Open science skills in Danish research libraries

Open Science is gaining more and more ground among academics. This has consequences for research libraries and their staff tasked with services supporting the entire research life cycle, from providing access to relevant databases, to research data management, to scholarly publishing. To stay relevant, research library services have to be developed and adapted to support Open Science research activities. Therefore, it is important to investigate what competencies and skills are needed to provide a given library service, both in terms of continuing education and training of existing library staff and of curriculum development in library and information science education. There are several international initiatives that either facilitate the upskilling of researchers and research staff within Open Science (e.g. the EC’s “Open Science Skills Working Group report” [1] and FOSTER’s materials and online courses [2]) or provide a framework for research libraries of how to engage in Open Science support (e.g. LIBER’s “Open Science Roadmap” [3]). These initiatives lay out general lines of action that can serve as starting points for more locally focused activities. Furthermore, the EDISON project has provided competency profiles for data professionals that can be used for curriculum design within higher and continuing education [4]. In our poster, we present a project, currently funded by Denmark’s Electronic Research Library (DEFF), that investigates, models, and deploys Open Science skills for Danish research librarians. The project comprises three subprojects that focus on 1) a general model of Open Science competencies and skills for research librarians, 2) an overview of Danish digital collections, with a focus on openness and applicability, 3) the identification of current and future RDM services and tools at Danish research libraries and a model of RDM competencies and skills for research librarians. The project started in March 2018 and will run until March 2020. We present initial considerations and the research design of the subprojects 1) and 3). We provide insights into the challenges encountered when introducing general international frameworks into a national context.</p

Thought experiment: Decoding cognitive processes from the fMRI data of one individual

Wegrzyn M, Aust J, Barnstorf L, et al. Thought experiment: Decoding cognitive processes from the fMRI data of one individual. PLOS ONE. 2018;13(9): e0204338.Cognitive processes, such as the generation of language, can be mapped onto the brain using fMRI. These maps can in turn be used for decoding the respective processes from the brain activation patterns. Given individual variations in brain anatomy and organization, analyzes on the level of the single person are important to improve our understanding of how cognitive processes correspond to patterns of brain activity. They also allow to advance clinical applications of fMRI, because in the clinical setting making diagnoses for single cases is imperative. In the present study, we used mental imagery tasks to investigate language production, motor functions, visuo-spatial memory, face processing, and resting-state activity in a single person. Analysis methods were based on similarity metrics, including correlations between training and test data, as well as correlations with maps from the NeuroSynth meta-analysis. The goal was to make accurate predictions regarding the cognitive domain (e.g. language) and the specific content (e.g. animal names) of single 30-second blocks. Four teams used the dataset, each blinded regarding the true labels of the test data. Results showed that the similarity metrics allowed to reach the highest degrees of accuracy when predicting the cognitive domain of a block. Overall, 23 of the 25 test blocks could be correctly predicted by three of the four teams. Excluding the unspecific rest condition, up to 10 out of 20 blocks could be successfully decoded regarding their specific content. The study shows how the information contained in a single fMRI session and in each of its single blocks can allow to draw inferences about the cognitive processes an individual engaged in. Simple methods like correlations between blocks of fMRI data can serve as highly reliable approaches for cognitive decoding. We discuss the implications of our results in the context of clinical fMRI applications, with a focus on how decoding can support functional localization

Mapping of Open Science Professional Networks in Europe

This presentation was given at the monthly meeting of the Community of Practice for Training Coordinators in June 2023 (13-06-2023). The presentation gives a short introduction to the Skills4EOSC project and presents the project deliverable D6.1 "Mapping of existing professional networks" that provides an overview of the current landscape of Open Science related professional networks in Europe

Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly

Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.publishe

A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst

Abstract With the advent of serial X-ray crystallography on microfocus beamlines at free-electron laser and synchrotron facilities, the demand for protein microcrystals has significantly risen in recent years. However, by in vitro crystallization extensive efforts are usually required to purify proteins and produce sufficiently homogeneous microcrystals. Here, we present InCellCryst, an advanced pipeline for producing homogeneous microcrystals directly within living insect cells. Our baculovirus-based cloning system enables the production of crystals from completely native proteins as well as the screening of different cellular compartments to maximize chances for protein crystallization. By optimizing cloning procedures, recombinant virus production, crystallization and crystal detection, X-ray diffraction data can be collected 24 days after the start of target gene cloning. Furthermore, improved strategies for serial synchrotron diffraction data collection directly from crystals within living cells abolish the need to purify the recombinant protein or the associated microcrystals

Pals1 prevents Rac1-dependent colorectal cancer cell metastasis by inhibiting Arf6

Loss of apical-basal polarity and downregulation of cell-cell contacts is a critical step during the pathogenesis of cancer. Both processes are regulated by the scaffolding protein Pals1, however, it is unclear whether the expression of Pals1 is affected in cancer cells and whether Pals1 is implicated in the pathogenesis of the disease. Using mRNA expression data and immunostainings of cancer specimen, we show that Pals1 is frequently downregulated in colorectal cancer, correlating with poorer survival of patients. We further found that Pals1 prevents cancer cell metastasis by controlling Rac1-dependent cell migration through inhibition of Arf6, which is independent of the canonical binding partners of Pals1. Loss of Pals1 in colorectal cancer cells results in increased Arf6 and Rac1 activity, enhanced cell migration and invasion in vitro and increased metastasis of transplanted tumor cells in mice. Thus, our data reveal a new function of Pals1 as a key inhibitor of cell migration and metastasis of colorectal cancer cells. Notably, this new function is independent of the known role of Pals1 in tight junction formation and apical-basal polarity