NCube/papyrus huggingface dataset:
L'ADN: dans l'enquête et au tribunal - Étude de cas du tueur en série Robert William Pickton

Several factors can affect the flow of DNA traces in the judicial process. This work is a case study on the Pickton case, a serial killer from Vancouver. This case study is specifically interested in the motivation behind the selection of DNA traces throughout the investigation and at the level of admissibility of DNA evidence at trial. The literature review provides an overview of studies ranging from the role of DNA traces from collection traces to the admissibility of DNA evidence in court. The analysis is based on DNA traces collected, analyzed and presented to the Court, the data were obtained in four different data sources. This analysis demonstrated that most of the analyzed DNA traces were presented to the Court. In the Pickton case, those that have been deemed ineligible were for procedural reasons.

Keyphrases: Judicial process, DNA, Case study, Serial killer, Eligibility, Proof
Perceptions du «bien manger» chez des intervenants clés agissant auprès d’enfants fréquentant des services de garde préscolaires

Context: Preschool age represents an important period for the acquisition of healthy eating habits. With their knowledge, attitudes, beliefs, practices and perceptions with regard to eating and nutrition, several stakeholders influence children: parents, but also foodservice managers and educators in childcare centres.   Objectives: This study describes and analyzes the perceptions of “eating well” of 113 foodservice managers, 302 educators and 709 parents of 2 to 5-year-old children in childcare centres of Quebec.   Methodology: This study focuses on an open-ended question, repeated in three self-administered questionnaires taken from the research Offres et pratiques alimentaires revues dans les services de garde au Québec. Data collected between 2009 and 2010 was analyzed using a coding grid crafted by induction and deduction.   Results: Qualitative data analysis revealed the recurrence of several themes such as variety, balance, moderation, vegetables and fruits, as well as the emergence of pleasure, health, Canadian Food Guide, organoleptic qualities, coercive practices and commensality. Findings indicate that variety, health and balance are perceptions common to all three categories of stakeholders, while the Canadian Food Guide, pleasure, healthy eating and organoleptic qualities are specific to certain stakeholders.   Conclusion: This portrait sheds some light on how “eating well” is understood by stakeholders who play an important role in the development of 2 to 5-year-old children. It also informs actors developing public health messages, interventions and policies promoting healthy eating and encouraging the set up of environments supporting the adoption of healthy eating habits in childcare centres of Quebec, as well as in households.

Keyphrases: perception, services de garde, Québec, parent, healthy eating, qualitative, childcare centre, preschool, Quebec, educator, foodservice responsible
Investigation du rôle de Myo9b dans la migration des interneurones GABAergiques corticaux

Epileptic encephalopathies are early-onset diseases characterized by refractory epilepsy with developmental delay. To identify the underlying genetic cause of these disorders, Dr Rossignol’s laboratory has performed whole-exome sequencing in children with sporadic epileptic encephalopathies. They have identified a novel de novo mutation in the MYO9B gene in one patient. Myo9b is known to regulate cell migration in the immune system and in cancer cells. It is expressed in the developing rodent brain, but its roles during brain development are largely unknown. Recent evidence suggests that epilepsy can be caused by an imbalance between inhibition and excitation in cortical circuits. Indeed, defects in the development or the functions of cortical GABAergic interneurons (INs) have been associated with epilepsy in human and in mouse models. Therefore, we postulated that Myo9b might play a role in the development of INs. In this thesis, I show that Myo9b is expressed in INs from early embryonic ages to post-natal ages. Furthermore, I demonstrate that the ex vivo downregulation of Myo9b in INs in cortical embryonic organotypic cultures causes morphological defects in migrating INs, including aberrant polarization of these cells. These morphological changes might result in aberrant IN migration, which would be expected to perturb the cortical inhibitory-excitatory ratio.

Keyphrases: Myo9b, Myosine IXb, cytosquelette, actine, tubuline, tangential migration, GABAergic interneurons, epileptic encephalopathy, epilepsy, cytoskeleton, actin, tubulin
Analyse du métabolisme du soufre de la bactérie autotrophique acidophile Acidithiobacillus thiooxidans ATCC 19377

The environmental impact of mining extraction is important. The action of microorganisms using their sulfur metabolism to metabolise compounds in mining waste contributes to reactions that may impact water quality and the environment. Few studies have been conducted on environmental microorganisms to advance the global comprehension of their sulfur metabolism in an attempt to study their impact on the environment. In this study, we cultivate an environmental bacterium, Acidithiobacillus thiooxidans, in an attempt to understand its sulfur metabolism in different growth media and at different levels of acidity. We used high-throughput RNA sequencing in association with sulfur biogeochemistry and electron microscopy to determine the expression of the genes encoding sulfur metabolism enzymes. The expression of genes encoding sulfur metabolism enzymes was media and pH-dependent. Also, the biogeochemical analysis showed the presence of reduced sulfur intermediates and of sulfuric acid in the medium. Finally, an electron microscopic analysis revealed that the bacteria stock sulfur in the cytoplasm. These results resulted in a better comprehension of its sulfur metabolism and it opens the possibility to predict reactions in mining operations that have impact on the environment.

Keyphrases: Acidithiobacillus thiooxidans, Transcriptome, Environment, Mining extraction, RNA sequencing, Biogeochemistry, Sulfur, Electron microscopy
Les oncogènes NUP98-PHF23 et NUP98-HOXD13 confèrent un potentiel aberrant d’auto-renouvellement aux progéniteurs thymiques

Early events in T-cell acute lymphoblastic leukemia (T-ALL) are regulated mostly by the activation of oncogenic transcription factors in the T lineage. We show that among those, two fusion genes, NUP98-PHF23 (NP23) and NUP98-HOXD13 (NHD13), reprogram normal thymocytes into pre-leukemic stem cells (pre-LSCs) with sustained self-renewal activity. By clonal analysis of serially transplanted thymocytes, we found that this population is organized in a hierarchy much like normal hematopoietic stem cells. These pre-LSCs were enriched in a subset of KIT+ immature thymocytes in which both NP23 and NHD13 activated a stem cell signature that includes Hoxa9, Hoxa10, Lyl1 and Hhex. Moreover, self-renewal activity was abrogated by RNA interference against Lyl1 or Hhex, indicating their functional importance downstream of NP23 or NHD13. Since these two genes are also required downstream of three other T-ALL oncogenes, SCL/TAL1, LMO1 and LMO2, we conclude that the levels of Lyl1 and Hhex set the threshold for thymocyte reprogramming into pre-LSCs.  In light of the evidence that pre-LSCs escape chemotherapy to cause relapse, our results provide new avenues for targeting pre-LSCs in the immature subgroup of T-ALL.

Keyphrases: thymocytes, NUP98-PHF23 (NP23), NUP98-HOXD13 (NHD13), T-cell acute lymphoblastic leukemia (T-ALL), preleukemic stem cell (pre-LSC), self-renewal, transgenic mouse model
Establishing a Robust In Vitro Embryonic Stem Cell Differentiation Assay to Monitor the Hematopoietic Potential of DELES Clones

To carry out functional studies on the mouse genome, our laboratory has generated a library of Embryonic Stem Cell (ESC) clones harboring random nested chromosomal deletions – DELES library. This library contains deletions covering ~ 25% of the mouse genome.  In the lab, we are interested in identifying novel hematopoietic cell fate determinants using this resource. A primary screen using benzidine to demonstrate the presence of hemoglobin in embryoid bodies (EBs) was able to identify several DELES clones exhibiting abnormal hematopoietic phenotype. Since this assay only tested for the presence of hemoglobin, the goal of my project is to establish a robust in vitro ESC differentiation assay to monitor the hematopoietic potential of DELES clones. My hypothesis is that the hematopoietic differentiation assay published by Dr. Keller can be used to observe hematopoietic commitment of the DELES clones. Using QRT-PCR and FACS assays I was able to monitor the kinetics of hematopoietic differentiation by observing the expression of hematopoietic genes and surface markers including CD41, C-KIT, RUNX1, GATA2, CD45, β-GLOBIN 1 and TER-119. This assay will be used to validate the hematopoietic potential of the candidate DELES clones identified in the primary screen.    My secondary project aims to use the same retro-viral Cre-loxP strategy used for the DELES library, in order to generate a library of KBM-7 leukemic cells harboring nested chromosomal deletions. My goal here is to test if the human near haploid KBM-7 cell line can be exploited using the DELES approach to create this library. The library of KBM-7 clones will be used to delineate the molecular activities of potential anti-leukemic drugs that we have identified in the lab to inhibit cell growth in several patient-derived acute-myeloid leukemia specimens. It will also allow me to identify molecular signaling pathways that, when genetically disrupted, can confer resistance to these drugs.

Keyphrases: Embryonic stem cells, hematopoietic differentiation, KBM-7 cells, chromosomal deletions
Regulation of lipocalin prostaglandin-D synthase expression by interleukin-1β in human chondrocytes

Osteoarthritis is a complex multifactorial disease; many factors are involved in its pathogenesis, among those factors prostaglandins. Some prostaglandins have inflammatory role and some have anti-inflammatory role. Prostaglandin D2 (PGD2) is a well-established anti-inflammatory PG which is synthesized by the Lipocalin prostaglandin-D synthase (L-PGDS) enzyme. Upon the initiation of the inflammatory process in osteoarthritis, chondrocytes try to save themselves by activating salvage pathways, among these pathways is the induction of L-PGDS gene. In this study we are addressing the signaling pathways involved in the regulation of (L-PGDS) gene expression, in chondrocytes treated with different inflammatory mediator. Rationale: understanding the regulation of L-PGDS will allow us to design therapeutic targets that can switch on the intrinsic anti-inflammatory pathway. Method and findings: In vivo, osteoarthritis was induced in mice knees surgically or naturally following aging, the development of osteoarthritis was then confirmed histologically. The expression levels of L-PGDS were detected by Immunohistochemistry. In vitro, human chondrocytes were treated with different inflammatory mediators (interleukin-1 beta, interleukin-17, hydrogen peroxide and tert-Butyl hydroperoxide). Interestingly, in most cases chondrocytes increased expression of L-PGDS in a dose and time dependent manner. We discovered that chondrocytes release L-PGDS into the extracellular space in response to inflammation, in vivo and in vitro. Lastly we observed different isoforms of L-PGDS generated in response to inflammation.

Keyphrases: Osteoarthritis, Lipocalin prostaglandin D synthase, Interleukin 1 beta, Prostaglandin D2, Lipocalin prostaglandine synthase D
L'implication de la Cycline B dans le processus de cytocinèse

Dysregulation of the cell cycle can cause cancer. During cytokinesis a contractile ring of actin and myosin forms, contracts and gives rise to a midbody ring which controls abscission. The process of cytokinesis is controlled by proteins such as the Rho GTPase, which activates cytokinesis and cyclin-Cdks that inhibit cytokinesis. Drosophila has 3 mitotic cyclins CycA, CycB and CycB3, which are successively degraded at the end of mitosis to allow the initiation of cytokinesis. The last step of abscission is a phenomenon that is still obscure. The ESCRTIII components VPS4 and CHMP4C protein linked to ANCHR will, in an Aurora B kinasedependent manner, promote abscission with recent studies implicating Cyclin B at this stage. Here, the aim was to test the role of cyclin B in cytokinesis and abscission, using real-time, high resolution microscopy of Drosophila melanogaster S2 cells expressing recombinant fluorescent proteins. This study was divided into two parts: gain and loss of function studies respectively using stable non-degradable cyclin B (CycBstable-GFP) and inhibition by using CycB double-stranded RNA (dsRNA). The CycBstable-GFP perturbed cytokinesis by inducing multiple contractile rings and midbodies. However CycB depletion had no detectable effect on the progression of cytokinesis nor on abscission despite the recruitment of CycB-GFP to the late midbody. In contrast, the protein Cdk1 seemed to play a role in abscission, since its depletion induced a delay. It therefore has potential implications for cytokinesis.

Keyphrases: Midbody, Abscission, Cyclin, Cytokinesis, Contractile ring
Dissection moléculaire de la sénescence cellulaire induite par le stress et la thérapie dans le cancer de l’ovaire et son impact sur la réponse des patientes

Human ovarian cancer (OvCa) is the deadliest gynecologic malignancy and existing surgical/chemotherapeutic treatment options have been relatively static for decades. We propose that understanding OvCa cell fate decisions taken in response to chemotherapy could guide new therapeutic opportunities. Damage-induced cellular senescence is often associated with TP53 activity, which is heavily mutated in high grade serous (HGS) OvCa (>90%), the most common form of this disease. Here, using patient derived tissues, we show that primary HGS-OvCa cultures predominantly trigger CDKN2A- associated (p16INK4A isoform) senescence following exposure to stress or chemotherapy. Key senescence hallmarks including altered morphology, senescence-associated-Betagalactosidase, DNA damage, cell cycle arrest and the senescence-associated secretory phenotype were evaluated and detected in damaged cells. Using tissue microarrays built from pre- and post-treatment human HGS-OvC tissue samples with accompanying clinical data, we quantified post-treatment hallmarks of senescence including reduced cell proliferation weeks after chemotherapy. Importantly, p16INK4A expression in pretreatment HGS-OvC samples correlated with increased patients survival, suggesting for the first time that senescence-competence in human cancer cells may have a beneficial impact on treatment outcomes for patients. In order to guide the potential improvement of existing human therapies via pharmacological senescence manipulation, our results suggests that it is important to determine for many types of human cancer whether treatment-induced senescence positively or negatively impacts disease progression and patient survival.

Keyphrases: Senescence, Therapy-induced senescence (TIS), High-grade serous ovarian cancer, Chemotherapy, Cell fate decisions, p16INK4A, Tissue Microarray (TMA)
Déficience dans la réparation par excision de nucléotides en phase S induite par la séquestration du facteur de réplication RPA

Introduction Replication-blocking UV-induced DNA adducts are removed by the highly-conserved nucleotide excision repair (NER) pathway. We previously demonstrated that ATR kinase, a preeminent responder to replicative stress, is required for efficient NER exclusively during S phase. Subsequent data suggested that this requirement is not a manifestation of ATR signaling per se, but rather more broadly reflects some consequence of replication stress. In this respect we emphasize that after UV treatment, heterotrimeric RPA plays essential and independent roles in both NER and restart of blocked replication forks. Hypothesis: In general, mutations which confer increased replicative stress engender excessive sequestration of RPA at blocked replications forks which in turn reduces the availability of this factor for NER.  Methods and Results: The powerful yeast model was chosen to address this hypothesis. We developed a cell-cycle-specific DNA repair assay to demonstrate that cells deleted for Mec1, the yeast ATR homolog, are defective in S phase-specific NER. Moreover several other yeast mutants, i.e., ones characterized by elevated levels of spontaneous DNA damage, exhibited a similar defect. These mutants also displayed increased frequency and intensity of RPA focus formation. Finally, degron-mediated depletion of RPA in wild-type cells resulted in significant inhibition of NER uniquely during S. Conclusion: Our data support the notion that RPA sequestration at blocked replication forks in yeast undergoing high levels of replication stress abrogates NER during S phase. This work in yeast facilitates elucidation of the analogous phenomenon in humans and, ultimately, harbours implications for undestanding the mechanism of UV-associated skin cancer development.

Keyphrases: Nucleotide excision repair, UV rays, DNA damage response
L'autisme, une autre intelligence: nouveauté ou recul?

In this article, we examine and evaluate Laurent Mottron's theory of autism as described in his book L'autisme : une autre intelligence (Mottron, 2004). This review article contains four parts. In the first part, we summarize Mottron's conception of Pervasive Developmental Disorders (PDD), with his focus on high functioning people, a group he considers much larger than formerly thought and neglected in current literature or service networks. He calls this group PDDWID (Pervasive Developmental Disorders Without Intellectual Deficiency) and creates an expanded new definition of autism. Secondly, we examine his theory of a different intelligence as displayed by ”autistic” people. We conclude that his conceptual assertions on this issue lack evidence-based validation, and lead to misinterpretation of the strengths and deficits of persons with ASD. Thirdly, we examine his appraisal of autism treatment. We conclude that he underestimates the value of early intensive behavioral intervention, and more generally of applied behavior analysis for the whole spectrum. His position on TEACCH as the main psychosocial and educational response for persons with ASD is inadequately justified, and anachronistic. Fourthly, Mottron's approach to the study of emotions based on autobiographical materials and introspection is a misleading avenue as a primary research method. Concluding comments question his dialectical stand contrasting autistics and non-autistics, his social activism for high functioning ASD persons, and his ideological endorsement of autism as a culture.

Keyphrases: Autisme, Intelligence, Autism, Treatment, Emotions
Qui utilise 10% de son cerveau?

This article discusses in 4 sections a widely held belief that humans use only 10 % of their brain. Firstly the pervasiveness of this belief is evaluated. Secondly the origins of the so-called « 10 % myth » are assessed. Thirdly, the authors demonstrate how this myth is invalid on the basis of neurobiological knowledge, which is reviewed according to the neuroanatomy of the brain, its neurophysiology, cerebral plasticity and evolution. The fourth section tries to account for the persistence of the myth still today.

Keyphrases: Brain, 10 % myth, Belief, Cerebral plasticity
Analyse de la distribution d'Escherichia coli, utilisée comme un marqueur microbiologique, dans un réseau de production porcin

Escherichia coli is an important constituent of the pig intestinal microbiota. The transmission of pathogenic E. coli between herds and a slaughterhouse in a production network, in particular to illustrate its dissemination in a zoonotic perspective, is not well characterized. The detection of E. coli virulence genes could be used as an indicator of contamination to describe transmission between herds and the slaughterhouse. The objective was to identify an E. coli contamination marker to describe some transmission modes of pathogenic E. coli in a well-defined swine production network. A defined geographical area containing 10 farms, a slaughterhouse, and a transportation network was selected. Environmental samples were collected at various sites inside and outside the farms (3 visits), at the slaughterhouse yard (2 visits), and on the vehicles of the animal transporter. Three consecutive production batches were followed during 12 months. The presence in the samples of virulence genes (eltB, estA, estB, faeG, stxA, stx2A, eae, cnf, papC, iucD, tsh, fedA) commonly associated with pathogenic E. coli was examined by conventional multiplex PCR. The monitoring of the virulence gene profile distribution both temporally and spatially resulted in the proposing of an ETEC/F4 contamination marker. ETEC\F4 positive samples were defined by the detection of at least one ETEC enterotoxin gene (estB, estA and eltB) in combination with the faeG gene encoding F4 fimbriae in samples by PCR. The distribution of ETEC/F4 positive samples suggests that the slaughterhouse yard may act as a reservoir of contamination frequently visited by transporters, which are mechanical vectors of contamination between herds. These results illustrated the need to improve the biosecurity relationship between herds and the slaughterhouse, both playing a role in dissemination of pathogenic (and potentially zoonotic) microorganisms in swine production.

Keyphrases: Escherichia coli, ETEC/F4, Source de contamination, Distribution, Contamination marker, Production network, Farms, Slaughterhouse, Swine, Environment, Contamination sources
Étude longitudinale à propos de l’espace occupé par les pseudosciences dans les librairies du Québec

In this article, we present the results of a longitudinal study on the proportion of space devoted, on the one hand, to books of pseudosciences (paranormal, the occult, new age, methods of divination, etc.) and of sciences for adults; and on the other hand, on the proportion of space devoted to books of spirituality and sciences for children in the bookstores of Quebec. Two measures were taken, one in 2001 in 55 bookstores, and the other one in 2011 in 72 bookstores. Statistical analyses were conducted only on the measures taken in the bookstores that were visited at the two measurement times. Results from correlational analyses show that those bookstores that devote more space to books of pseudosciences for adults (n = 40) and to books of spirituality for children (n = 38) are the same in 2001 and 2011. Moreover, a repeated measures ANOVA indicate that the proportion of space devoted to books of pseudosciences for adults had decreased at the second measurement time, which is not the case for books of spirituality for children. After briefly revisiting the methodology and results, we put forward four reasons that may explain the popularity of pseudosciences, as well as a few ethical and social consequences from their fashion. In our concluding remarks, we suggest two solutions to promote scientific reasoning among adolescents and children.

Keyphrases: Pseudosciences, Science, Bookstores, Longitudinal study