NCube/papyrus huggingface dataset:
Étude de la distribution de campylobacter à différentes étapes de la transformation primaire de la volaille dans des abattoirs du Québec

Campylobacter is responsible of the highest number of bacterial gastroenteritis worldwide. Most diseases in humans attributed to meat can be associated to consumption of or contact with poultry derived products; broiler chicken being involved in the majority of cases. The contamination of carcasses often occurs during the slaughter process. While many studies from various countries reported the distribution of Campylobacter among various critical steps of the slaughter process, none has been published, to our knowledge, in Canada regarding the presence and distribution of this bacterium within the abattoir. Our hypothesis was that it would be possible to identify key steps to control the contamination of carcasses by this bacterium by studying the presence and distribution of Campylobacter on carcasses and within the environment during the slaughter process. This study had two objectives. The first objective was to describe the distribution of Campylobacter within two selected slaughterhouses in Quebec in order to understand which processing step(s) play(s) a critical role in carcasses contamination. In the second objective, we aimed to verify if actual management procedures applied in these abattoirs were efficient in preventing consumer’s exposition. To meet these goals, four birds by production lot, one at each of the following steps (after bleeding, at transfer between killing and evisceration chain, after evisceration and after the cooling process) were sampled for a total of 379 birds from February 2017 to July 2017 in two slaughterhouses located in the province of Quebec. Furthermore, 217 environmental samples were collected during these visits in various sites possibly in contact with birds. Samples were suspended in peptone water and submitted to a PCR assay, using a specific 16S ribosomal probe, for detection of Campylobacter.  Overall, for the year of the study, we observed a significantly higher number of positive carcasses in summer compared to spring, while the environmental samples were more often positive in winter compared with summer. Furthermore, our results indicated that the number of positive carcasses decreased over the various processing steps, being either negative (air chilling) or low (water chilling) after the cooling process. Although we experienced some issues associated with the sensitivity of the procedure we used in this study to recover Campylobacter, taken together, these results suggest that the actual management procedures of Campylobacter in studied slaughterhouses are efficient.

Keyphrases: Campylobacter, Abattoirs, Broiler chicken, Slaughterhouses, Critical steps, Risk management
Utilisation de la vaccinologie réverse pour l’identification de protéines candidates vaccinales chez Clostridium perfringens causant l’entérite nécrotique aviaire

Avian necrotic enteritis caused by Clostridium perfringens is a disease with a major economical impact, generating losses up to 6 billion dollars for the poultry industry worldwide. This disease appears in broiler chicken flocks that no longer employ the use of antibiotics. To date, no alternative method allows for the efficient prevention of necrotic enteritis (NE) and a control by a vaccinal strategy would be mostly prized. A comparative genomics approach as well as comparative and subtractive reverse vaccinology identifying immunogenic bacterial surface proteins is one of the most promising methodologies for the rapid development of an efficient vaccine. A comparative genomic study was performed on 48 C. perfringens strains isolated from healthy broiler chickens and from broilers affected by necrotic enteritis. From this study, it was established that the genomes analyzed were composed of 155 700 distinct proteins where 13% were predicted to have an extracellular expression, 65% at the cytoplasma level and 22% within the plasma membrane. The evaluation of the immunogenic potential of these proteins was established with the prediction software VaxiJen v2.0 for which a 0.5 threshold score allowed for the identification of four score categories among the identified proteins, from 0.5 to 1.5. For the most part, proteins with the highest scores were associated with an extracellular localisation. The combination of the immunogenicity score and localisation of the analysed proteins led to the selection of 12 vaccinal candidate proteins that were mostly identified as hypothetical. A more in-depth description of these proteins would allow the assessment of their function, the evaluation of their true immunogenic potential by characterizing their interaction with the avian immune system and ultimately, evaluate their probable role in the pathogenesis of necrotic enteritis.

Keyphrases: Clostridium perfringens, vaccinologie reverse, vaccin, Broiler chickens, necrotic enteritis, reverse vaccinology, candidate proteins, vaccine
Amélioration des services de génomiques et de surveillance du virus du syndrome 
reproducteur et respiratoire porcin

Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen, costing over 130 million dollars annually in Canada. Surveillance is done by Sanger sequencing of the ORF5 gene, but we hypothesized that whole genome sequencing (WGS) of PRRSV genome will allow a better epidemiological monitoring of PRRSV compared to ORF5 gene sequencing. To develop an efficient method of PRRSV WGS, 149 PRRSV samples (sera, lungs, pool of tissues and others) collected for surveillance or from sick animals were tested. Viral RNA was concentrated using a poly(A) tailed RNA enrichment method, and sequencing was done on an Illumina platform. WGS was successful in 67.11% of cases. WGS was successful in some tissues and lungs samples with RT-qPCR cycle quantification (Cq) values up to 26.50, and in some sera with Cq value up to 34.13. The developed WGS methodology was 4650 times more sensitive for PRRSV WGS than previously described methods. To quantify the impact of WGS, 88 successful samples for the WGS of PRRSV were used to compare efficiency of WGS and ORF5 sequencing. Two different full-length genomes of PRRSV were found in four of those samples (coinfection rate of 4.55%). Six full-length PRRSV genomes (6.52% of PRRSV strains) were found to cluster differently compared to ORF5 sequencing. WGS of PRRSV also enabled a better classification or characterisation of 9.10% of the PRRSV infected samples compared to ORF5 sequencing. Thus, WGS can be both sensitive and more accurate then ORF5 classification for the characterisation of PRRSV strains.

Keyphrases: virus, coinfection, recombinant, porc, Porcine reproductive and respiratory syndrome, whole genome sequencing, high-throughput sequencing, classification, swine
Bronchial angiogenesis in asthmatic horses

Equine asthma is a chronic inflammatory disease of the lower airways characterized by structural changes that lead to bronchial wall thickening and airflow obstruction. Treatment for equine asthma partially reverse these remodeling changes. Angiogenesis has been shown to increase vascularization of the bronchial mucosa, which contributes to the thickening of the bronchial wall in humans with asthma, opening a new window for a targeted treatment. However, little information is available related to the occurrence of angiogenesis in asthmatic horses. The objective of this study is to document the presence of angiogenesis in the bronchi of asthmatic horses. Bronchial samples from seven asthmatic horses collected during an episode of exacerbation of the disease, seven asthmatic horses in clinical remission, and seven agematched healthy horses were studied. Immunohistochemistry analysis was performed with type IV collagen as a biomarker for basement membranes. The number of vessels, vascular density, vascular area and mean vessel size values were measured by histomorphometry using an image analysis software (Image J) and values from all three groups were compared using a one-way ANOVA (p <0.05). A Benjamini-Hochberg pairwise post hoc-test was performed to correct the alpha level for repeated measurements. A significant increase in the number of vessels in asthmatic horses in exacerbation (p = 0.007) and in horses in remission (p = 0.02) was observed in comparison to controls. Similarly, the vascular area was increased in horses with asthma in exacerbation when compared to controls (p = 0.02) and to horses in remission (p = 0.04). No other significant differences were observed. In conclusion, angiogenesis is present in the central airways of asthmatic horses, suggesting that it may contribute to the thickening of the airway wall. Further studies are warranted in order to assess the response to a targeted treatment.

Keyphrases: Asthma, Angiogenesis, Horses, Collagen IV
Implication des gènes curli dans un phénotype distinct d'autoagrégation et de formation de biofilm chez certaines souches Escherichia coli O157: H7

Enterohemorrhagic E. coli (EHEC) O157:H7 is an important foodborne pathogen that causes severe toxi-infections in humans. These bacteria have a higher capacity to form biofilm, impeding the control of the contamination in different environments and allowing their persistence. Some E. coli O157:H7 strains, including the Sakai reference strain, display a distinctive ability to autoaggregate and form strong biofilms. The aim of this work was to identify the genes involved in autoaggregation and biofilm formation in Sakai strain, and to verify the association between identified factors and the same phenotype in other EHEC O157: H7. We found that csgA, csgB and csgG curli genes were significantly overexpressed in strain Sakai compared to strain EDL933, a low biofilm-former and non-autoaglutinating strain. Sakai csgB and csgG Tn10 mutants formed significantly less biofilm and autoaggregation than the wild-type strain, and lost the curli-producing phenotype. Complementation restored the strong autoaggregation and biofilm formation phenotype, and the curliated morphotype of Sakai. In addition, E. coli O157: H7 isolates tested for curli formation, Sakai-like strains were curli-producing, whereas EDL933-like strains were non-curliated. These results suggest that overproduction of extracellular curli fibers in a subset of E. coli O157: H7 strains may be responsible for their particular phenotype of autoaggregation and strong biofilm formation. The project provides a better understanding of the mechanism of biofilm formation in EHEC, as well as reinforcing the hypothesis that curli fibers are an attractive target to counter the persistence of these bacteria in natural and industrial environments.

Keyphrases: Escherichia coli O157:H7, EHEC, biofilms, curli, autoaggregation, biofilm formation, curli fibers
Le développement des conduites agressives chez les élèves populaires au secondaire : l'affiliation à des amis populaires et agressifs comme facteur médiateur

Teenagers’ popularity is known to be linked to an increase in aggressive behaviors through time. However, few studies have explored the mechanisms that can explain this association. This study aims to assess to which extent friends’ popularity and aggressivity can possibly play a mediating role to explain the relationship between popularity and aggressivity at the beginning of high school. The sample of this longitudinal study consists of 621 students in 7th and 8th grade from disadvantaged socio-economic backgrounds who attended three public high schools in the Montreal area. The participants’ popularity and aggressivity scores were measured using a peer nominated protocol and assessed three times over a period of one year. Friends’ identity and characteristics were also measured repeatedly using the same procedure. Results show that participants’ popularity in the beginning of 7th grade promotes friendships with peers who are more and more popular and aggressive at the beginning of 8th grade. In return, friendships with aggressive peers can explain the increase in aggressive conducts at the end of 8th grade. The association between perceived popularity and aggressivity, for both boys and girls, can be explained by friends’ characteristics. The discussion focuses on the importance of the relational context when it comes to accounting for the developmental consequences associated with being perceived as popular in early adolescence.

Keyphrases: Adolescence, Perceived popularity, Aggressivity, Friends' characteristics
Bayesian modeling of biological motion perception in sport

The ability to recover information (e.g., identity or type of activity) about a moving living object from a sparse input is known as Biological Motion perception. This sparse input has been created and introduced by Johansson in 1973, using only light points placed on an individual's strategic joints. Biological motion perception/recognition proves to play a significant role in activities that are critical to the survival and social life of humans and primates. In this regard, the study of visual analysis of human action had the attention of scientists for decades. These studies are mainly focused on: kinematics information of the different movements (such as type of activity, emotional states), motor role in the perception of actions and underlying mechanisms, and associated neurobiological substrates. The latter being the main focus of the present study, a new descriptive risk-averse Bayesian simulation model, capable of discerning the ball’s direction from a set of complex biological motion soccer-kick stimuli is proposed. Inspired by the previous, neurophysiologically plausible, biological motion perception models and recent studies, the simulation model only represents the dorsal pathway as a motion information processing section of the visual system according to the two-stream theory, while the stimuli used have been obtained from a previous psychophysical study on athletes. Moreover, using the psychophysical data from the same study and tuning a set of parameters, the model could successfully simulate the psychometric function and average reaction time of the athlete participants of the aforementioned study. 5 Although it is established that the visual system optimally integrates all available visual cues in the decision-making process, the results conform to the speculations favouring motion cue importance over dynamic form by only depending on motion information processing. As a functioning simulator, the present simulation model not only introduces some insight into the subject at hand but also shows promise for industry use. For example, predicting the impact of the lens-induced distortions, caused by various lens designs, on human decision-making. Keywords: Biological motion, Bayesian, Dorsal pathway, Hierarchical simulation model, Psychometric function, Reaction time

Keyphrases: Bayesian, Hierarchical Simulation Model, Biological Motion, Biological Motion Perception, Computational Modeling, Dorsal pathway, Reaction-time, Psychometric Function
Élucidation des rôles des voies Wnt et Hippo dans le développement et la fonction du tractus reproducteur femelle chez la souris

The development of the female reproductive tract arises from the coordination of numerous signaling pathways regulating processes such as proliferation, differentiation and apoptosis during embryogenesis. The Wnt and Hippo pathways are known to be involved in these processes. Wnt pathway activation, via its specific ligands, results in the stabilisation and increased transcriptional activity of β-catenin. The Hippo pathway does not possess any specific ligands. In contrast to Wnt, inactivation of the Hippo pathway (via Lats1 and Lats2 kinases) is required for the stabilization and increased activity of the transcriptional coactivators YAP and TAZ. The Wnt pathway is known to be involved in the development of the female reproductive tract. Further evidence also suggests the possibility of functional redundancy amongst certain WNT ligands such as Wnt4 and Wnt5a. The Hippo pathway is not known to be implicated in the development of the female reproductive tract. However, numerous interactions have been reported between both pathways, suggesting a possible unknown role of Hippo in that context. The objective of this project was to elucidate the roles of Wnt4, Wnt5a, Lats1 and Lats2 in the Müllerian mesenchyme and the development of the uterus. Results from our first study confirmed the partially redundant roles of Wnt4 and Wnt5a in the development of the uterus. Our model was notably characterized by developmental abnormalities and loss of uterine functions resulting in in vivo decidualization defects and loss of conceptus viability. Results from our second study confirmed the redundant roles of Lats1 and Lats2 in the maintenance of Müllerian mesenchymal cell multipotency. We observed premature differentiation of Müllerian mesenchymal cells into myofibroblasts in absence of both Lats1 and Lats2. These changes were in part due to the increased expression of the target gene Ctgf. Our additional results could not demonstrate any potential interactions between the Wnt and Hippo pathways that could explain the phenotypic changes. In conclusion, our studies confirmed and further discovered novel roles of these pathways in the development of the Müllerian ducts. These models could also lead to better understanding of the pathophysiology of certain uterine diseases and the discovery of potential therapeutic approaches.

Keyphrases: B-catenin, Wnt4, Wnt5a, Lats1, Lats2, YAP, TAZ, Müllerian ducts, Wnt pathway, Hippo pathway, Myofibroblasts
L'approche codesign comme une stratégie d'apprentissage de la conception dans l'atelier de projet

The studio is at the heart of design education and presents itself as a simulation of professional practice. It is based on learning-by-doing, in a project-based approach. Moreover, critiques are the common educational practice in the studio. They are based on exchanges between the teacher and the students, in order to learn the design process and the design thinking. However, these critiques face a gap between the nature of the learning they carry (learning-by-doing) and the difficulties of explaining how it works to the students. Indeed, being an expert in the design process, the teacher is supposed to transfer his experience and his know-how, through exchanges with his students. Though, the teacher faces the challenge of externalizing his design thinking and a knowledge often tacit, to students who are expected to start designing without knowing how to do it. Besides, nowadays, and with the use of CAD tools, critiques are often reduced to a quick and individual verbal exchange at the teacher's table, accentuating the hierarchy, in addition to being focused on productivity more than the process itself. This is why it is necessary to bring some transformations to the actual way of doing critiques and bring further understandings of the learning situations in the studio. This doctoral thesis explores a new strategy using codesign approach for learning the process of designing in the studio. Through observations from a studio lead by codesign approach, in a natural context, this research aims to understand the unfolding critiques by this approach, its characteristics and its contributions to design learning. The nature of codesign, as a social activity and where thinking is done aloud naturally, has allowed the study of design processes in a learning context, without intrusiveness. Our methodology is innovative, since we used immersive retrospective interviews, which evoke memory, for the first time in the study of studio pedagogy, to combine the data collected in direct observations. We have contributed to the development of knowledge regarding the understanding of design learning situations, by shedding light on the progress of project critiques using the codesign approach. We have developed knowledge on the strategies (knowing-in-action in educational context) used by the teacher, on the contributions of all participants and the engagements of the students in the learning situations. Besides, we constructed an overview on this approach advantages compared to the traditional critiques and the learnings perceived by students themselves. Finally, we have developed some educational recommendations addressed to studio teachers.

Keyphrases: Codesign, Design studio, Project critiques, Learning, Design process
La criminalité soldatesque au Canada sous le Régime français

Since the arrival of social history in the 1960s, the military history of Canada under the French Regime has been enriched by several studies of soldiers. Historians of justice have also investigated the rank and file as a social group. These studies – which were not exclusively devoted to soldiers – adopted a quantitative approach. Though historians have viewed various aspects of soldiers’ lives, none have singled out criminality. That is precisely what this thesis attempts to do, by exploiting principally the judicial archives. More precisely, it analyzes criminal trials involving soldiers, relying as well on Ancien Regime jurisprudence to help place soldiers’ criminality in perspective. The trials offer a view of the different forms of this criminality and of some of the contributing factors. Lastly, several trials in addition to the colonial correspondence show that the army, not just a war machine, also played role in the rehabilitation of soldiers inclined to criminal behavior.

Keyphrases: violence, indubordination, soldier, New France, criminality, insecurity