The "problem" of predatory publishing remains a relatively small one and should not be allowed to defame open access

A recent investigation led by an international group of journalists raised concerns over the scale of the problem of deceptive publishing practices, with many researchers of standing and reputation found to have published in "predatory" journals. However, while the findings of this investigation garnered significant media attention, the robustness of the study itself was not subject to the same scrutiny. To Tom Olijhoek and Jon Tennant, the profile afforded to investigations of this type causes some to overstate the problem of predatory publishing, while often discrediting open access publishing at the same time. The real problem here is one of education around questionable journals, and should not distract from more urgent questions around the shifting scholarly ecosystem

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

Co-display of diverse spike proteins on nanoparticles broadens sarbecovirus neutralizing antibody responses

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants poses continuous challenges in combating the virus. Here, we describe vaccination strategies to broaden SARS-CoV-2 and sarbecovirus immunity by combining spike proteins based on different viruses or viral strains displayed on two-component protein nanoparticles. First, we combined spike proteins based on ancestral and Beta SARS-CoV-2 strains to broaden SARS-CoV-2 immune responses. Inclusion of Beta spike improved neutralizing antibody responses against SARS-CoV-2 Beta, Gamma, and Omicron BA.1 and BA.4/5. A third vaccination with ancestral SARS-CoV-2 spike also improved cross-neutralizing antibody responses against SARS-CoV-2 variants, in particular against the Omicron sublineages. Second, we combined SARS-CoV and SARS-CoV-2 spike proteins to broaden sarbecovirus immune responses. Adding SARS-CoV spike to a SARS-CoV-2 spike vaccine improved neutralizing responses against SARS-CoV and SARS-like bat sarbecoviruses SHC014 and WIV1. These results should inform the development of broadly active SARS-CoV-2 and pan-sarbecovirus vaccines and highlight the versatility of two-component nanoparticles for displaying diverse antigens

Directory of Open Access Journals - Certificate of excellence in reviewing - 2016

È un certificato del Doaj che riconosce la mia attività di revisione per il 2016

Criteria for open access and publishing

Çelik, Sönmez (Dogus Author)Bu makale DOAJ’ın tarihsel gelişimi ve bugünkü durumuna ilişkin genel bir değerlendirme sunmaktadır. Makalede DOAJ tarihine kısaca değinildikten sonra DOAJ’ın açık erişim, fikri mülkiyet hakları ve kuşku uyandıran yayıncılarla ilgili politikaları detaylı biçimde anlatılmaktadır. Makalenin büyük bir kısmını, DOAJ’ın açık erişim dergi değerlendirme sürecinde yeni belirlenen değerlendirme kriterlerinin nasıl kullanıldığına ilişkin açıklamalar ve DOAJ Seal’ı nitelendirmek için seçilen yedi yeni değerlendirme kriterinin arkasında yatan gerekçeler oluşturmaktadır. Son bölüm, DOAJ’ın yakında akademisyen ve yayıncılara sunacağı veri tabanı arama ve üst veri yükleme ile ilgili genişletilmiş seçeneklere ayrılmıştır. Sonuç, daha güçlü bir platform ve daha istikrarlı bir veri tabanı sunan, yükleme ve üst verinin derlenebilmesi için gelişmiş hizmetlere izin veren yenilenmiş bir DOAJ’dır.This article gives an overview of the history and current status of the DOAJ. After a brief historical overview, DOAJ policies regarding open access, intellectual property rights and questionable publishers are explained in detail. The larger part of this article is a much requested explanation on how DOAJ uses its new set of criteria for the evaluation of open access journals and the rationale behind choosing the seven extra criteria that qualify for the DOAJ Seal. A final section is devoted to the extended possibilities that DOAJ will be offering shortly to scholars and publishers for searching the database and for uploading metadata. The result is a renewed DOAJ that offers a more robust platform, a more stable database and enhanced services to allow the upload and collection of metadata

Criteria for open access and publishing

Olijhoek, T., Bjørnshauge, L. ve Mitchell, D. (2015). Criteria for open access and publishing. ScienceOpen Research, (8s.) makalesinin çevirisidir.Bu makale DOAJ’ın tarihsel gelişimi ve bugünkü durumuna ilişkin genel bir değerlendirme sunmaktadır. Makalede DOAJ tarihine kısaca değinildikten sonra DOAJ’ın açık erişim, fikri mülkiyet hakları ve kuşku uyandıran yayıncılarla ilgili politikaları detaylı biçimde anlatılmaktadır. Makalenin büyük bir kısmını, DOAJ’ın açık erişim dergi değerlendirme sürecinde yeni belirlenen değerlendirme kriterlerinin nasıl kullanıldığına ilişkin açıklamalar ve DOAJ Seal’ı nitelendirmek için seçilen yedi yeni değerlendirme kriterinin arkasında yatan gerekçeler oluşturmaktadır. Son bölüm, DOAJ’ın yakında akademisyen ve yayıncılara sunacağı veri tabanı arama ve üst veri yükleme ile ilgili genişletilmiş seçeneklere ayrılmıştır. Sonuç, daha güçlü bir platform ve daha istikrarlı bir veri tabanı sunan, yükleme ve üst verinin derlenebilmesi için gelişmiş hizmetlere izin veren yenilenmiş bir DOAJ’dır.This article gives an overview of the history and current status of the DOAJ. After a brief historical overview, DOAJ policies regarding open access, intellectual property rights and questionable publishers are explained in detail. The larger part of this article is a much requested explanation on how DOAJ uses its new set of criteria for the evaluation of open access journals and the rationale behind choosing the seven extra criteria that qualify for the DOAJ Seal. A final section is devoted to the extended possibilities that DOAJ will be offering shortly to scholars and publishers for searching the database and for uploading metadata. The result is a renewed DOAJ that offers a more robust platform, a more stable database and enhanced services to allow the upload and collection of metadata.DOA

A public antibody class recognizes an S2 epitope exposed on open conformations of SARS-CoV-2 spike

Delineating the origins and properties of antibodies elicited by SARS-CoV-2 infection and vaccination is critical for understanding their benefits and potential shortcomings. Therefore, we investigate the SARS-CoV-2 spike (S)-reactive B cell repertoire in unexposed individuals by flow cytometry and single-cell sequencing. We show that ∼82% of SARS-CoV-2 S-reactive B cells harbor a naive phenotype, which represents an unusually high fraction of total human naive B cells (∼0.1%). Approximately 10% of these naive S-reactive B cells share an IGHV1-69/IGKV3-11 B cell receptor pairing, an enrichment of 18-fold compared to the complete naive repertoire. Following SARS-CoV-2 infection, we report an average 37-fold enrichment of IGHV1-69/IGKV3-11 B cell receptor pairing in the S-reactive memory B cells compared to the unselected memory repertoire. This class of B cells targets a previously undefined non-neutralizing epitope on the S2 subunit that becomes exposed on S proteins used in approved vaccines when they transition away from the native pre-fusion state because of instability. These findings can help guide the improvement of SARS-CoV-2 vaccines

Antigenic cartography using sera from sequence-confirmed SARS-CoV-2 variants of concern infections reveals antigenic divergence of Omicron.

Large-scale vaccination campaigns have prevented countless hospitalizations and deaths due to COVID-19. However, the emergence of SARS-CoV-2 variants that escape from immunity challenges the effectiveness of current vaccines. Given this continuing evolution, an important question is when and how to update SARS-CoV-2 vaccines to antigenically match circulating variants, similarly to seasonal influenza viruses where antigenic drift necessitates periodic vaccine updates. Here, we studied SARS-CoV-2 antigenic drift by assessing neutralizing activity against variants of concern (VOCs) in a set of sera from patients infected with viral sequence-confirmed VOCs. Infections with D614G or Alpha strains induced the broadest immunity, whereas individuals infected with other VOCs had more strain-specific responses. Omicron BA.1 and BA.2 were substantially resistant to neutralization by sera elicited by all other variants. Antigenic cartography revealed that Omicron BA.1 and BA.2 were antigenically most distinct from D614G, associated with immune escape, and possibly will require vaccine updates to ensure vaccine effectiveness