NCube/papyrus huggingface dataset:
HIV-1 envelope glycoprotein amino acids signatures associated with clade B transmitted/founder and recent viruses

Background: HIV-1 transmitted/founder viruses (TF) are selected during the acute phase of infection from a multitude of virions present during transmission. They possess the capacity to establish infection and viral dissemination in a new host. Deciphering the discrete genetic determinant of infectivity in their envelope may provide clues for vaccine design. Methods: One hundred twenty-six clade B HIV-1 consensus envelope sequences from untreated acute and early infected individuals were compared to 105 sequences obtained from chronically infected individuals using next generation sequencing and molecular analyses. Results: We identified an envelope amino acid signature associated with TF viruses. They are more likely to have an isoleucine (I) in position 841 instead of an arginine (R). This mutation of R to I (R841I) in the gp41 cytoplasmic tail (gp41CT), specifically in lentivirus lytic peptides segment 1 (LLP-1), is significantly enriched compared to chronic viruses (OR = 0.2, 95% CI (0.09, 0.44), p = 0.00001). Conversely, a mutation of lysine (K) to isoleucine (I) located in position six (K6I) of the envelope signal peptide was selected by chronic viruses and compared to TF (OR = 3.26, 95% CI (1.76–6.02), p = 0.0001). Conclusions: The highly conserved gp41 CT_ LLP-1 domain plays a major role in virus replication in mediating intracellular traffic and Env incorporation into virions in interacting with encoded matrix protein. The presence of an isoleucine in gp41 in the TF viruses’ envelope may sustain its role in the successful establishment of infection during the acute stage.

Keyphrases: HIV-1, Acute/early infection, Transmitted/founder viruses, Recent viruses, Envelope, Amino acids, Genetic signatures, Signal peptide, Cytoplasmic domain, Lentivirus lytic peptide segment 1
Artifacts of technoculture : excommunication in the nonhuman theatre

The aim of this article is to form a conceptual framework for analyzing and understanding the latest intermedial practice within the field of new technologies. In order to achieve this, it suggests two converging theoretical strategies. Firstly, the introduction emphasizes on concept of “excommunication,” coined by Alexander R. Galloway in his 2013 book, in order to provide a better understanding of the scenic mediation that encompasses a great number of contemporary productions. More specifically, by both following and criticizing Galloway’s stance on three different media modalities, a fourth mediation vector will be isolated - The Water Principle - incorporated in the mythology of Neptune. Such a theoretical orientation is primarily guided by an ambition to associate intermedial theory with watery elements that appear in two different stage examples analyzed within this paper. Secondly, two different performances will be analyzed: Romeo Castellucci’s “M#10 Marseille” (2002) and “Fontaine Boréale” (2018). Prompted by intermedial issues, these two productions question the ontological claims of the human presence on stage by establishing digital stage simulation as a para-performative phenomenon. By analyzing these plays, I will demonstrate that in both examples, the Water Principle delivers a privileged media model through which aesthetic force is achieved. Finally, on a broader level, the paper suggests that the artistic trajectory of these productions calls for a new perspective on the nature of performance; a perspective emphasizing an aesthetics of disappearance and nonhuman structural impact.

Keyphrases: Technoculture, Excommunication, Nonhuman theatre, The water principle
‘They installed a speed bump’ : children’s perceptions of traffic-calming measures around elementary schools

Growing scientific literature evaluates the impact of traffic-calming devices in terms of mobility behavior and safety, but little is known about their perceived impact from the point of view of children. Our study asks children about their perceptions of different traffic-calming measures around their schools. It draws on data gathered through eight focus groups, followed by walking tours with Grade 6 children (11–12 years old) (n = 65, 27 boys, 38 girls) from elementary schools in different urban contexts in Quebec, Canada. Qualitative analysis of the discussions shows that (a) vehicle speed is the main perceived threat for participant children; (b) children are confident about the effectiveness of self-enforcing traffic-calming devices that reshape the street geometry; and (c) they are skeptical about the effectiveness of ‘informative’ measures such as signs and lines (marked pavement). Our findings inform public policy for a more effective promotion of walking and cycling among children.

Keyphrases: Travel, Schools, Traffic calming, Perceptions, Risk, Urban design
La bibliométrie : au-delà de l'évaluation des performances

En plus de permettre l’évaluation de la recherche, la bibliométrie offre plusieurs données utiles. Par exemple, elle permet de mieux comprendre l’évolution d'une discipline ou encore de soutenir les décisions relatives aux politiques scientifiques. Pour illustrer ces usages plus descriptifs, une étude sur l’influence des disciplines en criminologie est présentée.

Keyphrases: Bibliométrie, Criminologie
Un visage, un nom ou l’art de la rencontre entre les archives et le public.

Le projet Un visage, un nom vise à faire participer les communautés autochtones à la description des vastes collections photographiques hébergées à BAC portant sur les Inuits, les Premières Nations et la Nation métisse. Il a rencontré un succès important, tant auprès des communautés autochtones que des milieux archivistiques. En faisant participer les communautés autochtones à la description de ses collections, BAC trouve un excellent moyen de parfaire le traitement documentaire de ses fonds d’archives et ouvre la voie à un renouvellement profond des pratiques archivistiques. Rapidement, le projet dépasse les attentes du cercle des professionnels de l’archivistique et prend une dimension nouvelle en comblant les attentes exprimées par les communautés autochtones. L’intérêt de l’étude est de mettre en lumière la place centrale occupée par l’archiviste dans ce processus. En adoptant une attitude proactive, en supervisant l'intervention des usagers dans des domaines qui lui étaient jusque-là réservés, il contribue au renouvellement de sa profession et ouvre de nouvelles perspectives. En étant l'artisan volontaire d'une rencontre entre le document et le public, l'archiviste devient le maître d’œuvre de l'exploitation des archives.

Keyphrases: Archivistique, Description collaborative, Communautés autochtones, Sensibilité, Émotion, Approche classique, Approche postmoderne, Exploitation des archives, Diffusion des archives
Youth-driven tactics of public space appropriation in Hanoi : the case of skateboarding and parkour

Starting in the 2000s, there has been a rise in youth-led appropriation of public spaces in Hanoi, Vietnam. Through case studies of skateboarders and traceurs (practitioners of parkour) in two of the city’s formal public spaces, we explore and analyze the tactics deployed by these young urbanites to claim a part of the characteristically overcrowded and socio-politically restrictive public spaces of the Vietnamese capital. These case studies show that, by seeking to access public spaces for their new activities, skaters and traceurs have had to confront multiple sets of rules, imposed by not only the state, but also corporate actors and resident-driven surveillance. We find that skateboarders and traceurs deal with these forms of control largely through small-scale, non-ideological, and non-confrontational tactics. As a result, these youth practices have become normalized in Hanoi’s public spaces. These findings broaden the discourses on everyday urbanism and social-political transformations in post-socialist urban contexts, and shed light on the ways in which contemporary youths engage with the city.

Keyphrases: Youth, Skateboarders, Traceurs, Everyday urbanism, Spatial appropriation tactics public space, Hanoi, Vietnam, Doi moi, Street discipline, bo mon duong pho
Amyloid burden and white matter hyperintensities mediate age-related cognitive differences

This study examined the additive versus synergistic contribution of beta-amyloid (Aβ) and white matter hyperintensities (WMHs) across 7 cognitive domains in 104 cognitively normal older adults. It also measured the extent to which age-related differences in cognition are driven by measurable brain pathology. All participants underwent neuropsychological assessment along with magnetic resonance imaging and Pittsburg compound B-positron emission tomography imaging for Aβ quantification. WMH severity was quantified using the age-related white matter changes scale. Stepwise regressions, moderation, and mediation modeling were performed. Our findings show that Aβ deposition single-handedly predicts poorer episodic memory performance and that Aβ and WMHs contribute additively to poorer performance in working memory and language while carrying synergistic associations with executive functions and attention. Through mediation modeling, we demonstrated that the influence of age over episodic memory, working memory, executive functions, and language is fully mediated by brain pathology. This study permits to conclude that, in healthy older adults, (1) Aβ burden and WMHs have synergistic associations with some cognitive domains and (2) age-related differences in most cognitive domains are driven by brain pathology associated with dementia.

Keyphrases: Alzheimer's disease, Cognitive aging, Neuroimaging
Estimating treatment importance in multidrug-resistant tuberculosis using
Targeted Learning : an observational individual patient data network
meta-analysis

Persons with multidrug‐resistant tuberculosis (MDR‐TB) have a disease resulting from a strain of tuberculosis (TB) that does not respond to at least isoniazid and rifampicin, the two most effective anti‐TB drugs. MDR‐TB is always treated with multiple antimicrobial agents. Our data consist of individual patient data from 31 international observational studies with varying prescription practices, access to medications, and distributions of antibiotic resistance. In this study, we develop identifiability criteria for the estimation of a global treatment importance metric in the context where not all medications are observed in all studies. With stronger causal assumptions, this treatment importance metric can be interpreted as the effect of adding a medication to the existing treatments. We then use this metric to rank 15 observed antimicrobial agents in terms of their estimated add‐on value. Using the concept of transportability, we propose an implementation of targeted maximum likelihood estimation, a doubly robust and locally efficient plug‐in estimator, to estimate the treatment importance metric. A clustered sandwich estimator is adopted to compute variance estimates and produce confidence intervals. Simulation studies are conducted to assess the performance of our estimator, verify the double robustness property, and assess the appropriateness of the variance estimation approach.

Keyphrases: Double robustness, Individual patient data, Meta-analysis, Multidrug-resistant tuberculosis, Targeted maximum likelihood estimation, Transportability, Treatment importance
Inconsistances entre les mesures évaluant les difficultés cognitives chez des survivants de leucémie aigüe lymphoblastique : description et compréhension

Introduction – Le taux de survie de la leucémie aigüe lymphoblastique (LAL) dépasse aujourd’hui 90 %. En dépit de traitements moins toxiques, environ 50 % des survivants leucémie aigüe lymphoblastique (LAL) présentent au moins une séquelle cognitive cliniquement significative à long terme. Un problème central quant à l’évaluation cognitive est la présence d’écarts entre les résultats aux tests et les plaintes auto-rapportées. Les hypothèses émises pour expliquer ce phénomène sont nombreuses et mal connues. Objectifs – (1) Décrire les écarts entre les difficultés testées et celles auto-rapportées pour les domaines de la mémoire de travail et de l’attention. (2) Évaluer si la détresse émotionnelle, la dépression, l’anxiété, les affects positifs et négatifs et la fatigue permettent d’expliquer ces écarts. Méthodes – Nous avons utilisé les données disponibles pour 138 adultes survivants de LAL pédiatrique (cohorte PETALE). La mémoire de travail et l’attention des survivants ont été évaluées avec le WAIS-IV et via des questionnaires auto-rapportés (BRIEF-SR et CAARS-S:L). L’évaluation affective incluait la détresse émotionnelle (BSI-18), les affects (PANAS) et la fatigue (PedsQL-MFS). Nous explorons les écarts à l’aide d’indices diagnostiques, et les expliquons dans des modèles de régression multivariés. Résultats – Les déficits en mémoire de travail et en attention sont rapportés par 10 à 11 % des survivants, alors qu’ils sont objectivés chez 15 à 21 % d’entre eux. Les mesures auto-rapportées ne permettent pas d’identifier les déficits objectifs (sensibilité = 0.05-0.16). L’affectivité négative permet d’expliquer partiellement les écarts individuels retrouvés entre ces deux types de mesures au profit des difficultés auto-rapportées. Conclusions – L’évaluation cognitive testée et celle auto-rapportée par les survivants doivent être considérées comme des réalités différentes dont les écarts sont probablement influencés par le statut psychologique des répondants.

Keyphrases: Survivant, Cancer pédiatrique, Difficultés cognitives, Questionnaire auto-rapporté, Test cognitif, Attention, Mémoire de travail, Neuropsychologie clinique
Data-adaptive longitudinal model selection in causal inference with collaborative targeted minimum loss-based estimation

Causal inference methods have been developed for longitudinal observationalstudy designs where confounding is thought to occur over time. In particular,one may estimate and contrast the population mean counterfactual outcomeunder specific exposure patterns. In such contexts, confounders of thelongitudinal treatment‐outcome association are generally identified usingdomain‐specific knowledge. However, this may leave an analyst with a largeset of potential confounders that may hinder estimation. Previous approaches todata‐adaptive model selection for this type of causal parameter were limited tothe single time‐point setting. We develop a longitudinal extension of acollaborative targeted minimum loss‐based estimation (C‐TMLE) algorithmthat can be applied to perform variable selection in the models for theprobability of treatment with the goal of improving the estimation of thepopulation mean counterfactual outcome under a fixed exposure pattern. Weinvestigate the properties of this method through a simulation study, comparingit to G‐Computation and inverse probability of treatment weighting. We thenapply the method in a real‐data example to evaluate the safety of trimester‐specific exposure to inhaled corticosteroids during pregnancy in women withmild asthma. The data for this study were obtained from the linkage ofelectronic health databases in the province of Quebec, Canada. The C‐TMLEcovariate selection approach allowed for a reduction of the set of potentialconfounders, which included baseline and longitudinal variables.

Keyphrases: Collaborative double robustness, Saturated marginal structural model, Targeted minimum loss‐based estimation
Understanding and diagnosing the potential for bias when using machine learning methods with doubly robust causal estimators

Data-adaptive methods have been proposed to estimate nuisance parameters when using doubly robust semiparametric methods for estimating marginal causal effects. However, in the presence of near practical positivity violations, these methods can produce a separation of the two exposure groups in terms of propensity score densities which can lead to biased estimates of the treatment effect. To motivate the problem, we evaluated the Targeted Minimum Loss-based Estimation procedure using a simulation scenario to estimate the average treatment effect. We highlight the divergence in estimates obtained when using parametric and data-adaptive methods to estimate the propensity score. We then adapted an existing diagnostic tool based on a bootstrap resampling of the subjects and simulation of the outcome data in order to show that the estimation using data-adaptive methods for the propensity score in this study may lead to large bias and poor coverage. The adapted bootstrap procedure is able to identify this instability and can be used as a diagnostic tool.

Keyphrases: Causal inference, Positivity, Doubly robust, IPTW, Super learner
Hotspot or blind spot? Historical perspectives on surveillance and response to epidemics in the Central African Republic

Objectives The Central African Republic (CAR), a site of recurrent disease emergence, developed a noteworthy epidemiological surveillance system from the colonial period, but its health measures have remained among the world’s lowest. To understand this disparity between surveillance and public health, we examined selected moments in its history of surveillance and changing relations with public health structures. Methods We conducted archival research in CAR and French archives and 18 semi-structured interviews with key researchers working in CAR. Results We find long-term continuities in privileging surveillance over the health system and population health, making the CAR a ‘‘hotspot’’ for emerging diseases and a ‘‘blind spot’’ of primary health care. From the colonial period, the country attracted considerable support for surveillance, without concomitant investment in public health system. Political disputes and financial constraints have obscured real primary care needs on the ground. Conclusions As both a hotspot and a blind spot for global health, the CAR signals the need to reorient health interventions to address the long-term health of Central African people.

Keyphrases: Surveillance, Disease emergence, Epidemics, Central Africa, History, Pasteur
Blockchain technology and corporate governance : the issue of smart contracts — current perspectives and evolving concerns

Traditional contracts are being replaced in an increasing number of instances by smart contracts that is, “decentralized agreements built in computer code and stored on a blockchain”, which are able to automatically execute the terms within the contract and control the relations between parties so that no further “explicit but redundant” negotiations are needed. This paper assesses current and evolving concerns regarding the adoption of blockchain technology in the areas of financial services, and corporate and public governance. The author evaluates the risks and benefits of the utilization of smart contracts and assesses their suitability (in terms of transparency, accountability, responsibility and fairness) for use in the public services’ “space”. It concludes that while the benefits outweigh the disadvantages, great care should be exercised in terms of design and use because this is still a developing area in terms of both the technology itself and the regulatory environment. Les contrats traditionnels sont remplacés dans un nombre croissant de cas par des contrats intelligents, c'est-à-dire «des accords décentralisés construits en code informatique et stockés sur une blockchain», qui sont capables d'exécuter automatiquement les termes du contrat et de contrôler les relations entre les parties afin qu’aucune autre négociation «explicite mais redondante» ne soit nécessaire. Cet article évalue les préoccupations actuelles et leurs évolutions concernant l'adoption de la technologie blockchain dans les domaines des services financiers et de la gouvernance d'entreprise et publique. L’auteur évalue les risques et les avantages de l’utilisation de contrats intelligents et évalue leur aptitude (en termes de transparence, de responsabilité, d’équité) à une utilisation dans «l’espace» des services publics. Il conclut que même si les avantages l'emportent sur les inconvénients, une grande prudence doit être exercée en termes de conception et d'utilisation, car il s'agit toujours d'un domaine en développement en termes à la fois de technologie et d'environnement réglementaire.

Keyphrases: Philosophy, Ethics, Economics, Smart contracts, Blockchain, Corporate governance, Financial and public services, Philosophie, Éthique, Économie, Blockchain, Gouvernance d'entreprise, Services financiers et publics
Causal inference with multiple concurrent medications: a comparison of methods and an application in multidrug-resistant tuberculosis

This paper investigates different approaches for causal estimation under multiple concurrent medications. Our parameter of interest is the marginal mean counterfactual outcome under different combinations of medications. We explore parametric and non-parametric methods to estimate the generalized propensity score. We then apply three causal estimation approaches (inverse probability of treatment weighting, propensity score adjustment, and targeted maximum likelihood estimation) to estimate the causal parameter of interest. Focusing on the estimation of the expected outcome under the most prevalent regimens, we compare the results obtained using these methods in a simulation study with four potentially concurrent medications. We perform a second simulation study in which some combinations of medications may occur rarely or not occur at all in the dataset. Finally, we apply the methods explored to contrast the probability of patient treatment success for the most prevalent regimens of antimicrobial agents for patients with multidrug-resistant pulmonary tuberculosis.

Keyphrases: Causal inference, Concurrent medications, Generalized propensity score, Machine learning, Multidrug-resistant tuberculosis, Targeted maximum likelihood estimation
La philosophie au secours des rapports de responsabilité sociale de l’entreprise, ou comment dépasser les limites d’un discours "aphilosophique" sur la responsabilité :
Deuxième Partie – Responsabilité et relations moi- autrui

Martin Buber and Emmanuel Levinas have been influenced by the Heideggerian Being-in-the-world. However, Buber’s philosophy as well as Levinas’ philosophy have given birth to new paths of humanizing the world, particularly business corporations, while requiring deep changes in the way the relational fabric of groups, organizations and social institutions is evolving. Buber and Levinas have emphasized the need to develop an authentic relation with radical otherness, starting with the existentiell positioning of being in-face-of-others. In doing so, Buber and Levinas have overcome the state of existential fallenness, while considering radical otherness as an unavoidable dimension of the in-the-worldliness. Influencés par l’Être-dans-le-monde heideggerien, Martin Buber et Emmanuel Levinas ont ouvert, par leur philosophie respective, de nouvelles voies d’humanisation du monde, en particulier le milieu des affaires, tout en imposant un lourd fardeau de changements pour que le tissu relationnel des groupes, organisations et institutions sociales devienne véritablement imprégné d’une relation authentique avec l’altérité radicale, à partir de la position existentielle d’être-en-face-de-l’autre, avec toutes les responsabilités concrètes qui en découlent pour tout un chacun. De cette manière, Buber et Levinas ont dépassé l’être-jeté dans l’existence, en faisant de l’altérité radicale une dimension inévitable de l’intramondanéité.

Keyphrases: Philosophy, Ethics, Economics, Buber, Martin, Levinas, Emmanuel, Heidegger, Martin, Responsibility, Otherness, Philosophie, Éthique, Économie, Responsabilité, Altérité