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Clades of huge phages from across Earth’s ecosystems
Bacteriophages typically have small genomes
1
and depend on their bacterial hosts for replication
2
. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems.
Genomic analyses of major clades of huge phages sampled from across Earth’s ecosystems show that they have diverse genetic inventories, including a variety of CRISPR–Cas systems and translation-relevant genes.
Journal Article
From Classroom to Resource: Co-Creating a User-Centered English-Romanian Psychology Dictionary
This paper details the four-year long lexicographic, terminological and translational process of gathering and editing terms for an English-Romanian dictionary of psychology with the help of sources licensed under Creative Commons. It discusses the process of collaboration between four teachers and students in Psychology from the West University. At the same time, it seeks to expound on a previously published paper (Bran & Pele, “Bridging the Language Gap in Psychology. Challenges in Developing and English-Romanian Dictionary,” 2025) with further theoretical content, more figures, and different examples. As we shall discuss, the result is a specialized bilingual dictionary suitable for anyone interested in psychological concepts and terminology.
Journal Article
Dados de pesquisa subjacentes a artigos científicos
Este artigo analisa questões do direito autoral relacionadas a dados de pesquisa subjacentes a artigos de revistas científicas. A análise é feita tendo como pano de fundo a abertura e o compartilhamento de dados de pesquisa, operação que também comporta práticas colaborativas em nível internacional. Tais práticas podem esbarrar em diversos tipos de proteção jurídica, de diferentes legislações nacionais, de cultura e interpretações distintas, que acabam gerando áreas de diferença que podem inibir o reúso de dados subjacentes. Desta forma, efetuamos um estudo do direito autoral como possível proteção de dados de pesquisa, sob a perspectiva da comunicação científica. Para tanto, foram realizadas pesquisas bibliográfica e documental. A bibliográfica incluiu livros e artigos nas áreas jurídica, biomédica e biológica, por meio de buscas no repositório PubMed Central da Biblioteca Nacional de Medicina do National Institutes of Health dos Estados Unidos e em outras bases bibliográficas que abrigam periódicos dessas áreas, como o Portal de Periódicos da Capes, Springer Link, entre outras. A pesquisa documental consistiu em consultas a leis sobre direitos autorais, direitos sui generis sobre bases de dados e proteção a dados pessoais da União Europeia; lei de direitos autorais dos Estados Unidos; leis brasileiras que regulam o direito autoral e a proteção a dados pessoais; e a Constituição brasileira. Conclui-se que o direito autoral, naturalizado e, ao mesmo tempo, pouco pesquisado como elemento formador da área científica, revela-se provavelmente inadequado para regular relações jurídicas no universo científico cuja matéria-prima é a produção de conhecimento.
Journal Article
Empowering knowledge through AI: open scholarship proactively supporting well trained generative AI
Generative AI has taken the world by storm over the last few years, and the world of scholarly communications has not been immune to this. Most discussions in this area address how we can integrate these tools into our workflows, concerns about how researchers and students might misuse the technology or the unauthorised use of copyrighted work. This article argues for a novel viewpoint that librarians and publishers should be encouraging the use of their scholarly content in the training of AI algorithms. Inclusion of scholarly works would advance the reliability and accuracy of the information in training datasets and ensure that this content is included in new knowledge discovery platforms. The article also argues that inclusion can be achieved by improving linkage to content, and, by making sure that licences explicitly allow inclusion in AI training datasets, it advocates for a more collaborative approach to shaping the future of the information landscape in academia.
Journal Article
Dalla scienza moderna alla scienza aperta, pubblicare in ambito scientifico: copyright, Creative Commons e… oltre
Il concetto di tutela autorale si afferma e sviluppa nel corso della storia per favorire la massima diffusione dell’informazione. Dopo ben due secoli dalla sua affermazione, sviluppo e maturazione, il sistema tradizionale entra in piena crisi, minato nelle sue fondamenta dall’innovazione digitale e dalle trasformazioni socio-culturali del XX secolo. L’evoluzione del sistema tradizionale ha introdotto elementi oggi limitanti per la libera circolazione dell’informazione scientifica e di ostacolo all’accesso alla conoscenza. Le licenze Creative Commons (CC) offrono un modello di gestione più flessibile dei diritti d’autore, permettendo agli autori di riservarsi alcuni diritti e cederne altri. Esistono diverse varianti di licenze CC: alcune sono compatibili con l’accesso aperto, altre no. Per un cambiamento significativo verso una scienza più aperta, è necessario restituire maggiore potere contrattuale agli autori, modificando la legge sul diritto d’autore, e la gestione della produzione scientifica agli scienziati.
Journal Article
IMÁGENES DE ACCESO ABIERTO Y LOS BANCOS DE IMAGEN: ESTUDIO DE CASOS
At present, stock photography websites, have proliferated in correlation with the presence of digital images on the Web. In this context, this paper includes a study of representative cases of free image banks, such as Pixabay, Stocksnap or the INTEF. This analysis applies to the short of images these sites offer, as well as their conditions of use, and the possibilities of collaborative creation that they allow. Finally, the most relevant results and conclusions are presented and discussed. In addition, a list of websites of this type is given offered, which could be a very useful source of images for potential users.
Journal Article
The Future of the Monograph in the Arts, Humanities and Social Sciences: Publisher Perspectives on a Transitioning Format
A web-based survey of academic publishers was undertaken in 2021 by a team at Oxford International Centre for Publishing into the state of monograph publication in the arts, humanities, and social sciences. 25 publishing organisations responded, including many of the larger presses, representing approximately 75% of monograph output. Responses to the survey showed that the Covid 19 pandemic has accelerated the existing trend from print to digital dissemination and that Open Access (OA) titles receive substantially greater levels of usage than those published traditionally. Responses also showed that for most publishers OA publication stands at under 25% of output and that fewer than 10% of authors enquire about OA publication options. Continuing problem areas highlighted by respondents were the clearing of rights for OA publication and the standardisation of title and usage metadata. All responding organisations confirmed that they expect to be publishing monographs in ten years’ time, but that they anticipate the format and/or the model will be different, with open access expected to play a key part in the future, perhaps in the context of a mixed economy of OA and ‘toll access’ publication.
Journal Article
Copyright implications for the aggregation of audiovisual content in Greece
Purpose
This paper aims to attempt to provide an overview of the copyright legal framework for audiovisual resources in Europe and Greece, how Audiovisual (AV) content is currently licensed by Greek providers and how licenses or copyright exceptions enable its reuse. The motivation for this work was the development of an aggregation service for audiovisual resources in Greece, the Open AudioVisual Archives (OAVA) platform.
Design/methodology/approach
Copyright licenses and exceptions in the European Union and in Greek Legislation have been thoroughly reviewed along with the reuse of content, based on the terms of Fair Use, Rights Statements and Creative Commons. Licensing issues for the most well-known aggregation services, such as Europeana, Digital Public Library of America, Trove, Digital New Zealand and the National Digital Library of India, have also been studied and considered. Audiovisual content providers in Greece have been recorded, and their licensing preferences have been analyzed. Pearson’s chi-square test was applied to test the relationship between the provider’s type, resources’ genre and licenses used.
Findings
Despite the abundance of copyright legislation in the European Union and in Greece, audiovisual content providers in Greece seem to ignore it or find it difficult to choose the right license. More than half of them choose to publish their resources on popular audiovisual platforms using the default licensing option provided. Creative Commons licenses are preferred for audiovisual content that falls into the following categories: open courses (almost exclusively) and interviews and digital collection/research projects (about half of the content).
Originality/value
This paper examines audiovisual content aggregation, in the EU and Greece, from a legal point of view. To the best of the authors’ knowledge, it is the first attempt to record and analyze the licensing preferences of Greek AV content providers.
Journal Article
The Plan S Rights Retention Strategy is an administrative and legal burden, not a sustainable open access solution
The Plan S Rights Retention Strategy (RRS) requires authors who are submitting to subscription journals to inform publishers that the author accepted manuscript (AAM) will be made available under a Creative Commons Attribution (CC BY) licence. The laudable stated aim of the RRS is to achieve immediate open access to research outputs, while preserving journal choice for authors. However, proponents of the RRS overlook the significant administrative and legal burdens that the RRS places on authors and readers. Even though compliance with existing green open access (self-archiving) policies is poor at best, the RRS is likely to rely on authors to successfully execute the CC licensing of their work in the face of publisher resistance. The complexity of copyright law and CC licensing gives many reasons to doubt the legal validity of an RRS licence grant, which creates legal risk for authors and their institutions. The complexity of RRS CC BY licensing also creates legal risk for readers, who may not be able to fully rely on the reuse rights of a CC BY licence on the AAM. However, cOAlition S has released no legal advice that explains why the RRS is valid and legally binding. Publishers of legacy subscription journals have already begun implementing strategies that ensure they can protect their revenue streams. These actions may leave authors having to choose between paying publication fees and complying with their funding agreements. The result is that the RRS increases the complexity of the copyright and licensing landscape in academic publishing, creates legal risk and may not avoid author fees. Unless increased complexity and conflict between authors and publishers drives open access, the RRS is not fit for its stated purpose as an open access strategy.
Journal Article