The Open Access Journals Toolkit

Contents: Getting Started 5 • Scope, aims and focus 5 • Choosing a title for your journal 6 • Types of content accepted 7 • Kick-off and ongoing funding 11 • Disciplinary considerations 16 • Journal setup checklist and timeline 18 • Running a journal 20 • Article selection criteria 20 • Publication frequency and journal issues 23 • Attracting authors 25 • Peer review and quality assurance 27 • The costs of running an online open access journal 31 • Running a journal in a local or regional language 34 • Flipping a journal to open access 36 • Indexing 38 • Building and maintaining a profile 38 • Journal and article indexing 41 • Search engine optimisation and technical improvements 43 • Journal and article level metrics 45 • Staffing 49 • Roles and responsibilities 49 • Recruiting journal staff 51 • Building an editorial board 54 • Training and staff development 57 • Policies 59 • Developing author guidelines 59 • Publication ethics and related editorial policies 61 • Compliance with funder policies and mandates 64 • Copyright and licensing 66 • Displaying licensing information 68 • Corrections and retractions 70 • Infrastructure 72 • Software and technical infrastructure 72 • Journal appearance and web design 74 • Article and journal metadata 76 • Structured content 79 • Persistent Identifiers 81 • About the Open Access Journals Toolkit 83 • About 83 • What is an open access journal? 86 • Frequently asked questions 89 • Glossary 92 • Further reading 9

Ten Myths around Open Scholarly Publishing

The changing world of scholarly communication and the emergence of ‘Open Science’ or ‘Open Research’ has brought to light a number of controversial and hotly-debated topics. Yet, evidence-based rational debate is regularly drowned out by misinformed or exaggerated rhetoric, which does not benefit the evolving system of scholarly communication. The aim of this article is to provide a baseline evidence framework for ten of the most contested topics, in order to help frame and move forward discussions, practices and policies. We address preprints and scooping, the practice of copyright transfer, the function of peer review, and the legitimacy of ‘global’ databases. The presented facts and data will be a powerful tool against misinformation across wider academic research, policy and practice, and may be used to inform changes within the rapidly evolving scholarly publishing system

Ten Hot Topics around Scholarly Publishing

The changing world of scholarly communication and the emergence of a new wave of 'Open Science' or 'Open Research' has brought to light a number of controversial and hotly-debated topics. Yet, evidence-based rational debate is regularly drowned out by misinformed or exaggerated rhetoric, which does not benefit the evolving system of scholarly communication. The aim of this article is to provide a baseline evidence framework for ten of the most contested topics, in order to help frame and move forward discussions, practices and policies. We address issues around preprints and scooping, the practice of copyright transfer, the function of peer review, predatory publishers, and the legitimacy of 'global' databases. The presented facts, arguments and data will be a powerful tool against misinformation across wider academic research, policy and practice, and may be used to inform changes within the rapidly evolving scholarly publishing system

A MOOC approach for training researchers in developing countries

We report on an online course in research writing offered in a massive open online course (MOOC) format for developing country researchers. The concepts of cognitive presence, teacher presence, and social presence informed the design of the course, with a philosophy of strong social interaction supported by guest facilitators. The course was developed with low-bandwidth elements and hosted on a Moodle site. It was offered twice as a MOOC and 2830 learners from more than 90 countries, mainly in the developing world, took part. The average completion rate was 53%. Female learners and learners who were active in the forums were more likely to complete the course. Our MOOC approach may be a useful model for continuing professional development training in the developing world

Correction: Economic sanctions and academia: Overlooked impact and long-term consequences.

[This corrects the article DOI: 10.1371/journal.pone.0222669.]

Ten Myths around Open Scholarly Publishing

The changing world of scholarly communication and the emergence of ‘Open Science’ or ‘Open Research’ has brought to light a number of controversial and hotly-debated topics. Yet, evidence-based rational debate is regularly drowned out by misinformed or exaggerated rhetoric, which does not benefit the evolving system of scholarly communication. The aim of this article is to provide a baseline evidence framework for ten of the most contested topics, in order to help frame and move forward discussions, practices and policies. We address preprints and scooping, the practice of copyright transfer, the function of peer review, and the legitimacy of ‘global’ databases. The presented facts and data will be a powerful tool against misinformation across wider academic research, policy and practice, and may be used to inform changes within the rapidly evolving scholarly publishing system

Whole-genome sequencing provides new insights into the clonal architecture of Barrett's esophagus and esophageal adenocarcinoma

The molecular genetic relationship between esophageal adenocarcinoma (EAC) and its precursor lesion, Barrett's esophagus, is poorly understood. Using whole-genome sequencing on 23 paired Barrett's esophagus and EAC samples, together with one in-depth Barrett's esophagus case study sampled over time and space, we have provided the following new insights: (i) Barrett's esophagus is polyclonal and highly mutated even in the absence of dysplasia; (ii) when cancer develops, copy number increases and heterogeneity persists such that the spectrum of mutations often shows surprisingly little overlap between EAC and adjacent Barrett's esophagus; and (iii) despite differences in specific coding mutations, the mutational context suggests a common causative insult underlying these two conditions. From a clinical perspective, the histopathological assessment of dysplasia appears to be a poor reflection of the molecular disarray within the Barrett's epithelium, and a molecular Cytosponge technique overcomes sampling bias and has the capacity to reflect the entire clonal architecture.</p