Open science- who is left behind?

Open Access initiatives promise to extend access to scholarly conversations. However, the dominant model of Article Processing Charges, whilst lowering financial barriers for readers, has merely erected a new paywall at the other end of the pipeline, blocking access to publication for less-privileged authors. In this post, Tony Ross-Hellauer, Angela Fessl, and Thomas Klebel, ask ... Continue

Training researchers with the MOVING platform

The MOVING platform enables its users to improve their information literacy by training how to exploit data and text mining methods in their daily research tasks. In this paper, we show how it can support researchers in various tasks, and we introduce its main features, such as text and video retrieval and processing, advanced visualizations, and the technologies to assist the learning process

Dynamics of cumulative advantage and threats to equity in open science: a scoping review

Open Science holds the promise to make scientific endeavours more inclusive, participatory, understandable, accessible and re-usable for large audiences. However, making processes open will not per se drive wide reuse or participation unless also accompanied by the capacity (in terms of knowledge, skills, financial resources, technological readiness and motivation) to do so. These capacities vary considerably across regions, institutions and demographics. Those advantaged by such factors will remain potentially privileged, putting Open Science's agenda of inclusivity at risk of propagating conditions of ‘cumulative advantage’. With this paper, we systematically scope existing research addressing the question: ‘What evidence and discourse exists in the literature about the ways in which dynamics and structures of inequality could persist or be exacerbated in the transition to Open Science, across disciplines, regions and demographics?’ Aiming to synthesize findings, identify gaps in the literature and inform future research and policy, our results identify threats to equity associated with all aspects of Open Science, including Open Access, Open and FAIR Data, Open Methods, Open Evaluation, Citizen Science, as well as its interfaces with society, industry and policy. Key threats include: stratifications of publishing due to the exclusionary nature of the author-pays model of Open Access; potential widening of the digital divide due to the infrastructure-dependent, highly situated nature of open data practices; risks of diminishing qualitative methodologies as ‘reproducibility’ becomes synonymous with quality; new risks of bias and exclusion in means of transparent evaluation; and crucial asymmetries in the Open Science relationships with industry and the public, which privileges the former and fails to fully include the latter

ATP-induced asymmetric pre-protein folding as a driver of protein translocation through the Sec machinery

Funding: Royal Society for a University Research Fellowship; Wellcome Multi-User Equipment Grant (099149/Z/12/Z) (JEL).Transport of proteins across membranes is a fundamental process, achieved in every cell by the 'Sec' translocon. In prokaryotes, SecYEG associates with the motor ATPase SecA to carry out translocation for pre-protein secretion. Previously, we proposed a Brownian ratchet model for transport, whereby the free energy of ATP-turnover favours the directional diffusion of the polypeptide [Allen et al. eLife 2016]. Here, we show that ATP enhances this process by modulating secondary structure formation within the translocating protein. A combination of molecular simulation with hydrogen-deuterium-exchange mass spectrometry and electron paramagnetic resonance spectroscopy reveal an asymmetry across the membrane: ATP induced conformational changes in the cytosolic cavity promote unfolded pre-protein structure, while the exterior cavity favours its formation. This ability to exploit structure within a pre-protein is an unexplored area of protein transport, which may apply to other protein transporters, such as those of the endoplasmic reticulum and mitochondria.Publisher PDFPeer reviewe

MOVING: A User-Centric Platform for Online Literacy Training and Learning

Part of the Progress in IS book series (PROIS)In this paper, we present an overview of the MOVING platform, a user-driven approach that enables young researchers, decision makers, and public administrators to use machine learning and data mining tools to search, organize, and manage large-scale information sources on the web such as scientific publications, videos of research talks, and social media. In order to provide a concise overview of the platform, we focus on its front end, which is the MOVING web application. By presenting the main components of the web application, we illustrate what functionalities and capabilities the platform offer its end-users, rather than delving into the data analysis and machine learning technologies that make these functionalities possible

How many bird and mammal extinctions has recent conservation action prevented?

Aichi Target 12 of the Convention on Biological Diversity (CBD) aims to ‘prevent extinctions of known threatened species’. To measure its success, we used a Delphi expert elicitation method to estimate the number of bird and mammal species whose extinctions were prevented by conservation action in 1993 - 2020 (the lifetime of the CBD) and 2010 - 2020 (the timing of Aichi Target 12). We found that conservation prevented 21–32 bird and 7–16 mammal extinctions since 1993, and 9–18 bird and 2–7 mammal extinctions since 2010. Many remain highly threatened, and may still become extinct in the near future. Nonetheless, given that ten bird and five mammal species did go extinct (or are strongly suspected to) since 1993, extinction rates would have been 2.9–4.2 times greater without conservation action. While policy commitments have fostered significant conservation achievements, future biodiversity action needs to be scaled up to avert additional extinctions

How many bird and mammal extinctions has recent conservation action prevented?

Aichi Target 12 of the Convention on Biological Diversity (CBD) contains the aim to ‘prevent extinctions of known threatened species’. To measure the degree to which this was achieved, we used expert elicitation to estimate the number of bird and mammal species whose extinctions were prevented by conservation action in 1993–2020 (the lifetime of the CBD) and 2010–2020 (the timing of Aichi Target 12). We found that conservation action prevented 21–32 bird and 7–16 mammal extinctions since 1993, and 9–18 bird and two to seven mammal extinctions since 2010. Many remain highly threatened and may still become extinct. Considering that 10 bird and five mammal species did go extinct (or are strongly suspected to) since 1993, extinction rates would have been 2.9–4.2 times greater without conservation action. While policy commitments have fostered significant conservation achievements, future biodiversity action needs to be scaled up to avert additional extinctions.https://wileyonlinelibrary.com/journal/conlMammal Research Institut

Components of a Research 2.0 infrastructure

In this paper, we investigate the components of a Research 2.0 infrastructure. We propose building blocks and their concrete implementation to leverage Research 2.0 practice and technologies in our field, including a publication feed format for exchanging publication data, a RESTful API to retrieve publication and Web 2.0 data, and a publisher suit for refining and aggregating data. We illustrate the use of this infrastructure with Research 2.0 application examples ranging from a Mash-Up environment, a mobile and multitouch application, thereby demonstrating the strength of this infrastructure

ATP-induced asymmetric pre-protein folding as a driver of protein translocation through the Sec machinery

Transport of proteins across membranes is a fundamental process, achieved in every cell by the 'Sec' translocon. In prokaryotes, SecYEG associates with the motor ATPase SecA to carry out translocation for pre-protein secretion. Previously, we proposed a Brownian ratchet model for transport, whereby the free energy of ATP-turnover favours the directional diffusion of the polypeptide [Allen et al. eLife 2016]. Here, we show that ATP enhances this process by modulating secondary structure formation within the translocating protein. A combination of molecular simulation with hydrogen-deuterium-exchange mass spectrometry and electron paramagnetic resonance spectroscopy reveal an asymmetry across the membrane: ATP induced conformational changes in the cytosolic cavity promote unfolded pre-protein structure, while the exterior cavity favours its formation. This ability to exploit structure within a pre-protein is an unexplored area of protein transport, which may apply to other protein transporters, such as those of the endoplasmic reticulum and mitochondria