NCube/papyrus huggingface dataset:
Comparaison des méthodes d'analyse de l'expression différentielle basée sur la dépendance des niveaux d'expression

Microarrays remain an important tool for the measurement of gene expression, and a myriad of methods for their pre-processing or statistical testing of differential expression has been proposed in the past. However, insufficient and sometimes contradictory evidence has prevented the emergence of a strong consensus over a preferred methodology. This leaves microarray practitioners to somewhat arbitrarily decide which method should be used to analyze their data. Here we present a novel approach to the problem of comparing methods for the identification of differentially expressed genes. Over eight hundred analytic pipelines were applied to more than a hundred independent microarray experiments. The accuracy of each analytic pipeline was assessed by measuring the average level of co-regulation uncovered across all data sets. This analysis thus relies on a varied set of biologically relevant data, does not confound reproducibility for accuracy and can easily be extended to future analytic pipelines. This procedure identified FARMS summarization and the TREAT gene ordering statistic as algorithms significantly more accurate than other alternatives. Most interestingly, our results corroborate recent findings about the importance of taking the magnitude of change into account along with an assessment of statistical significance.

Keyphrases: microarrays, fold-change, differential expression
L'autre Basque

Basque nationalism has emerged several centuries ago, however, it experienced a global resonance only since the last fifty years with the formation of the armed Basque nationalist and separatist organization Euskadi Ta Askatasuna (ETA).   Formed to fight the Franco regime, the organization is now considered as a terrorist group by the entire international community. The organization will, however, raise a Basque national consciousness on the question of belonging to the same people, and today, the conflict for self-determination for the Basque country echoes back in both the Spanish and French territories. This nationalist movement is indissociable between south and north. Different modes of expression are still observed even if the Basque nationalism will always be linked to political violence. The present research work allowed to apprehend the "subjective perceptions" of the Basque population on this political violence and, thus, to highlight a violence from both Spanish and French States. This State violence is mainly characterized by a symbolic violence but it will sometimes lead to physical violence. Therefore, much more than the separate historical and institutional contexts Spanish and French States, the un-harmonized State violence is the distinguishing factor of nationalist violence experienced on French and Spanish territories.

Keyphrases: basque nationalism, terrorism, political violence, state violence, symbolic violence, social movements
Analyse du lien séquentiel entre les comportements d'anxiété et d'évitement lors d'interactions parent-enfant

Anxiety disorders are common among children. They can have serious consequences on their development, and tend to persist or even get worst over time. Avoidance behaviors are often used by anxious people, including children, to escape the object of their fear and to decrease their anxiety level. Dysfunctionnal anxious cognitions that support avoidance tend to develop early in childhood and are partially related to parent-child interactions. The objective of the present study was to examine sequential dependency between anxious and avoidant behaviours, by means of sequential analysis of parent-child interactions. The sample included 20 parent-child dyads, children being aged between 4 and 7 years. A story-completion task was administered in order to arouse anxious feelings in participants.  Results of the present study did not suggest a dependency between anxious and avoidant behaviours among dyads. The discussion proposes avenues for future research to explore.

Keyphrases: Anxiety disorders, parent-child interactions, avoidance, sequential analysis
Caractérisation de l’ubiquitin-fold modifier (UFM1) dans un modèle C. elegans

The ubiquitin-fold modifier (UFM1) is part of the type 1 class of the family of ubiquitin-like protein (Ubl). UFM1 and Ub have very little sequence homology but share remarkable similarities in their tertiary structure. Like Ub and most other UBLS, UFM1 binds covalently to its substrates through an enzymatic cascade. It is frequently reported that UBLs are involved in human diseases. UFM-1 is overexpressed in mice developing a myocardial ischemia and in the islets of patients suffering from type 2 diabetes. UFM1 and its specific enzymes, UBA5, UFL1, and UFC1 are conserved in metazoans and plants suggesting an important role in multicellular organisms. Caenorhabditis elegans is one of the the simplest animal models used in biology. Some features such as morphology, visible phenotypes and cell lineage have completely been described. The short lifecycle of C. elegans makes it easy to observe gene effects on longevity. This model allows us to easily manipulate the expression of the Ufm1 gene and learn more about its putative functions. To study putative functions of Ufm1, we decreased the expression of ufm-1 using RNA interference introduces through feeding. No gross morphological disturbances were observed; worms resembled wild type and had a normal brood size. However, worms exposed to ufm-1 RNAi had a significantly shorter lifespan than the controls. This effect is independent of the insulin/IGF pathway, which is a major axis of longevity genetics. In C. elegans longevity and cellular stress resistance are intimately linked. We have observed no effect of ufm-1 on thermal, osmotic or oxidative stress, but it is required for protection against proteotoxic stress. It is also necessary to maintain neuronal integrity during aging. Together, our results shed light on putative functions of Ufm1 gene.

Keyphrases: Caenorhabditis elegans, Ufm1, Caenorhabditis elegans, Ufm1, Longevity, Aging, RNA interference, Neuronal integrity
Stomatite prothétique, candidose orale et leur évolution dans le temps

Objectives: To assess the evolution of denture stomatitis in term of frequency and severity and its association with potential risk factors over a two-year period.   Methods: One hundred thirty five healthy edentulous elders who were randomly rehabilitated with a maxillary complete denture opposed by a conventional denture or an implant-supported overdenture retained by two ball attachments were followed over two years. Demographic and clinical data concerning oral and general health, smoking, denture status and hygienic habits were obtained from oral examination and standard questionnaires. Denture stomatitis was evaluated according to Newton’s classification. Microbiological analyses consist of detection of Candida species in denture plaque and inoculation in selective growth medium. Pearson Chi-square and McNemar tests were used to analyse the frequency of denture stomatitis, its association with potential risk factors and it’s evolution over time. Odds ratios and their 95% confidence intervals were calculated to determine the strength of association between risk factors and denture stomatitis.   Results: The prevalence of denture stomatitis increased between the first (63.6%) and second year follow-up (88.7%) with an incidence rate of 78.8%. Those individuals suffering from type 2 or type 3 denture stomatitis and who brushed their palate had approximately 6 times more chance of observing a decrease in the severity of their condition [p=0.04 OR 5.88 CI (1.1-32.2)].  There was no statistically significant association between the frequency of denture stomatitis and classical risk factors at both follow-ups. The carriage rate of Candida species remained stable over time (45.8% and 49.2% first and second year of follow-up consecutively, p > 0.05). There was no association between the presence of oral candidiosis and denture stomatitis or its potential risk factors.  Conclusion: The results of this study suggest that denture stomatitis progresses overtime independent of Candida carriage. Palatal brushing could be a preventive approach to minimise the inflammation in individuals suffering from type 2 or type 3 denture stomatitis.

Keyphrases: Implant overdenture, Dental protheses, Denture stomatitis, Randomised controlled trial, Oral health
Exploration des conceptions de la performance privilégiées par des infirmières et des membres de l’équipe d’encadrement impliqués dans l’offre de services infirmiers : une étude qualitative exploratoire

Background : Healthcare organizations face pressure to supply care and services that meet the highest level of performance and to show accountability in regards to this performance. These pressures come from different individuals ranging from the users of the healthcare system to political leaders. Since the nursing staffs occupy an important part in the supply of the healthcare services, there is a growing interest to put in place actions that would increase the performance of the nursing services as well as measure it. However, as part of this process, healthcare organizations often face conflictual notions of what performance is and how to properly measure it. Objectives : This qualitative exploratory study aims to explore the different notions of what performance is as seen by management teams involved in the nursing services delivery and by the field nurses to determine how much these notions are similar to each other or rather in opposition. Methodology: Semi-directed interviews have been held with five management teams’ members and also with three nurses. A content analysis has been made to illustrate the various notions of what performance is and those that show up the most. The framework used in this study is an adaptation of Donabedian’s model which includes three components: structure, process and results (Unruh & Wan, 2004). Findings: Ten distinct but related performance notions that focus on nursing’s process and impact on the users have been identified from data collected from management team members. On the nurses’ side, nine notions have been identified and put the focus mainly on the adequacy of nursing human resources with the nursing process. Some differences and similarities have also been identified between the performance notions of the two groups. Conclusion : This study gives a better understanding of the different performance notions that come from the various individuals involved in the nursing supply. The integrator model that result from the mix of these different notions will be useful in the creation of performance measurement tools directly linked with the nursing services, which will help respond to the accountability demand towards these services.

Keyphrases: Perception, Nursing performance, Nursing indicators, Nursing-sensitive outcomes, Quality of care, Perception, Nurse leader, Nurse administrator, Nursing performance measurement
Facteurs influençant la réponse immunitaire humorale suite à la vaccination avec un vaccin vivant contre la maladie de Gumboro chez le poulet de chair

In Quebec, Canada, broilers chickens are slaughtered from 33 to 40 days of age depending on the targeted market. Considering the withdrawal period of 21 days following vaccination, chickens would have to be vaccinated in the presence of maternally derived antibodies (MDA). The purpose of this study was to determine the effectiveness of high dose of vaccine and high dietary concentration of vitamin E in circumventing the MDA. A normal dose vaccine containing 104.35 TCID50/ml/bird and a higher dose containing 105.35 TCID50/ml/bird were used on 1200 chickens, which were divided into 4 groups housed in 8 pens: a high dose of vaccine in which all chickens were given 105.35 TCID50/ml (HD100%), a high dose in which 10% of the birds were vaccinated (HD10%), a normal dose as prescribed by the manufacturer in which all birds received 104.35 TCID50/ml (ND100%), and unvaccinated control groups. Each group was divided into 2 sub-groups; one was supplemented with 50 to 100 IU/kg of vitamin E and the other was supplemented with 20 to 27 IU/kg. The result of this study showed that the vaccine virus was able to circumvent the MDA, which persisted until 20 days of age, and to initiate a high antibody response. The study also showed that the vaccine virus was able to spread by direct and indirect contact within the pen and to the next pens. No reversion to the virulence or mutation of VP2 nucleotide was detected from the contact vaccinated birds. Vitamin E at the concentration of 50 to 100 IU/kg of the diet induced significantly elevated antibody response against IBDV.

Keyphrases: dose, vaccin, IBD, high vaccine dose, vitamin E, maternal antibodies
Évaluation de stratégies pour améliorer l'observance de la biosécurité sur les fermes avicoles au Québec

Biosecurity compliance issue is present in all types of animal productions, Therefore, it is essential to define strategies to improve the implementation of biosecurity measures. This study described the application of biosecurity measures when entering and exiting 24 poultry barns in Québec, Canada. The effect of audits and visible cameras on compliance was investigated, as well as determinants of compliance. Also, the relationship between compliance and personality profiles, experience and education has been described. Application of biosecurity measures was evaluated using hidden cameras. Short term (first two weeks) and medium term (six months later) compliance were determined.   Based on the control group, 44 different biosecurity breaches were observed when getting in and out of poultry barns. Most were related to area delimitation (clean versus contaminated). The nature and frequency of errors suggest a lack of understanding of biosecurity principles. Overall, video viewing revealed 3055 visits done by 277 different individuals (136 employees, 123 visitors, 3 supervisors and 15 growers). Results showed that audits did not have any impact on employee compliance. Visible cameras had a significant impact on changing boots and respecting areas during the visit for the short term period. However, six months later, compliance significantly declined and was no longer statistically higher compared to the control group. Duration and moment of the visit, presence of the grower or an observer, barn entrance design, number of barns, number of biosecurity measures requested, type of boots, gender and being a member of a grower’s family were significantly associated with compliance with some biosecurity measures. Finally, three personality traits were significantly associated with compliance: responsibility, action-oriented and complexity, as well as the number of years of experience and the level of education.   There is a need to improve biosecurity training by making training material available to all poultry personnel demonstrating why and how to apply biosecurity measures. Educational meetings should also address issues related to visit and farm characteristics. Improving barn entrance design should contribute to enhance and maintain compliance. The identification of personality traits associated with compliance may have implications for the selection of job applicants or task attribution, and for developing educational materials and training programs.

Keyphrases: Biosecurity, Compliance, Video surveillance, Audits, Poultry, Personality
Efficacité de deux méthodes d'enseignement d'hygiène orale chez les patients atteints de maladies rénales

Renal diseases are known to cause oral changes that can increase the risk of developping a bacteraemia.  Even if infective endocarditis is a rare condition in patients with renal disease, it is associated with nosocomial infections.  In the past, antimicrobial therapy was recommended for haemodialysis patients to prevent infective endocarditis and indwelling venous catheter-related infections.  The administration of prophylactic antibiotics is no longer supported, given the lack of evidence concerning this approach.  To prevent patients from developing a transitory bacteraemia, home oral care has to be improved.  The goal of this study is to assess the efficacy of two oral health instruction methods in children with renal disease. Objectives The objectives of this study are to assess the knowledge on infective endocarditis and its link to the oral health of parents with children who present with renal disease; to evaluate the perception of parents in relation with their child’s oral health and their dental behaviour and finally to compare the impact of the oral health instruction methods on the plaque index of children with renal disease. Hypothesis The two hypotheses of this study are a) parents of children suffering from renal diseases know and respect the guidelines published by the American Heart Association and b) that the improvement of the plaque index is better in the group who receives oral health instructions from the audio-visual material compared to the one receiving instructions from the nephrologist.  Methods An ethic’s certification was obtained from the Centre Hospitalier Universitaire Sainte-Justine for children.  Of the 38 recruited patients, 37 patients (19 girls, 18 boys) ranging in age from 6 to 16 years participated in this transversal study.  Consent was obtained prior to randomised assignment to either oral hygiene delivered by means of an audio-visual aid (groupe 1) or by a nephrologist (group 2).  A questionnaire investigating parental knowledge on renal disease linked with oral health was administered.  An initial plaque index was taken before applying oral health instructions.  A final plaque index using disclosing tablets was measured by two observers tested for intra and inter-reliability through intra-oral pictures. Results The statistical analyses do not show any significant differences between the two oral health instruction groups.  No significant relation was found between oral health status and age, gender, dental follow up, frequency of home dental hygiene and motivation.  The only significant relationship found was as parents perception of their child’s oral health increases, the initial plaque index decreases.  Conclusion The results indicate that even if there is no statistically significant difference between the two methods of oral health instruction, both techniques are capable of reducing the plaque index of children suffering from renal disease.

Keyphrases: renal disease, vascular access infection, infective endocarditis, oral hygiene instruction
Relation entre la satisfaction et la qualité de vie reliée à la santé bucco-dentaire chez les patients totalement édentés

Statement of problem: Patients’ satisfaction and oral health-related quality of life (OHRQoL) are two commonly used patient-reported outcomes. Convincing evidence is lacking to demonstrate the relation between these two outcomes in completely edentate patients who receive prosthodontic treatments. In addition, it is still unclear which elements of denture satisfaction share the best association with OHRQoL.  Objectives: To evaluate the level of association between patients’ denture satisfaction and OHRQoL in edentulous patients, and to identify the determinants of satisfaction that best predict OHRQoL. Methods: Data from 255 edentulous elders who participated in a randomized clinical trial were used to analyze the relationship between OHRQoL and denture satisfaction. OHRQoL was evaluated with the Oral Health Impact Profile (OHIP-20) questionnaire. The McGill Denture Satisfaction Instrument was used to assess patients’ satisfaction with treatment. Outcomes were measured prior to treatment and 6 and 12 months after delivery of new dentures. Simple and multiple linear regressions analyses were performed to statistically assess the relationship between the variables. Results: A highly positive association exists between oral health-related quality of life and denture satisfaction ratings. Chewing ability (P = .005) and oral condition (P = .002) are the aspects of satisfaction presenting the best association with OHRQoL. These two variables explained 46.4% (P = .0001) of the variance in OHIP’s change score following treatment. This association varied with time, but not with type of treatment or socio-demographic variables. Conclusions: Within the limitations of this study, a highly positive association exists between OHRQoL and denture satisfaction. Chewing ability and oral condition are the determinant of denture satisfaction best associated with OHRQoL, predicting 46.4% of its improvement following a treatment.

Keyphrases: satisfaction, randomized clinical trial, oral health related quality of life, satisfaction, conventional denture, mandibular implant overdenture
Analyse de l'influence des paramètres esthétiques sur l’attrait du sourire tel que perçu par des non-experts : étude transversale exploratoire

Despite all the information in aesthetic dentistry, evidence-based literature has not yet fully embraced the field of cosmetic dentistry, its rules and effects. The main goal of this study is to raise this level of knowledge and therefore, determine the influence of aesthetic parameters on the overall smile attractiveness as perceived by laypeople.  A request to answer an anonymous survey was sent to the University de Montreal’s community, trough its institutional email lists. 467 questionnaires were started, but only 263 were completed and kept in this study. According to this survey, « Teeth alignment » was the only objective criteria proven to have a significant statistical effect on the overall smile appreciation (p = .028). Straight (p = .012) and crowded teeth (p = .009) raised the appreciation over the rotated ones. When the data was correlated with laypeople’s belief, « superior dental median line angle » and « incisal plane incline » also had a statistical effect. From a patient’s point of view and within the suggested vocabulary, tooth wear and tooth position are the most important subjective elements that may vary with smile attractiveness.  Within the limitations of this study, the conclusions are the following : (1) « teeth alignment, « incisal plane inclination » and « superior medial dental line angulation » all have proven a significant statistical effect on the smile appreciation. (2) « Teeth alignment » is the only objective criteria, by which overall appreciation can vary significantly on a statistical aspect. (3) The high degree of correlation within each smiles rating, leads us to believe that the appreciation of smile attractiveness is a reflex action. Practical application: treatments aiming whitening and correcting teeth alignment or tooth wear, all have the potential to rise smile attractiveness as perceived by laypeople.

Keyphrases: Smile, Perception, Satisfaction, Aesthetic, Cosmetic, Visual Perception, Attractiveness, Criteria, Parameter