1,062 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
Analysis of Mathieu Equation Stable Solutions in the First Zone of Stability
No full textAbstractThe paper presents the results of a homogeneous Mathieu equation studies. Mathieu equation solutions are oscillations, modulated in amplitude and frequency. In the computational experiments we found dependences of the given oscillations on the ratio of the coefficients. These dependences are shown in graphs that can be used for an approximate estimation of the Mathieu equation solutions without integration
Pensar las escalas para pensar las luchas: Autor: Mathieu UHEL
No full textA través de un título sugerente, “pensar las escalas para pensar las luchas”, Mathieu Uhel entreteje la construcción teórico-crítica del concepto escala, generada por la geografía radical anglosajona de finales del siglo XX, con la necesidad/utilidad práctica de la escala para concienciar las luchas sociales. El artículo cumple un doble propósito: por un lado, delinear los elementos de lectura sobre el concepto escala; y, con ello, promover la atención de esta problemática en las luchas contemporáneas. En un primer apartado, Uhel ubica las discusiones académicas en torno a la escala, como herramienta metodológica útil para comprender la complejidad de las sociedades capitalistas; en el segundo apartado, el autor avanza la exposición en torno al contexto de la dimensión escalar del imperialismo capitalista; finalmente, el autor se centra en el rol de la actividad política a escala nacional en la tensa relación entre las imposiciones del capital y la lucha social.Por meio de um título sugestivo, “pensando escalas para pensar lutas”, Mathieu Uhel entrelaça a construção teórico-crítica do conceito de escala, gerado pela geografia radical anglo-saxônica do final do século XX, com a necessidade / utilidade prática escala para aumentar a consciência das lutas sociais. O artigo tem um duplo propósito: por um lado, delinear os elementos de leitura sobre o conceito de escala; e, com isso, promover atenção a esse problema nas lutas contemporâneas. Na primeira seção, Uhel localiza as discussões acadêmicas em torno da escala, como uma ferramenta metodológica útil para compreender a complexidade das sociedades capitalistas; na segunda seção, o autor avança a exposição em torno do contexto da dimensão escalar do imperialismo capitalista; por fim, o autor enfoca o papel da atividade política em escala nacional na tensa relação entre as imposições do capital e a luta social.Mathieu Uhel\u27s suggestive title, “Thinking about scales to think about struggles”, he interweaves the theoretical-critical construction of concept scale, generated by radical Anglo-Saxon geography in the late 20th century, with it´s practical utility to social struggles. The article serves two purposes: on the one hand, Uhel locates academic discussion around scale; and, with this, he promotes attention to this problem in contemporary struggles. In the first section, Uhel locates academic discussions around scale, as a useful methodological tool to understand the complexity of capitalist societies; in the second section, the author advances the argument around the context of the scalar dimension of capitalist imperialism; finally, the author focuses on the role of political activity on a national scale in the tense relationship between the impositions of capital and the social movement
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
Mathieu Ichou, Les Enfants d’immigrés à l’école
No full textIt is common to hear in the fields of educational and immigration sociology that on average, the children of immigrants do not perform as well in school as children of native-born parents. Mathieu Ichou offers an innovative sociological analysis on a topic that is heavily exploited by political and media discourse, and subject to much scientific controversy. The author takes distance from the homogenized vision of a “second generation” of students who have totally failed academically, and rep..
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
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