106 research outputs found
JASPAR TFBS LOLA databases - Part 2
No full textThis repository contains the second part of the JASPAR 2022 LOLA databases used by the JASPAR TFBS enrichment tool. We provide the LOLA databases for the human (hg38) JASPAR 2022 TFBS sets as compressed directories containing a set of .RDS R objects.
Due to file sizes, we had to split the repository into two different parts. Part 1 of the repository containing the rest of databases can be found here
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
No full textInternational audienceAbstract JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release and 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing profiles and provided orthogonal support for 72 profiles from the previous release's UNVALIDATED collection. Altogether, the JASPAR 2024 update provides a 20% increase in CORE profiles from the previous release. A trimming algorithm enhanced profiles by removing low information content flanking base pairs, which were likely uninformative (within the capacity of the PFM models) for TFBS predictions and modelling TF-DNA interactions. This release includes enhanced metadata, featuring a refined classification for plant TFs’ structural DNA-binding domains. The new JASPAR collections prompt updates to the genomic tracks of predicted TF binding sites (TFBSs) in 8 organisms, with human and mouse tracks available as native tracks in the UCSC Genome browser. All data are available through the JASPAR web interface and programmatically through its API and the updated Bioconductor and pyJASPAR packages. Finally, a new TFBS extraction tool enables users to retrieve predicted JASPAR TFBSs intersecting their genomic regions of interest
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
No full textInternational audienceJASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups. In this 9th release, we expanded the CORE collection with 341 new profiles (148 for plants, 101 for vertebrates, 85 for urochordates, and 7 for insects), which corresponds to a 19% expansion over the previous release. We added 298 new profiles to the Unvalidated collection when no orthogonal evidence was found in the literature. All the profiles were clustered to provide familial binding profiles for each taxonomic group. Moreover, we revised the structural classification of DNA binding domains to consider plant-specific TFs. This release introduces word clouds to represent the scientific knowledge associated with each TF. We updated the genome tracks of TFBSs predicted with JASPAR profiles in eight organisms; the human and mouse TFBS predictions can be visualized as native tracks in the UCSC Genome Browser. Finally, we provide a new tool to perform JASPAR TFBS enrichment analysis in user-provided genomic regions. All the data is accessible through the JASPAR website, its associated RESTful API, the R/Bioconductor data package, and a new Python package, pyJASPAR, that facilitates serverless access to the data
Resilient power plant operations through a self-evaluation method
No full textWell trained operators are essential for safety. This study presents a self-evaluation method to be applied after simulator training by power plant operators. The method was created collaboratively with training developers at a nuclear power plant. Inspiration was drawn from education theory as well as from resilience engineering literature. In particular, we considered the line of study that suggest that ‘interpretive practices’ (which involve, e.g., robust communication and the use of various information sources critically) support system resilience. Drawing from this line of study, the developed training method encourages operators to reflect on their own work practices. In practice, the method consists of individual self-evaluation and group discussions. The method was tested with four operator shifts. A brief analysis on the group discussions is presented. It suggest that applying the method might be beneficial for system resilience because a significant proportion of the discussions supported reflection concerning issues that may support system resilience: collaboration, understanding of plant dynamics and the use of procedures. We assume that this kind of ‘developmental reflection’ could potentially enhance work practices. Overall, we suggest that developmental reflection may open avenues for supporting the learning dimension of interpretive practice and thus also resilience
Building an "Adaptive Safety Culture" in a Nuclear Construction Project:Insights to Safety Practitioners
No full textNuclear power plant construction projects are challenging for safety management due to many of their inherent characteristics, which include high levels of organizational turbulence, changes in lifecycle phases, unanticipated events, interactions between multiple parties and the challenges of multicultural environment. This means that traditional approaches to improving safety might not be sufficient. To address this issue, we will view safety management from the perspective of Resilience Engineering and complexity thinking and propose a novel perspective to the practical development of safety culture in dynamic environments. We describe a revised model of adaptive safety management and use four well-known safety culture improvement methods as illustrative examples of how they can be utilized in building an adaptive safety culture
Resilient power plant operations through a self-evaluation method
No full textWell trained operators are essential for safety. This study presents a self-evaluation method to be applied after simulator training by power plant operators. The method was created collaboratively with training developers at a nuclear power plant. Inspiration was drawn from education theory as well as from resilience engineering literature. In particular, we considered the line of study that suggest that ‘interpretive practices’ (which involve, e.g., robust communication and the use of various information sources critically) support system resilience. Drawing from this line of study, the developed training method encourages operators to reflect on their own work practices. In practice, the method consists of individual self-evaluation and group discussions. The method was tested with four operator shifts. A brief analysis on the group discussions is presented. It suggest that applying the method might be beneficial for system resilience because a significant proportion of the discussions supported reflection concerning issues that may support system resilience: collaboration, understanding of plant dynamics and the use of procedures. We assume that this kind of ‘developmental reflection’ could potentially enhance work practices. Overall, we suggest that developmental reflection may open avenues for supporting the learning dimension of interpretive practice and thus also resilience
Building an "Adaptive Safety Culture" in a Nuclear Construction Project:Insights to Safety Practitioners
No full textNuclear power plant construction projects are challenging for safety management due to many of their inherent characteristics, which include high levels of organizational turbulence, changes in lifecycle phases, unanticipated events, interactions between multiple parties and the challenges of multicultural environment. This means that traditional approaches to improving safety might not be sufficient. To address this issue, we will view safety management from the perspective of Resilience Engineering and complexity thinking and propose a novel perspective to the practical development of safety culture in dynamic environments. We describe a revised model of adaptive safety management and use four well-known safety culture improvement methods as illustrative examples of how they can be utilized in building an adaptive safety culture
Modelling organizational learning from successes in the nuclear industry:Staff meetings as forums of knowledge sharing and acquisition
No full textUtilizing lessons learned from successful experiences in the context of safety-critical organizations has been receiving increasing interest among both scientific and practitioner communities. However, despite the attention, there is a need to better understand how success-related knowledge can be utilized to ensure safety and what tools and practices can be used to facilitate this process. In this paper, we focus on staff meetings as forums of knowledge sharing and acquisition. We describe staff meeting practices from empirical case studies, carried out at two Nordic nuclear power plants, and examine how the staff meetings contribute to organizational learning from successes. Based on these insights, we propose an integrative framework that aims to identify the factors that facilitate or hinder organizational learning from successes
Dopaminergic modulation of inhibition and cognitive control: A candidate-genes approach.
No full textCognitive inhibition, one of the main executive functions, allows to suppress the production of predominant but inappropriate responses in order to promote more adapted ones. These mechanisms are regulated by cognitive control processes, varying in a context-dependent manner, and responsible for the active maintenance of tasks goals and goal-related information. The role of the neurotransmitter dopamine (DA) in modulating executive functioning (behavior and brain-related activity) received increased interest over the last decade (Barnes et al., 2011), particularly through the effect of the COMT Val158Met polymorphism (Witte and Floël, 2012), well-known to impact the level of prefrontal DA (Chen et al., 2004). However, unsolved issues remains such as (1) the variability of the influence of the dopaminergic system with regard to different form of inhibition, and (2) the effects of DA-mediated signaling on the antero-posterior network underlying interference resolution and on the implementation of different cognitive control strategies during the processing of interfering events.In that context, the general objective of this research work was to capitalize on a candidate-gene approach as a means to investigate the interactive effect of an intrinsic factor (the dopaminergic activity) and an extrinsic factor (the context) on performance and brain-related activity associated with specific inhibitory mechanisms.By means of behavioral and functional magnetic resonance imaging (fMRI) studies, we explored the effects of the prefrontal level of DA, and DA receptors activity, on behavioral efficiency and brain-related activity during tasks involving inhibition. Various inhibitory tasks were administered outside the MRI scanner to participants genotyped for the COMT rs4680, DRD1 rs4532 and MAOA rs6323 polymorphisms; three genetic variants affecting the level of DA or the activity of the DA D1-receptors (DRD1). Within the scanner, modified versions of the Stroop and Sternberg tasks (Sternberg, 1966; Stroop, 1935) were administered to three groups of young adults varying according to their COMT Val158Met genotype [Val/Val (VV; low DA level), Val/Met (VM; intermediate DA level) and Met/Met (MM; high DA level)]. Based on the theory of dual mechanisms of control (Braver et al., 2007), the tasks were built up to induce proactive or reactive control processes according to the tasks context. Our results demonstrated for the first time that: (1) the inhibition of automatic saccades is influenced by the interaction between the level of DA and the DRD1 activity (Study 1); (2) proactive control during a verbal inhibitory task is specifically associated with an increased activity in the anterior cingulate cortex in individuals with a high cortical level of DA (Met-allele carriers), while an increased activity was observed in the middle frontal gyrus in carriers of the Val allele (Study 2); (3) during reactive control, the antero-posterior functional connectivity linked to interference resolution is influenced by the COMT genotype, such that fronto-temporal areas appeared more « connected » in individuals with a low level of DA (VV homozygous) (Study 4); (4) during proactive control, interference resolution during a working memory task is specifically associated to an increased activity in a large frontal network in VV homozygous individuals, especially in the left superior frontal gyrus during the transition from storage to recognition processes (Study 3). As a whole, these results suggest the level of DA as well as the activity of the DRD1 receptors are crucial factors to simultaneously take into account when investigating the influence of the dopaminergic system on inhibitory functioning. From a cognitive viewpoint, task context but also the kind of working memory representations (stable vs. flexible) during interference resolution seems particularly important to understand the effect of dopaminergic modulation on inhibitory efficiency
Modelling organizational learning from successes in the nuclear industry:Staff meetings as forums of knowledge sharing and acquisition
No full textUtilizing lessons learned from successful experiences in the context of safety-critical organizations has been receiving increasing interest among both scientific and practitioner communities. However, despite the attention, there is a need to better understand how success-related knowledge can be utilized to ensure safety and what tools and practices can be used to facilitate this process. In this paper, we focus on staff meetings as forums of knowledge sharing and acquisition. We describe staff meeting practices from empirical case studies, carried out at two Nordic nuclear power plants, and examine how the staff meetings contribute to organizational learning from successes. Based on these insights, we propose an integrative framework that aims to identify the factors that facilitate or hinder organizational learning from successes
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