PubPeer: Never Heard of It? You Have Now.

Information for authors and editorial policies

The work required to collect, clean and publish biodiversity datasets is significant, and those who do it deserve recognition for their efforts. Researchers publish studies using open biodiversity data available from GBIF—the Global Biodiversity Information Facility—at a rate of about two papers a day. These studies cover areas such as macroecology, evolution, climate change, and invasive alien species, relying on data sharing by hundreds of publishing institutions and the curatorial work of thousands of individual contributors. With more than 90 per cent of these datasets licensed under Creative Commons Attribution licenses (CC BY and CC BY-NC), data users are required to credit the dataset providers. For GBIF, it is crucial to link these scientific uses to the underlying data as one means of demonstrating the value and impact of open science, while seeking to ensure attribution of individual, organizational and national contributions to the global pool of open data about biodiversity. Every single authenticated download of occurrence records from GBIF.org is issued a unique Digital Object Identifier (DOI). These DOIs each resolve to a landing page that contains details of the search parameters used to generate the download a quantitative map of the underlying datasets that contributed to the download a simple citation to be included in works that rely on the data the search parameters used to generate the download a quantitative map of the underlying datasets that contributed to the download a simple citation to be included in works that rely on the data When used properly by authors and deposited correctly by journals in the article metadata, the DOI citation establishes a direct link between a scientific paper and the underlying data. Crossref—the main DOI Registration Agency for academic literature— exposes such links in Event Data, which can be consumed programmatically to report direct use of individual datasets. GBIF also records these links, permanently preserving the download archives while exposing a citation count on download landing pages that is also summarized on the landing pages of each contributing datasets and publishers. The citation counts can be expanded to produce lists of all papers unambiguously linked to use of specific datasets. In 2018, just 15 per cent of papers based on GBIF-mediated data used DOIs to cite or acknowledge the datasets used in the studies. To promote crediting of data publishers and digital recognition of data sharing, the GBIF Secretariat has been reaching out systematically to authors and publishers since April 2018 whenever a paper fails to include a proper data citation. While publishing lags may hinder immediate effects, preliminary findings suggest that uptake is improving—as the number of papers with DOI data citations during the first part of 2019 is up more than 60 per cent compared to 2018. Focusing on the value of linking scientific publications and data, this presentation will explore the potential for establishing automatic linkage through DOI metadata while demonstrating efforts to improve metrics of data use and attribution of data providers through outreach campaigns to authors and journal publishers.

Salami slicing, shingling, and meat extending are all fanciful terms for a thorny and often overlooked issue. Publication overlap—the presentation of redundant ideas or data in multiple papers by the same authors—is a practice that warrants serious discussion. When there is little to no publication overlap, the findings in one paper lead to new ideas and the collection of new data, producing a paper trail of scientific progress that moves the field forward (Fig. 1). At the other extreme, authors present the same text and data in two papers, which is usually a clear violation of journal copyright policies ("dual publication," Merrill 2015). In between these two extremes are different degrees and forms of overlap that may result in multiple low-impact papers. For example, authors may ask the same question with different datasets, or they may ask different questions with the same dataset. In these cases, authors have to critically evaluate whether publishing multiple separate but overlapping papers is in the best interest of the science community or whether it is self-serving. We aim to spur conversation about the consequences of publication overlap in the ecology and evolutionary biology (EEB) community, where discussions of this issue are lacking despite the pressure to "publish or perish." We offer generic examples of three forms of publication overlap that may commonly occur in EEB and other fields. Authors offer several justifications for producing overlapping publications. These include having a large project with multiple endpoints, quickly disseminating initial results without waiting for additional data to be collected, publishing in multiple languages, reaching different audiences in different journals, publishing in high profile journals with strict page limits, proving to funding sources that progress is being made on a project, and addressing significantly different questions that would not result in a single cohesive paper (Buddemeir 1981, Refinetti 1990, Susser and Yankauer 1993, Schein and Paladugu 2001, Tobin 2002, Statzner and Resh 2010). Scientists may also be unaware of the concept of publication overlap and may receive little to no training on this issue (Lazaridou et al. 2017). However, we suspect that publication overlap is often the deliberate result of scientists wanting to inflate their research productivity and increase their publication number. In a publish-or-perish world, researchers may be willing to sacrifice research quality and impact for publication count. Combining overlapping publications into a single paper has negative consequences for readers, journals, and authors, and the ethics of publication overlap have been called into question (Alfonso et al. 2005, Benos et al. 2005). With an explosion in publication number (Grossman 2014), readers must spend their time sorting through overlapping publications, identifying novel results, and comparing papers by the same authors that answer similar questions (Berk 1996). Publication overlap can also lead to practical problems in meta-analyses, and excluding duplicate results and identifying non-overlapping data is an essential step to prevent bias in meta-analyses (Tramer et al. 1997). Furthermore, when a large dataset is split apart to answer similar questions, the separate but overlapping publications fail to offer a cohesive picture. These issues are compounded when authors fail to cite their previous overlapping publications, an unethical and stagnating practice called covert duplication (Jefferson 1998, Smart 2017) that occurs surprisingly frequently in some disciplines (Schein and Paladugu 2001). Overlapping publications also contribute to a backlog of papers needing to be reviewed and requires the time of editors and journal resources (Statzner and Resh 2010, Grossman 2014). Finally, authors waste time and resources finding new ways to present similar questions or data in multiple publications. Severe forms of publication overlap risk retraction, which can be damaging to the reputations of all authors involved. In a published survey of science editors, publication overlap was the top issue of concern across disciplines (Wager et al. 2009). However, during our initial research on publication overlap, we were intrigued by how frequently the issue is discussed in the medical field relative to other disciplines. We searched the Web of Science Core Collection using a query that encompassed many synonyms and forms of publication overlap (7 March 2018; see Appendix S1). This query returned 912 articles. We excluded correspondences about retracted articles, publications not discussing publication overlap, and duplicate publications (e.g., the same editorial printed in multiple journals). Of the 459 remaining articles, 346 (75%) were in the medical field (Fig. 2). Seven articles (1.5%), published between 1981 and 2015, were specific to EEB (see Appendix S1). It is possible that the medical field dominates the discussion on publication overlap because this issue is a bigger problem in medicine than in EEB and other fields. To investigate this possibility, we searched the Retraction Watch Retraction Database (Retraction Watch 2018) on 9 March 2018 for retracted peer-reviewed publications in medicine and EEB. We defined EEB publications as either those tagged with "ecology" or those having both the tags "env" (i.e., environment) and either "zoology" or "plant biology/botany." We tabulated the number of articles retracted because of duplication of the article, data, images, or text, "euphemisms for duplication," or salami slicing. The medical field had about 20 times more retracted articles than EEB. However, EEB and medicine had similar proportions of articles retracted due to publication overlap (Fig. 3). Given that many cases of publication overlap may be unethical but not retraction-worthy, these numbers most likely highly underestimate the prevalence of potentially problematic overlap in both fields. For example, in a systematic screening of medical publications, 14% were suspected of some form of overlap, especially salami slicing (Schein and Paladugu 2001). Our results suggest that publication overlap is a problem in both fields, and that the EEB community, though smaller than the medical field, should be vigilant of its occurrence and negative effects. Authors should critically consider whether publishing a single comprehensive paper or multiple overlapping papers would be more appropriate to present the information concisely and cohesively. If multiple papers are needed, authors should take care to self-cite to avoid covert duplication. Though the onus for preventing publication overlap is primarily on authors, journals can help by defining publication overlap and making their policies explicit. To investigate current EEB journal policies, we selected the top 20 journals listed by Scimago Journal Rankings in the "Ecology" category and the "Ecology, Evolution, Behavior and Systematics" category (see Appendix S1). We excluded journals that only publish reviews, leaving 32 journals that were listed in one or both categories. We surveyed each journal's instructions to authors, editorial processes, and permissions web-pages to determine what policies on publication overlap were available to authors before submitting manuscripts. Of the journals surveyed, 31% (n = 10) asked authors to include descriptions of any overlapping publications in the cover letter. Interestingly, 12.5% (n = 4) required authors to submit several similar publications. Though the rationale for identifying similar publications is to ground the work in a body of literature and aid in the selection of reviewers, it could also help editors identify possible cases of overlap. Only 9% (n = 3) of the journals had statements explicitly discouraging salami slicing. Some resources for investigating possible cases of publication overlap exist. For example, Alfonso et al. (2005) provide a list of criteria to help editors identify publication overlap. Similarly, many journals belong to the Committee on Publication Ethics (COPE), which provides guidelines, action flowcharts, and resources for journal editors to use when investigating possible ethical issues, including publication overlap. Seventy-eight percent (n = 25) of the journals we surveyed were members of COPE. However, of the members, only 60% (n = 15) referred to COPE's guidelines in their instructions for authors, making the resources provided by COPE that define publication overlap unlikely to be accessed by authors before submission. We suggest that discussions of the definition and consequences of publication overlap be incorporated into university ethics training, graduate student journal clubs, academic reading groups, online forums, and laboratory meetings. We hope that these conversations will help scientists recognize and evaluate problematic cases of publication overlap that are a disservice to science. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

The following article has been retracted by the Editor and publishers of Psychological Science at the request of the lead author, Lawrence J. Sanna: Sanna, L. J., Chang, E. C., Parks, C. D., & Kennedy, L. A. (2009). Construing collective concerns: Increasing cooperation by broadening construals in social dilemmas. Psychological Science, 20, 1319–1321. doi:10.1111/j.1467-9280.2009.02458.x In a letter to the Editor (Eric Eich), Dr. Sanna wrote: The data reported in this article are invalid and should not be considered part of the scientific literature. The responsibility for this problem rests solely with the first author, Lawrence J. Sanna. Coauthors Edward C. Chang, Craig D. Parks, and Lindsay A. Kennedy are in no way responsible for this problem. In response, the Editor noted that Psychological Science follows the retraction guidelines developed by the Committee on Publication Ethics (COPE). Dr. Sanna was urged to follow these guidelines carefully in drafting a retraction notice, particularly with respect to stating the reasons for the retraction, to distinguish misconduct from honest error. To assist Dr. Sanna with this task, the Editor provided Dr. Sanna with a copy of the COPE guidelines (http://publicationethics.org/resources/guidelines) and a link to a retraction notice that was published in Psychological Science last year. This notice was considered a “model” by Retraction Watch, and Dr. Sanna was advised that, in keeping with this notice, he “must specify clearly the reasons for the retraction in such language that all of your coauthors agree to it.” While awaiting Dr. Sanna’s reply, the Editor sought to contact Dr. Sanna’s three coauthors. Although one coauthor was aware of Dr. Sanna’s request to retract the 2009 Psychological Science article, the other two were not. All of the coauthors have agreed to retraction of the article, and each has received a copy of this notice. Dr. Sanna replied by noting with regret that “research errors” have made it necessary for him to request retraction. The letter concluded with the following: “At the direction of legal counsel, I am unable to say anything further than that contained in my previous letter at this time.” Because it is unclear when, if ever, details on these research errors will be forthcoming, the Editor owes it to the journal’s readership to retract the article now, even though this notice does not reflect COPE guidelines or journal policy.

The proliferation of open access (OA) publishing has been accompanied by a rise in unsolicited academic correspondence, often originating from so-called "predatory" publishers. Early-career surgeons may be particularly vulnerable to predatory journals due to pressure to publish in order to enter and advance through training. This observational study aims to characterize the nature and volume of unsolicited emails received by a surgical trainee following the publication of a single paper. All unsolicited emails received by the author between September 10th 2024 and December 31st 2024, were collated and analysed. Emails were assessed for their origin, journal/publisher, structure, requested contribution, relevance and associated Article Processing Charges (APCs). Where emails lacked this information, it was sought from journal and publisher websites. Publication legitimacy was assessed by the journal or publisher's presence on Beall's list of potential predatory journals, inclusion in the Directory of Open Access Journals (DOAJ) and the Committee on Publication Ethics (COPE). A total of 264 emails were received, 227 of which were soliciting journal articles. These represented 109 individual journals, comprising 44 publishers and 10 standalone journals. High levels of flattery (92.95%) and poor grammar (91.19%) were noted in the emails. In terms of legitimacy, 87.15% (n=95) were on Beall's list whereas 8 (7.3%) were members of COPE and 2 (1.8%) listed in DOAJ. APCs were mentioned in 36.56% of emails and clearly stated in 11.45%. The mean APC was 2006.18 USD, median APC was 1988.5 USD. Withdrawal fees were charged by 58.7% (n=64) of journals with a mean cost of 1039.68 USD and median cost of 680.25 USD. The remaining emails included conference invites (n=28), editorial board invites (n=6) and book chapter requests (n=3). This study highlights the high volume and typical characteristics of predatory journal solicitations following a single publication. With increasing pressure on surgical trainees to publish, awareness of predatory practices is essential. Transparent vetting tools and guidance from training bodies are needed to safeguard academic standards in surgical training.

Research integrity: time for global action

The world seems to be divided into two groups of people: those who “get” Twitter, and those who don't. I say this because whenever the use of Twitter comes up in a conversation, those who shout loudest are the ones who say “I don't get Twitter.” This group often contains people who have a Twitter account-but have found it difficult—and not tried it further than setting it up and leaving it at that. I am not sure what they expected to happen. Maintaining a Twitter account is not without effort. However, the effort is worthwhile and it does not have to become a major investment in time and it need not become an obsession. Using my experience of running the Journal of Advanced Nursing (JAN) Twitter site, which I set up in December 2011, I hope to illustrate this. Here are some questions to ask yourself if you are considering setting up a Twitter account: The worst answer here is “because everyone else seems to be doing it.” On the other hand, there is no best answer and no correct answer. Clearly, if you are considering using Twitter then you probably have some idea of what Twitter is about. You cannot have failed to notice the widespread use of Twitter by individuals, companies and journals. The Twitter logo is now common and usually offers a hyperlink to the Twitter site that you are being invited to follow. One of the best ways to find out what Twitter is all about is to click on some of these links, see what a Twitter account looks like and read what people say in their Twitter feeds. Try to find some Twitter feeds that are close to your interests. If you are an academic then look at the Twitter feeds of other academics; if you are an editor then look at the Twitter feeds of journals and other editors. Essentially, you should want to set up a Twitter account because you have something to say, and, in seeing what others with similar interests to you say, then you will begin to get some ideas. Frankly, some people share a remarkable amount of trivia on Twitter, and this is what gives Twitter a bad name. However, it is usually individuals who do this, and if you want to read trivia and share yours with others, then set up your own account and tell people what you are doing right now. The best Twitter sites are informative. They share useful information about the product or organisation they are linked to, they keep you up to date on developments, and, given the limited number of characters you are permitted to use (140), they also provide weblinks where further information can be obtained. For example, on the JAN Twitter site we mainly provide links to our Early View articles before they appear in volumes of JAN. In addition, we provide links to the current issue of JAN as it appears online. We also provide links to abstracts of a wide selection of our articles; for example, we always “tweet” about our editorials, systematic reviews, open access papers and a selection of the remaining papers. Other Twitter content related to the journal includes links to updated author guidelines, our LinkedIn page and the JAN blog. We appear to be doing something right because in 2 years, we have accumulated nearly 5,000 followers. Some people worry about using Twitter because they think they have nothing to say; this cannot be true of any academic or journal editor. Some people worry that what they say on Twitter will get them into trouble, and it will if you are careless. If you have a tendency to make indiscreet remarks then avoid “tweeting” when you are angry, tired or under the influence of alcohol. If you are running a Twitter account for an organisation or journal, make sure that you do not also use this as a personal account. There is no harm in having more than one Twitter account. If you are concerned about Twitter etiquette and how to use an account, some excellent guidance is available, for example, from Mollett et al (2011) and Reed and Evely (undated). Both of these guides contain glossaries of Twitter terms, some of which I have used here (e.g, “re-tweet”). At JAN we have found it useful, in addition to material about the journal, to “re-tweet” material related to the journal such as links to good practice guidelines from organisations such as COPE (The committee on Publication Ethics), CONSORT (Consolidated Standards of Reporting Trials) and PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses). Whenever we do this, we try to include the “Twitter handle” of the relevant organisations in the form, for example, of @cope and @prisma. In this way these organisations will note that we have “tweeted” about their work, and, with any luck, they will “re-tweet” our “tweet”. JAN will get a mention and others may decide to follow us. Twitter is not the only form of social networking media we use at JAN to reach out beyond our usual readership and authorship, but it is the most effective. I am a great enthusiast, and if you have never tried it, I strongly encourage you to set up a Twitter account, follow a few interesting people and journals, and without pressure just take it from there. Roger Watson, PhD, FAAN, is Editor-in-Chief of Journal of Advanced Nursing and Professor of Nursing, University of Hull, UK. His email is R.Watson@hull.ac.uk Follow him on Twitter: @rwatson1955.

Malvertising is a malicious activity that leverages advertising to distribute various forms of malware. Because advertising is the key revenue generator for numerous Internet companies, large ad networks, such as Google, Yahoo and Microsoft, invest a lot of effort to mitigate malicious ads from their ad networks. This drives adversaries to look for alternative methods to deploy malvertising. In this paper, we show that browser extensions that use ads as their monetization strategy often facilitate the deployment of malvertising. Moreover, while some extensions simply serve ads from ad networks that support malvertising, other extensions maliciously alter the content of visited webpages to force users into installing malware. To measure the extent of these behaviors we developed Expector, a system that automatically inspects and identifies browser extensions that inject ads, and then classifies these ads as malicious or benign based on their landing pages. Using Expector, we automatically inspected over 18,000 Chrome browser extensions. We found 292 extensions that inject ads, and detected 56 extensions that participate in malvertising using 16 different ad networks and with a total user base of 602,417.

Existem várias formas de recuperação da informação periódica na Internet, mas não de maneira eficiente, como, por exemplo, através de um identificador persistente de objeto. Com essa preocupação, o Portal de Periódicos Eletrônicos Científicos (PPEC), vinculado ao Sistema de Bibliotecas da UNICAMP (SBU), manifestou, junto à Coordenação Geral da Universidade (CGU), o pedido de afiliação à CrossRef / PILA (Publisher International Linking Association) por meio da Associação Brasileira de Editores Científicos (ABEC), visando a aquisição do Digital Identifier Object (DOI), a ser atribuído aos periódicos vinculados e credenciados no PPEC. O presente trabalho tem como objetivo apresentar o processo de atribuição e controle do DOI nos periódicos do PPEC, a fim de garantir a sua identificação persistente na Internet para efeito da busca e recuperação dos metadados qualificados. Metodologicamente, os editores e assistentes da Universidade vinculados ao PPEC verificam, após a publicação do fascículo, se o mesmo está em conformidade com os metadados. Após essa verificação, é iniciado o processo de validação desse fascículo e seus artigos na CrossRef. A ferramenta que subsidia esse processo de atribuição é Open Journal System (OJS/SEER), que já possui integrado ao sistema plug-in de habilitação para o DOI, tanto para o fascículo quanto para os artigos dos periódicos. Optou-se pelo controle por artigos, pois ele facilita a validação de cada DOI junto à CrossRef, cujo pagamento é efetuado a cada três meses por meio da ABEC. Existem duas formas de realizar a validação do DOI: gerando um arquivo na linguagem XML ou selecionando os artigos e os registrando dentro do próprio sistema. A diferença é que enviando o XML, recebemos a comunicação de validação por e-mail. Já no registro dentro do sistema, a verificação da validação só é possível através da conexão à CrossRef. Após a realização da validação, é realizado um controle, em uma planilha Excel, para fins de pagamento e também do que está sendo enviado à CrossRef. Obtivemos de imediato, junto a CGU, a contemplação para atribuição de 17.000 DOIs a toda coleção de periódicos de 2000 a 2016 da UNICAMP, o que garantirá aos periódicos a internacionalização dos seus artigos. Concluímos, assim, que esse trabalho planejado, organizado e de total relevância para a Universidade aumentará cada vez mais o impacto na busca por seus periódicos, evidenciando, dessa forma, o quanto uma publicação qualificada e estruturada é capaz de promover a visibilidade e a aceitação junto à comunidade científica.

Living guideline maintenance is underpinned by manual approaches toward evidence retrieval, limiting long-term sustainability. Our study aimed to evaluate the feasibility of using only PubMed, Embase, OpenAlex, or Semantic Scholar in automatically retrieving articles that were included in a high-quality international guideline - the 2023 international polycystic ovary syndrome (PCOS) guidelines. The digital object identifiers (DOIs) and PubMed ID (PMIDs) of articles included after full-text screening in the 2023 international PCOS guidelines were extracted. These IDs were used to automatically retrieve article metadata from all tested databases. A title-only search was then conducted on articles that were not initially retrievable. The extent of coverage, and overlap of coverage, was determined for each database. An exploratory analysis of the risk of bias (RoB) of articles that were unretrievable was then conducted for each database. OpenAlex had the best coverage (98.6%), followed by Semantic Scholar (98.3%), Embase (96.8%), and PubMed (93.0%). However, 90.5% of all articles were retrievable from all four databases. All articles that were not retrievable from OpenAlex and Semantic Scholar were either assessed as medium or high RoB. In contrast, both Embase and PubMed missed articles that were of high quality (low RoB). OpenAlex should be considered a single source for automated evidence retrieval in living guideline development, due to high coverage, and low risk of missing high-quality articles. These insights are being leveraged as part of transitioning the 2023 international PCOS guidelines toward a living format.

<p>GBIF—the Global Biodiversity Information Facility—and its network of more than 1,500 institutions maintain the world's largest index of biodiversity data (https://www.gbif.org), containing nearly 1.4 billion species occurrence records. This infrastructure offers a model of best practices, both technological and cultural, that other domains may wish to adapt or emulate to ensure that its users have free, FAIR and open access to data.</p><p>The availability of community-supported data and metadata standards in the biodiversity informatics community, combined with the adoption (in 2014) of open Creative Commons licensing for data shared with GBIF, established the necessary preconditions for the network's recent growth.</p><p>But GBIF's development of a data citation system based on the uses of DOIs—Digital Object Identifiers—has established an approach for using unique identifiers to establish direct links between scientific research and the underlying data on which it depends. The resulting state-of-the-art system tracks uses and reuses of data in research and credits data citations back to individual datasets and publishers, helping to ensure the transparency of biodiversity-related scientific analyses.</p><p>In 2015, GBIF began issuing a unique Digital Object Identifier (DOI) for every data download. This system resolves each download to a landing page containing 1) the taxonomic, geographic, temporal and other search parameters used to generate the download; 2) a quantitative map of the underlying datasets that contributed to the download; and 3) a simple citation to be included in works that rely on the data.</p><p>When authors cite these download DOIs, they in effect assert direct links between scientific papers and underlying data. Crossref registers these links through Event Data, enabling GBIF to track citation counts automatically for each download, dataset and publisher. These counts expand to display a bibliography of all research reuses of the data.This system improves the incentives for institutions to share open data by providing quantifiable measures demonstrating the value and impact of sharing data for others' research.</p><p>GBIF is a mature infrastructure that supports a wide pool of researchers publish two peer-reviewed journal articles that rely on this data every day. That said, the citation-tracking and -crediting system has room for improvement. At present, 21% of papers using GBIF-mediated data provide DOI citations—which represents a 30% increase over 2018. Through outreach to authors and collaboration with journals, GBIF aims to continue this trend.</p><p>In addition, members of the GBIF network are seeking to extend citation credits to individuals through tools like Bloodhound Tracker (https://www.bloodhound-tracker.net) using persistent identifiers from ORCID and Wikidata IDs. This approach provides a compelling model for the scientific and scholarly benefits of treating individual data records from specimens as micro- or nanopublications—first-class research objects that advancing both FAIR data and open science.</p>

Despite its prominent position as one of the leading for-profit scholarly publishers of subscription and open access (OA) journals, and its membership of the Committee on Publication Ethics (COPE), Directory of Open Access Journals (DOAJ), and Open Access Scholarly Publishers Association (OASPA), Springer Nature can be criticized for taking a vague approach in its editorial policies pertaining to “predatory” publishing. While cautioning authors and/or editors about the citation of papers that are published in “predatory” journals, the advice presented in the policies itself is flawed due its limitation to OA journals – thus apparently excluding the possibility that subscription journals might also be “predatory” and failing to specify precisely which journals authors and editors should be careful of, i.e., no source for the “predatory” definition of OA journals is indicated. Moreover, this vague set of policies does not have a publication date, nor is any authorship specified. The opacity of these aspects of these editorial policies limits their usefulness and weakens their objectives, namely in ostensibly offering scholarly advice to protect editors and authors. I argue that the Springer Nature policies pertaining to “predatory” publishing as they currently stand are not useful, and if left unchanged, can be a source of confusion or error for authors and editors of Springer Nature journals. In this connection, the identified risk is that if the poor advice indicated in those policies is heeded, it may encourage abuse, insults and/or indiscriminate profiling of academics, including those associated with Springer Nature journals. While assuming Springer Nature’s genuine intention to alert editors and authors against citing papers published in suspect scholarly venues, I argue that this editorial set of policies should either be rewritten to rely on clearer parameters, including a definitive list of journals for which “predatory” criteria have been defined, or abandoned as they are overly broad. The criticism is aimed at stimulating a discussion among other editors and publishers, especially COPE members.

Focuses on open science practices in suicide research. Specifically, the authors use examples from their own and others' work to demonstrate the opportunities for future-proofing research by implementing open science practices, and they discuss some of the challenges and their potential solutions. They cover implementing open science practices in new, ongoing, and concluded studies, and discuss practices in order of being 'low' to 'high' threshold to implement (based on Kathawalla et al., 2021). Space constraints preclude an extensive presentation of all open science practices although they briefly describe the strategies of providing preprints, sharing study materials and codes, preregistration of studies and registered reports, and sharing research data. To highlight the open science work of as many researchers as possible, examples are provided in Electronic Supplementary Material 1 (ESM 1) rather than in the text. The authors ask for readers' help in adding to these examples via their 'living' reading list (https://osf.io/v6y3t/).

It is a joy to browse the information on drugs here, ranging from chemical structures to illustrated clinical applications. RxList was initiated by a group of pharmacists in 1995 to collate pharmaceutical information about brand-name and generic drugs. They claim (with justification) to be the premier internet drug resource. Articles are written by pharmacists and physicians, supplemented by data obtained from other sources such as the FDA. Medications can be found using the A–Z drug list (an alphabetical listing of both brand and generic drug names), or by entering the generic or brand drug name in the search box at the top of the page. I came to this site during a search for information on the drug Nexium® (esomeprazole magnesium) and found that the active ingredient in Nexium is bis(5-methoxy-2-[(S)-[(4-methoxy-3,5-dimethyl-2-pyridinyl)methyl]sulfinyl]-1H-benzimidazole-1-yl) magnesium trihydrate, a compound that inhibits gastric acid secretion. Fortunately, the Nexium chemical structure was also given as a clear structural drawing. More chemical and clinical detail followed. Above the entry I located an invitation to view a slide show on digestive disease myths, an appropriate offering to link to a drug that inhibits gastric acid secretion. I took the slide show and then proceeded through several more slide shows illuminating common medical conditions and their treatment. I particularly commend the slide show on adult skin problems. The services here are multilayered and comprehensive, so allow some browsing time to take it all in. If you want some teaching material then you may find the series of articles on drug families will provide useful information on the actions and side effects of commonly prescribed medications. The drug families described are ACE inhibitors (high blood pressure medications), angiotensin receptor blockers, antacids, antidepressants, benzodiazepines, beta blockers, calcium channel blockers, COX-2 inhibitors, diuretics, medications used in dentistry, nonsteroidal antiinflammatory drugs, sleep disorder drugs, statins (cholesterol lowering drugs), and tricyclic antidepressants. PLoS Computational Biology is a peer-reviewed journal published monthly by the Public Library of Science (PLoS) as the journal of the International Society for Computational Biology. I was introduced to the journal and its rigorous editorial standards when invited to refer a paper. The current impact factor for PLoS Computational Biology is 6.2, which places it highest in the category of mathematical and computational biology. Although this is a niche journal, it has a wide appeal in content, because of many intersections of computing with everything from ecology to genomics. For example, the current issue when reviewed included the article “Evolutionary Sequence Modeling for Discovery of Peptide Hormones” contributed by eight US authors from major laboratories. The abstract for this article introduces the circumstance that there are a large number of orphan G-protein-coupled receptors whose endogenous ligands (peptide hormones) are unknown. Identification of these peptide hormones for understanding disease and treatment opportunities is an important, but a difficult problem. The article describes a computational approach that models structure along the genomic sequence linked with a model of temporal evolutionary path structures across species. Such cross-genomic sequence comparisons can be used to discover new functional molecules, in particular the peptide hormones. Returning to the nature of the journal, the policy is stated as the publication of works of exceptional significance that further the understanding of living systems from molecules to patient populations and ecosystems, through the application of computational methods. Research articles for publication are required to demonstrate both scientific novelty and new biological insights. Extending the research content are reviews and tutorials (including multimedia presentations) that teach concepts in the field of computational biology. You can go to the archive of issues and easily step through the content of each. The cover artwork for each issue is excellent (see Fig. 1). The creative commons attribution license of the journal allows authors to retain copyright for their articles, and anyone can use the articles for teaching or other purposes as long as the original authors and source are cited (no permission is required from the authors or the publishers). PLoS Computational Biology has an author publication fee of US$2,200, with a waiver for authors who do not have funds. The International Society for Computational Biology (www.iscb.org), the professional parent society of the journal, also provides additional publications, meetings, training, education, employment, and information relating to computer applications in life sciences. Cover artwork from PLoS Computational Biology, November 2007, titled “Trinucleotide disease as a genetic time bomb.” Trinucleotide diseases such as Huntington's occur when a subject inherits a DNA region consisting of a three-letter code abnormally repeated many times. The age at which the disease strikes the patient is encoded by the number of repeats. A universal mechanism by which this molecular time bomb operates in this family of hereditary diseases has been suggested. Image credit: Genia Brodsky, Weizmann Institute of Science. The primary resources for teaching in this website are under Training and Publications. The Department of Health Promotion and Education (DHPE) was found in 1946 in the United States by the state directors of health education and the deans of health education. The objectives of DHPE are to share program efforts, ideas, and materials between the state authorities. In the 1980s the US Centers for Disease Control began to cooperate in running national conferences and expanding DHPE activities. There is a section of fact sheets that relate comprehensively to infectious diseases and it was the sheet on cytomegalovirus that led me to this site. I discovered here that cytomegalovirus is a member of the herpes virus family that includes the causative agents of chickenpox, infectious mononucleosis, fever blisters, and genital herpes. These viruses share the ability to remain alive, but dormant, in the body lifelong. A first infection with cytomegalovirus usually causes no symptoms and the virus persists without causing obvious damage or illness. It rarely becomes active when the immune system weakens and is no longer able to hold the virus in check. An estimated 80% of adults in the United States are infected with cytomegalovirus. These facts and more are summarized in the DHPE fact sheet. You can work through an alphabetic list of numerous infectious diseases. I was previously unaware of cat-scratch disease, but in the United States about 24,000 people suffer from this bacterial disease each year. Under Training and Publications you can find a folio of papers on health policy and human–environment case studies, many relating to smoking and diet. Each year I print an updated version of my identities and passwords that I use to get access to publications, professional society sites, and financial services. I paste the list into my hard-copy diary that travels around with me at most times. I include some (although not enough) cryptic codes and it is possible that my identities could be stolen if my diary was lost. My local newspaper alerted me to Access Manager, a genre of software that would save me from my inability to remember every password. Encrypted password data can be stored on a desktop computer or mobile device, or in a net-accessible location. A single password used to enter the Access Manager will divulge all the others. The article about Access Managers that I read reviewed four products and rated eWallet from Iliumsoft as the best, relative to Password Plus, KeePass, and My Password Manager. A food industry journal alerted me to a new zero-calorie sweetener that is being marketed as Reb-A or PureVia™. Although it is a new commercial product, it has been used for centuries by South American natives as a sweetener. The product is Rebaudioside A, which is extracted from the leaves of the Stevia plant, a member of the chrysanthemum family that is native to Paraguay. It is rated as up to 450 times sweeter than sucrose. Reb-A joins a list of other low-energy sweeteners and has the “organic” advantage of being a completely natural product, unlike aspartame that has its origins in the synthetic laboratories of G.D. Searle when Jim Schlatter accidentally made it in 1965. Rebaudioside A is a triglycoside of steviol, a diterpene. The isoprenoid pathway leading to the terpenes has long held me in awe of the power of biochemical pathways to give rise to such diverse products as rubber and Reb-A. The isoprenoid pathways also illustrate how biochemically rich plants are relative to animals. Plants cannot flee from their predators or court a mate and so they produce a range of chemicals that achieve all of the functions that movement achieves for animals. It may seem odd that a product that makes Stevia leaves sweet to taste, and therefore attractive to be eaten by animals, would confer a selective Darwinian advantage. There are now large plantations of Stevia and so Darwin is vindicated yet again. The website given here introduces a lot of the ecofriendly aspects of growing and using the Stevia plant. Other information is needed to get the full picture, e.g., initial toxicity tests suggested that Reb-A was carcinogenic, but these tests were flawed and now Reb-A is considered safe for human consumption (this background can be found using Wikipedia). For a biotechnology course setting a project on this diterpene could bring together a lot of biochemistry and health issues while providing a case study for the commercialization of a natural product. The data base currently includes 5,374 proteins exhibiting 26,052 reactive sites, thereby making an average of 4.8 phosphorylation sites per protein in the data base. Of the 26,052 sites included in the data, serine phosphorylation sites represent 59.1%, tyrosine phosphorylation sites 25.1%, and threonine phosphorylation sites 15.8%. PhosphoNET can be searched for proteins using the Uniprot ID or a common name. A list of possible options for proteins is generated by entering at least three letters of the name and waiting for a list to appear. I chose to search for aquaporins and found that two were in the data base. For aquaporin zero (Uniprot ID P30301) the data base reveals that it is a channel protein having a mass of 28,122 Da, with 263 amino acids. Four sequences around separate serine phosphorylation sites were given and clicking on the reference button for each site led to the primary literature reference via PubMed. This data base is being actively expanded. CNET Networks Incorporated is a media company based in San Francisco. The company was founded in 1993 and was acquired by CBS in 2008 for US$1.8 billion. Initially the core business was providing television news and features. As the internet became central to communication technologies, the company added web-based functions. What is available now at CNET is a web supermarket with many departments and choices which makes possible to spend days sampling all the useful and interesting features. There are numerous subeditors for CNET who specialize in niche reports, often with a video of the subeditor making a presentation. The first recommended choice is to look at the selections available under the News banner. CNET news proclaims itself to be filtered by humans, not bots, and the quality of the summaries validates this claim. At the time of review, President Obama's energy policies were a leading feature. There is a Green Tech choice within the news categories, and this has excellent coverage of issues related to science and the environment, particularly new consumer technologies such as electric cars. Feature articles on medical science are not so conveniently clustered, but the search facility allows rapid location of targeted subjects. While browsing articles on cancer I located the information that the researchers at the Children's Hospital in Boston could directly view the internal organs of a new colony of zebrafish. Embryos of normal zebrafish have naturally transparent bodies but turn opaque when they get older. The new breed stays transparent throughout its lifetime, thus allowing the visualization of tumor development. In general, CNET is divided into seven major sections. These sections are 1) Reviews—product and service reviews, largely conducted in-house by CNET staff; 2) News—articles that are mostly dedicated to technology; 3) Tips and Tricks—a range of tutorials, guides, and tips for technology users; 4) TV—a selection of video content including reviews, first looks, and special features; 5) Shopper—a tool that aims to find the lowest prices on items from online retailers; 6) Blogs—comments from CNET personalities and external responses; 7) Download—provides Windows, Macintosh, and mobile software for download. CNET can be added as a Rich Site Summary (RSS) to your browser (see entry below). RSS has three interpretations in web terminology; Really Simple Syndication, Rich Site Summary or RDF (Resource Description Framework) Site Summary. These variant names describe the forms of web syndication used by news websites and blogs. An RSS provider, such as CNET above, downloads content to subscribers who choose filters to suit their needs. The downside is generally unsolicited advertising, but this is necessary to subsidize the service. The sites provided by RSS usually display an icon with the acronyms RSS, XML, or RDF to indicate that a feed is available. A user saves time, relative to individual visits, by obtaining filtered up-to-date content from multiple sites automatically. Hundreds of providers are listed at this RSS explained website. Under Health there are multiple providers within the subcategories of cancer, cardiovascular disorders, digestive disorders, endocrine disorders, immune disorders, infectious diseases, musculoskeletal disorders, neurological disorders, respiratory disorders, and sleep disorders. If you use Microsoft Outlook for email, this program can also serve to provide RSS feeds, and to make it easy, Outlook has a list of sites that you can choose from to get started. For complex integration of multiple sources, feed reader (news aggregator) software allows collection of RSS feeds. Popular readers are Amphetadesk, FeedReader, NewsGator, and Google Reader. The utility FeedReader was commended in the Websites of Note in the BAMBED issue of November/December 2008. If you want to use feeds, the RSS-explained site will provide the information needed.

Predatory publishing: what authors need to know.