Keyphrases: Tinnitus, Pitch, Loudness, Assessment, Simulated malingerers, Music training, Psychoacoustics
Le rôle du CD40 homodimère dans la réponse immunitaire

CD40 is a type I transmembrane glycoprotein belonging to the TNFRs family, which is expressed on the surface of immune, hematopoietic cells, vascular, epithelial, and other cell types, including a wide range of tumour cells. CD40 does not have a kinase domain. Thus, to induce a signal, CD40 interacts directly or indirectly with adapter proteins such as TRAFs and Jaks. The interaction of CD40 with its main ligand, CD154, plays an important role in regulating the immune response and homeostasis. The activation of CD40 on the surface of B cells increases its ability to promote antigen presentation, in addition to inducing proliferation, isotype switching, and apoptosis. Patients affected by mutations in the gene encoding the CD40 or its ligand are immunosuppressed and susceptible to opportunistic infections. Studies have shown that CD40, as other members of the family of TNFRs is capable of forming homodimers. More recently, it was shown that the formation of the CD40 homodimer is the result of the engagement of CD40 on B cells by CD154. In addition, the homodimerization of CD40 is important for the phosphorylation of Akt. The CD40/CD154 interaction can have a direct role in immunotherapy by inducing apoptosis of some cancer cells or an indirect role in activating antigen-presenting cells (APCs), thereby increasing the effectiveness of activation of cytotoxic T cells. Our results show that the induction of cell death by CD40 requires permeabilization of the lysosome, the release of cathepsin B, the presence of ROS and interaction with TRAF6, this programmed cell death is greater in the presence of the monomeric form of CD40, due to a mutation at the level of the cysteine 238. Moreover, the homodimerization of CD40 requires its translocation to lipid rafts and the presence of ROS. This homodimerization is necessary for the CD40 B-cell activation via the induction of expression of CD23, CD69 and CD80. In addition, our results show for the first time the involvement of the CD40 homodimer in the induction of CD23 expression via TLR4. Our results emphasize the importance of CD40 homodimer in signaling pathways and highlight the role of Cys-238 in the cooperation between receptors of the innate and adaptive immune response. All together our results will allow a better understanding of CD40 signaling pathways involved in several autoimmune diseases, which give a rise to a better therapeutic trial design.

Keyphrases: ROS, TRAF6, db-CD40 homodimer, cathepsin B, cell death, lipid rafts, B cell activation, toll-like receptors (TLR)
Charge virale des papillomavirus et transmission entre partenaires

The natural history and progression of genital HPV infection are well understood. However, less is known about transmission dynamics of HPV between sexual partners. A better knowledge of risk factors and dynamics of HPV transmission is needed to optimize prevention strategies through vaccination and contraceptive measures. Our study aims to determine if the viral load of HPV infection affects transmission between sexual partners. The association between human papillomavirus (HPV) loads in genital swabs and type-specific concordance of prevalent HPV infection was assessed in 250 heterosexual recently-formed couples to further characterize HPV transmission. Viral loads of HPV16 (r=0.30), HPV18 (r=0.50) and HPV51 (r=0.19) were significantly correlated (p<0.05) between partners in opposite to HPV31 (r=0.08) and HPV42 (r=-0.10). A higher HPV load increased significantly the rate of detection of HPV16, 31 and 51 in sexual partners (age-adjusted odds ratios from 1.64 to 7.71). In recently-formed heterosexual couples, higher HPV16, 31 or 51 load was associated with increased detection of the same HPV type in sexual partners.

Keyphrases: couple, transmission, HPV, heterosexual, viral load
Rôle de la ghréline dans la régulation du coactivateur transcriptionnel PGC-1alpha

The adaptation of an organism to its environment is essential to its survival. Energy homeostasis is defined as the balance between intakes, expenses and storage of energy. An excess of calories disrupts this process and leads to the development of the metabolic syndrome that is characterized by obesity, type II diabetes, cardiovascular diseases and dyslipidemia. During fasting, ghrelin participates in the maintenance of energy balance by stimulating hepatic production of glucose and lipid storage in adipose tissue. The transcriptional coactivator PGC-1alpha is overexpressed in the liver during fasting and is involves in the induction of the hepatic glucose production and fatty acid oxidation. Our hypothesis is that these two key performers in the energy metabolism constitute a common axis control. In this study, we show that ghrelin plays a role in the regulation of PGC-1alpha. The ghrelin receptor GHS-R1a is also involved because of its strong constitutive activity in absence of ligand. We found that GHS-R1a inhibited PGC-1alpha transcriptional activity whereas adding ghrelin to cells moderated this effect. PGC-1alpha activation by GHS-R1a correlated with a dose-dependent increase of PGC-1alpha acetylation. The stability of PGC-1alpha was also increased by ghrelin receptor in a manner involving the ubiquitin-independent proteasome pathway. Ghrelin decreased the ability of PGC-1alpha to bind to PPARbeta, one of its nuclear receptor partners. Furthermore, ghrelin decreased the ability of PGC-1alpha to coactivate PPARbeta in a ligand-dependent manner in hepatocytes. Together, these results identify PGC-1alpha as a metabolic target of GHSR-1a signaling and defines a new regulatory axis involving ghrelin/PGC-1alpha/PPARbeta in hepatocytes. A better understanding of this regulation axis will provide novel aspects in therapeutic targeting of diseases associated with the metabolic syndrome.

Keyphrases: PGC-1alpha, GHS-R1a, PPARbeta, PGC-1alpha, GHS-R1a, Ghrelin, Nuclear receptors, Transcriptional coactivator, Metabolic syndrome, PPARbeta
Façons de faire l’évaluation formative d’enseignants de français sénégalais : une analyse de leurs savoirs pratiques en contexte d’effectifs pléthoriques au Lycée

This research documents the ways formative assessment is operationalized by French teachers working in the context of overcrowded classrooms in a Senegalese High School. The recent choice for implementing the competency-based approach in this country invites teachers to promote the use of formative assessment which is geared towards the provision of high quality learning (Allal & Mottier Lopez, 2005, Black & Wiliam, 2009 Morrissette, 2010). However, Ministerial guidelines for its implementation are very general, and so far, research has not been carried out as regards its application in overcrowded classes. Building on the field of reflective practice (Schön, 1983) and an interactive situated vision of formative assessment (Mottier Lopez, 2007; Morrissette, 2010), I led a collaborative research with 14 French teachers working in the same High School. Six focus groups discussions were carried out which shed light on three dimensions related to formative assessment practices: contextual analysis of teacher practices, the negotiated construction of knowledge and the management of the overcrowded classrooms. Analysis of formative assessment practices in the context of « cultural strangeness » (free translation) (Douville, 2002) helped to conceptualize their know-how on evaluation in light of how they interpret the problems faced by students, their conception of what error constitutes and the ways they reinvent the traditional performance evaluation methods rooted in the school culture.

Keyphrases: formative assessment practices, French teachers, Senegalese High School, reflective practice, interactionist perspective, collaborative research, focus group, thematic analysis, operationalization of formative assessment practices in overcrowded classrooms, cultural strangeness
Sélection de gènes de référence pour la normalisation des expériences de PCR quantitative dans un modèle de dysfonction diastolique de lapin

Left ventricular diastolic dysfunction (LVDD) is characterized by the diminution of ventricle’s performance, its incapacity to relax normally and an increase of blood filling pressure. LVDD is considered as a main cause of heart failure in approximately 50% of patients suffering from this disease. However, the molecular mechanisms underlying LVDD remain unclear. Real-time quantitative PCR (RT-qPCR) is widely used in gene-expression studies. In this study we attempt to establish normalization genes for gene expression analysis in a rabbit model of LVDD. Eighteen New-Zealand white rabbits were exposed to normal (n=7) or 0.5% hypercholesterolemic (n=11) diet supplied by vitamin D2; an LVDD animal model previously characterized in our Laboratory. LVDD was assessed by echocardiography. RT-qPCR was performed using cDNA from left ventricle samples and measuring the stability of 10 candidate genes as normalisers (Gapdh, Hprt1, Ppia, Sdha, Rpl5, Actb, Eef1e1, Ywhaz, Pgk1, and G6pd).  We found that Sdha and Gapdh are the most stable genes using geNorm analysis with very high stability average M <0.2. By contrast, Hprt1 and Rpl5 were found to be the best combination for normalization with a stability value of 0.042 when using Normfinder. Comparison of both normalization strategies highlighted an increase of Anp, Bnp, Mcp-1 and Nox-2 mRNA expression in the hypercholesterolemic rabbits (p<0.05) compared to normal controls. This increase correlates with different DD parameters and validates the development of the disease in our model. To our knowledge, this is the first study highlighting stable reference genes for RT-qPCR normalization in a validated rabbit model of LVDD.

Keyphrases: RT-qPCR, Bnp, Diastolic dysfunction, Rabbit, RT-qPCR, Reference genes, Bnp
Back muscles activity and scoliosis in ataxic and dystrophic patients

To investigate the role of muscles in the development of adolescent idiopathic scoliosis (AIS), our group was initially interested in Duchenne muscular dystrophy (DMD) diseases where a muscular degeneration often leads to scoliosis. Few years ago the studies with those patients provided interesting results but were obtained only from few patients. To increase that number, the present project was initiated but recruitment of new DMD patients from Marie-Enfant hospital was found impossible. As an alternative, patients with Friedreich’s ataxia (FA) were recruited since they also suffer from a muscular deficiency which often induces a scoliosis. So, 4 FA patients and 4 healthy controls have been chosen to closely match the age, weight and body mass indexes (BMI) of the patients were enrolled in our experiments. As in the previous study, electromyography (EMG) activity of paraspinal muscles were recorded on each side of the spine during three types of contraction at 2 different maximum voluntary contractions (MVC). Moreover, the volume and skinfold thickness of these muscles were determined from ultrasound images (US) in order to facilitate the interpretation of EMG signals recorded on the skin surface. For the 3 FA right scoliotic patients, EMG activity was most of the time larger on the concave side of the deviation. The opposite was found for the 4th one (P4, left scoliosis, 32°) for whom EMG activity was larger on the convex side; it should however be noted that all his signals were of small amplitude. This was associated to a muscle weakness and a large skinfold thickness (12 mm) vs 7 mm for the 3 others. As for the paraspinal muscle volume, it was present on the convex side of P1, P3 and P4 and on the concave side for P2. As for skinfold thickness over this muscle, it was larger on the concave side for P1 and P2 and the opposite for P3 and P4. At the apex of each curve, the volume and skinfold thickness differences were the largest. Although the study covers only a small number of FA patients, the presence of larger EMG signals on the concave side of a spinal deformation is similar to pre-scoliotic DMD patients for whom the deformation is in its initial stage. It thus seems that our FA patients with more EMG activity on their concave side could see progression of their spinal deformation in the coming months in spite of their already important Cobb angle.

Keyphrases: DMD, Friedreich’s ataxia, Scoliosis, EMG, Ultrasound, Paraspinal muscles
Vector flow mapping using plane wave ultrasound imaging

Clinical diagnosis of cardiovascular disease is dominated by colour-Doppler ultrasound despite its limitations: angle-dependent velocity measurements and low frame-rate from conventional focusing. Two studies, varying in their approach, address these limitations using plane-wave imaging, post-processed with the delay-and-sum and autocorrelation methods. The aim of this study is to re-implement these methods, investigating some parameters which affect blood velocity estimation accuracy using 2D vector-Doppler. Through in vitro experimentation on stationary parabolic flow, using a Verasonics system, four parameters were tested on mapping accuracy: number of tilts per orientation, ensemble length for single titled images, cycles per transmit pulse, and orientation angle at various flow-rates. The optimal estimates were found for 7 compounded tilts per image, oriented at ±15° with 6 cycles per pulse. Reconstruction accuracies were comparable to conventional Doppler; however, maintaining frame-rates more than 10 to 20 times faster, allowing better characterization of fast transient events requiring higher temporal resolution.

Keyphrases: onde plane, plane-wave, vector flow, ultrafast ultrasound, blood flow