ITC's strategic plan for Open Science 2021-2025:towards an open future

Open Science (OS) is an umbrella term comprising principles to increase the transparency of research. Besides Open Access to scientific articles, these principles contain public availability of reusable methods (e.g., code and tools), data, and educational materials. This document outlines a plan to achieve the transition towards OS. ITC’s Strategic Plan for OS 2021-2025 - Towards an Open Future contains five initiatives: 1.OS at ITC aims to provide guidelines and OS capacity development to address the obstacles ITC researchers encounter when doing OS. 2.The ITC Knowledge Hub will provide services and tools to access, create, and publish open research, including scientific results based on qualitative/quantitative analyses using computational workflows. 3.Open Educational Resources will be addressed by exploring options to realise Open Educational Resources at ITC and providing lecturers with guidelines and support to create them. 4.The OS Community Twente serves as an inter-disciplinary, bottom-up community to promote, learn, share, and discuss OS practices. 5.Research & Funding aims to address challenges in OS through innovative developments and user studies. A further output is to generate funding to realise the ambitious aims presented in the plan. For a successful OS transition, the initiatives aim to address the Rewards & Recognition system, valorise Sharing & Collaboration, develop OS Knowledge & Skills, and foster Cultural change & Societal impact

Impacts of Bar-driven Shear and Shocks on Star Formation

Bars drive gas inflow. As the gas flows inward, shocks and shear occur along the bar dust lanes. Such shocks and shear can affect the star formation (SF) and change the gas properties. For four barred galaxies, we present Hα velocity gradient maps that highlight bar-driven shocks and shear using data from the PHANGS-MUSE and PHANGS-ALMA surveys, which allow us to study bar kinematics in unprecedented detail. Velocity gradients are enhanced along the bar dust lanes, where shocks and shear are shown to occur in numerical simulations. Velocity gradient maps also efficiently pick up H ii regions that are expanding or moving relative to the surroundings. We put pseudo-slits on the regions where velocity gradients are enhanced and find that Hα and CO velocities jump up to ∼170 km s−1, even after removing the effects of circular motions due to the galaxy rotation. Enhanced velocity gradients either coincide with the peak of CO intensity along the bar dust lanes or are slightly offset from CO intensity peaks, depending on the objects. Using the Baldwin–Philips–Terlevich BPT diagnostic, we identify the source of ionization on each spaxel and find that SF is inhibited in the high-velocity gradient regions of the bar, and the majority of those regions are classified as a low-ionization nuclear emission-line region (LINER) or composite. This implies that SF is inhibited where bar-driven shear and shocks are strong. Our results are consistent with the results from the numerical simulations that show SF is inhibited in the bar where the shear force is strong

A Comprehensive Analysis of Choroideremia: From Genetic Characterization to Clinical Practice.

Choroideremia (CHM) is a rare X-linked disease leading to progressive retinal degeneration resulting in blindness. The disorder is caused by mutations in the CHM gene encoding REP-1 protein, an essential component of the Rab geranylgeranyltransferase (GGTase) complex. In the present study, we evaluated a multi-technique analysis algorithm to describe the mutational spectrum identified in a large cohort of cases and further correlate CHM variants with phenotypic characteristics and biochemical defects of choroideremia patients. Molecular genetic testing led to the characterization of 36 out of 45 unrelated CHM families (80%), allowing the clinical reclassification of four CHM families. Haplotype reconstruction showed independent origins for the recurrent p.Arg293* and p.Lys178Argfs*5 mutations, suggesting the presence of hotspots in CHM, as well as the identification of two different unrelated events involving exon 9 deletion. No certain genotype-phenotype correlation could be established. Furthermore, all the patients´ fibroblasts analyzed presented significantly increased levels of unprenylated Rabs proteins compared to control cells; however, this was not related to the genotype. This research demonstrates the major potential of the algorithm proposed for diagnosis. Our data enhance the importance of establish a differential diagnosis with other retinal dystrophies, supporting the idea of an underestimated prevalence of choroideremia. Moreover, they suggested that the severity of the disorder cannot be exclusively explained by the genotype

The Azorean Biodiversity Portal: an internet database for regional biodiversity outreach

Copyright © 2010 The Natural History Museum.There is a growing interest in academia to provide biodiversity data to both the scientific community and the public. We present an internet database of the terrestrial lichens, bryophytes, vascular plants, molluscs, arthropods, vertebrates and coastal invertebrates of the Azores archipelago (Portugal, North Atlantic): the Azorean Biodiversity Portal (ABP, http://www.azoresbioportal.angra.uac.pt/). This is a unique resource for fundamental research in systematics, biodiversity, education and conservation management. The ABP was based on a regional species database (ATLANTIS), comprised of grid-based spatial incidence information for c. 5000 species. Most of the data rely on a comprehensive literature survey (dating back to the 19th century) as well as unpublished records from recent field surveys in the Azores. The ABP disseminates the ATLANTIS database to the public, allowing universal, unrestricted access to much of its data. Complementarily, the ABP includes additional information of interest to the general public (e.g. literature on Macaronesian biodiversity) together with images from collections and/or live specimens for many species. In this contribution we explain the implementation of a regional biodiversity database, its architecture, achievements and outcomes, strengths and limitations; we further include a number of suggestions in order to implement similar initiatives

Quinoa Phenotyping Methodologies: An International Consensus

Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally

A Ligand Peptide Motif Selected from a Cancer Patient Is a Receptor-Interacting Site within Human Interleukin-11

Interleukin-11 (IL-11) is a pleiotropic cytokine approved by the FDA against chemotherapy-induced thrombocytopenia. From a combinatorial selection in a cancer patient, we isolated an IL-11-like peptide mapping to domain I of the IL-11 (sequence CGRRAGGSC). Although this motif has ligand attributes, it is not within the previously characterized interacting sites. Here we design and validate in-tandem binding assays, site-directed mutagenesis and NMR spectroscopy to show (i) the peptide mimics a receptor-binding site within IL-11, (ii) the binding of CGRRAGGSC to the IL-11Rα is functionally relevant, (iii) Arg4 and Ser8 are the key residues mediating the interaction, and (iv) the IL-11-like motif induces cell proliferation through STAT3 activation. These structural and functional results uncover an as yet unrecognized receptor-binding site in human IL-11. Given that IL-11Rα has been proposed as a target in human cancer, our results provide clues for the rational design of targeted drugs

Mesenchymal Stem Cell Graft Improves Recovery after Spinal Cord Injury in Adult Rats through Neurotrophic and Pro-Angiogenic Actions

Numerous strategies have been managed to improve functional recovery after spinal cord injury (SCI) but an optimal strategy doesn't exist yet. Actually, it is the complexity of the injured spinal cord pathophysiology that begets the multifactorial approaches assessed to favour tissue protection, axonal regrowth and functional recovery. In this context, it appears that mesenchymal stem cells (MSCs) could take an interesting part. The aim of this study is to graft MSCs after a spinal cord compression injury in adult rat to assess their effect on functional recovery and to highlight their mechanisms of action. We found that in intravenously grafted animals, MSCs induce, as early as 1 week after the graft, an improvement of their open field and grid navigation scores compared to control animals. At the histological analysis of their dissected spinal cord, no MSCs were found within the host despite their BrdU labelling performed before the graft, whatever the delay observed: 7, 14 or 21 days. However, a cytokine array performed on spinal cord extracts 3 days after MSC graft reveals a significant increase of NGF expression in the injured tissue. Also, a significant tissue sparing effect of MSC graft was observed. Finally, we also show that MSCs promote vascularisation, as the density of blood vessels within the lesioned area was higher in grafted rats. In conclusion, we bring here some new evidences that MSCs most likely act throughout their secretions and not via their own integration/differentiation within the host tissue