Minimizing carry-over PCR contamination in expanded CAG/CTG repeat instability applications.

Expanded CAG/CTG repeats underlie the aetiology of 14 neurological and neuromuscular disorders. The size of the repeat tract determines in large part the severity of these disorders with longer tracts causing more severe phenotypes. Expanded CAG/CTG repeats are also unstable in somatic tissues, which is thought to modify disease progression. Routine molecular biology applications involving these repeats, including quantifying their instability, are plagued by low PCR yields. This leads to the need for setting up more PCRs of the same locus, thereby increasing the risk of carry-over contamination. Here we aimed to reduce this risk by pre-treating the samples with a Uracil N-Glycosylase (Ung) and using dUTP instead of dTTP in PCRs. We successfully applied this method to the PCR amplification of expanded CAG/CTG repeats, their sequencing, and their molecular cloning. In addition, we optimized the gold-standard method for measuring repeat instability, small-pool PCR (SP-PCR), such that it can be used together with Ung and dUTP-containing PCRs, without compromising data quality. We performed SP-PCR on myotonic-dystrophy-derived samples containing an expansion as large as 1000 repeats, demonstrating the applicability to clinically-relevant material. Thus, we expect the protocols herein to be applicable for molecular diagnostics of expanded repeat disorders

Statistical properties of groundwater noble gas paleoclimate models: Are they robust and unbiased estimators?

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95652/1/ggge1627.pd

Criteria for assessing grant applications: A systematic review

Criteria are an essential component of any procedure for assessing merit. Yet, little is known about the criteria peers use in assessing grant applications. In this systematic review we therefore identify and synthesize studies that examine grant peer review criteria in an empirical and inductive manner. To facilitate the synthesis, we introduce a framework that classifies what is generally referred to as 'criterion' into an evaluated entity (i.e. the object of evaluation) and an evaluation criterion (i.e. the dimension along which an entity is evaluated). In total, this synthesis includes 12 studies. Two-thirds of these studies examine criteria in the medical and health sciences, while studies in other fields are scarce. Few studies compare criteria across different fields, and none focus on criteria for interdisciplinary research. We conducted a qualitative content analysis of the 12 studies and thereby identified 15 evaluation criteria and 30 evaluated entities as well as the relations between them. Based on a network analysis, we propose a conceptualization that groups the identified evaluation criteria and evaluated entities into aims, means, and outcomes. We compare our results to criteria found in studies on research quality and guidelines of funding agencies. Since peer review is often approached from a normative perspective, we discuss our findings in relation to two normative positions, the fairness doctrine and the ideal of impartiality. Our findings suggest that future studies on criteria in grant peer review should focus on the applicant, include data from non-Western countries, and examine fields other than the medical and health sciences.Comment: Final versio

Dyadic pulsations as a signature of sustainability in correspondence networks

In this paper, we introduce the concept of dyadic pulsations as a measure of sustainability in online discussion groups. Dyadic pulsations correspond to new communication exchanges occurring between two participants in a discussion group. A group that continuously integrates new participants in the on-going conversation is characterized by a steady dyadic pulsation rhythm. On the contrary, groups that either pursue close conversation or unilateral communication have no or very little dyadic pulsations. We show on two examples taken from Usenet discussion groups, that dyadic pulsations permit to anticipate future bursts in response delay time which are signs of group discussion collapses. We discuss ways of making this measure resilient to spam and other common algorithmic production that pollutes real discussion

Contracting CAG/CTG repeats using the CRISPR-Cas9 nickase

CAG/CTG repeat expansions cause over 13 neurological diseases that remain without a cure. Because longer tracts cause more severe phenotypes, contracting them may provide a therapeutic avenue. No currently known agent can specifically generate contractions. Using a GFP-based chromosomal reporter that monitors expansions and contractions in the same cell population, here we find that inducing double-strand breaks within the repeat tract causes instability in both directions. In contrast, the CRISPR-Cas9 D10A nickase induces mainly contractions independently of single-strand break repair. Nickase-induced contractions depend on the DNA damage response kinase ATM, whereas ATR inhibition increases both expansions and contractions in a MSH2- and XPA-dependent manner. We propose that DNA gaps lead to contractions and that the type of DNA damage present within the repeat tract dictates the levels and the direction of CAG repeat instability. Our study paves the way towards deliberate induction of CAG/CTG repeat contractions in vivo

Breaking immersion: A theoretical framework of alienated play to facilitate critical reflection on interactive media

There is a growing interest in understanding how to best represent complexity using IDNs. We conceptualize this as the aim to make players of such IDNs reflect critically on the complexity being represented. We argue that current understandings of player experience do not lend themselves to this aim. Research on interactive media has assumed immersion to be a universal positive for the player experience. However, in this article we argue that immersion into the Magic Circle of an IDN could be antagonistic to a critical experience. This is because immersion persuades players into suspending their disbelief, rather than facilitating critical reflection. Instead we propose, on the basis of the Epic Theater, an alternative form of play called alienated play. Meaning, a form of play in which the player is playing, while also observing themselves play. This form of play should allow for players to benefit from the enjoyable nature of play, while simultaneously remaining at a critical distance. To illustrate our theory we design two models, one for immersed play and one for alienated play. Furthermore, we present examples of the design for alienation in commercial video games, as well as hypotheses to test out theory in future research. Therefore, this work contributes an initial theoretical and practical informed form of play, specifically designed to facilitate critical reflection on IDNs representing complexity

The quality of data collected online: An investigation of careless responding in a crowdsourced sample

Despite recent concerns about data quality, various academic fields rely increasingly on crowdsourced samples. Thus, the goal of this study was to systematically assess carelessness in a crowdsourced sample (N = 394) by applying various measures and detection methods. A Latent Profile Analysis revealed that 45.9% of the participants showed some form of careless behavior. Excluding these participants increased the effect size in an experiment included in the survey. Based on our findings, several recommendations of easy to apply measures for assessing data quality are given

Le « Solifonds » – Un modèle de coopération entre le mouvement des travailleurs et celui du développement

Après trois ans de discussions, l’USS, le PSS, l’OSED et dix autres organisations d’entraide et de développement, ont décidé à l’automne 1982 de créer le « Fonds de solidarité pour la lutte de libération sociale dans le Tiers Monde ». Le Solifonds doit permettre au mouvement ouvrier de se joindre aux organisations de développement dans leur action en faveur des mouvements de revendication sociale dans le Tiers Monde. Un tel rassemblement est unique en Europe.Le Solifonds s’orientera principalement vers la défense des droits de l’homme, des droits politiques et syndicaux. Il pourra intervenir dans des actions de solidarité syndicale et politique, qui ne sont pas appuyées par les pouvoirs publics, à cause de leur caractère spécifique. La décision d’entreprendre des actions doit être approuvée par les trois quarts des membres du Conseil de Fondation, qui compte treize membres. Les décisions doivent donc découler d’un large consensus au sein du Conseil. Le Solifonds ne veut pas être en concurrence avec la solidarité syndicale telle qu’elle s’exprime actuellement, mais veut plutôt jouer un rôle de complément.Les actions entreprises par le Solifonds doivent se concevoir à court terme, et de manière spontanée. Les projets qui demandent une conception à long terme sont du ressort traditionnel des organisations de solidarité

Der “Solifonds” – Ein Modell der Zusammenarbeit Zwischen Arbeiterbewegung und Entwicklungsbewegung

Après trois ans de discussions, l’USS, le PSS, l’OSED et dix autres organisations d’entraide et de développement, ont décidé à l’automne 1982 de créer le « Fonds de solidarité pour la lutte de libération sociale dans le Tiers Monde ». Le Solifonds doit permettre au mouvement ouvrier de se joindre aux organisations de développement dans leur action en faveur des mouvements de revendication sociale dans le Tiers Monde. Un tel rassemblement est unique en Europe.Le Solifonds s’orientera principalement vers la défense des droits de l’homme, des droits politiques et syndicaux. Il pourra intervenir dans des actions de solidarité syndicale et politique, qui ne sont pas appuyées par les pouvoirs publics, à cause de leur caractère spécifique. La décision d’entreprendre des actions doit être approuvée par les trois quarts des membres du Conseil de Fondation, qui compte treize membres. Les décisions doivent donc découler d’un large consensus au sein du Conseil. Le Solifonds ne veut pas être en concurrence avec la solidarité syndicale telle qu’elle s’exprime actuellement, mais veut plutôt jouer un rôle de complément.Les actions entreprises par le Solifonds doivent se concevoir à court terme, et de manière spontanée. Les projets qui demandent une conception à long terme sont du ressort traditionnel des organisations de solidarité