Manuscripts provide novel insights that reflect the authenticity and originality of the work when writing and sharing data. To combat plagiarism in manuscripts, CrossCheck (now Similarity Check) has been increasingly used to prevent plagiarism, or reduce the number of duplicate submissions. Similarity Check, powered by iThenticate, evolved as a collaboration between major publishers and CrossRef. It allows editors, publishers, authors, and readers to check submitted articles against a database of millions of other academic journals. This tool allows people to detect plagiarism using an automated text similarity checker.

Features of Similarity Check

After an article is uploaded, Similarity Check scans the manuscript for similarities to previously published content. It compares full-text manuscripts against more than 38 million articles and more than 20 billion web pages. You can check here if your journal uploads its information.

Of course, some writing will be very similar to various other articles. Hence, results are reviewed to determine the nature of the duplicated text. Nevertheless, several organizations use this software, including Springer, BiomedCentral, Adis, Birkhauser, and Bohn Stafleu van Loghum.  Meanwhile, other organizations, like the Institute of Electrical and Electronics Engineers (IEEE), require all papers for proceedings and conferences be screened via a plagiarism detection process.

Volunteers or staff of various organizations then review the reports generated by Similarity Check to determine the nature of the similarity and if any action is warranted.

A Quick User’s Guide

Staff members of various publishing organizations and publications volunteers (e.g., authors, editors, etc.) upload new manuscripts into the database. This can either be done manually or might require some help from the publications volunteer.

When a publication reaches a threshold, such as 30% (as recommended by the IEEE), the person who has uploaded the manuscript is notified electronically. This threshold can be modified to any amount and is linked to an email alert system.

The submission is then reviewed. A report is generated that highlights similarities, which must be carefully reviewed to discern actual plagiarism from coincidental writing. The report shows the combined or total score of individual similarities. These reports can be modified based on similarity, content tracking, or largest matches.

Similarity Check for Authors from Aries Systems Corporation on Vimeo.

Similarity Check for Editors from Aries Systems Corporation on Vimeo.

What Your Results Mean

The similarity reports have several features:

Text is highlighted in a color and indicated by a number

The original source is then indicated on a side panel and is colored and numbered to match the in-text coding

The percentage of similarity of the article to an individual source is indicated for each article or source that shares common language

The summation of individual article similarity scores is presented

An individual must review this report and consider several variables, such as the extent of the similarity, the originality of the copied material (e.g., standard or routine language), the context of the similar material, and the attribution to author or source. When considering the individual similarity scores of each source, Springer recommends that a score of 1-5% requires no checking, >10% requires quick checking, and >20% requires thorough checking.

Important Considerations

Given the nature of publishing and academic writing, duplicated text might become unnecessarily flagged for several reasons. These can include when updating a systematic review, mentioning contributions of an author, self-citation, or “patch writing” that involves several small segments of routine language

In some instances, cultures vary on the nature of plagiarism. Some communities may believe that copying is a sign of respect while others value individuality or uniqueness. Furthermore, senior authors may not have been aware of a junior author’s missteps. Alternatively, authors may have granted permission to duplicate or reuse the text.

Ultimately, the integrity of a scientist is paramount to ensure that the research work is perceived with trust. Using Similarity Check’s report, an author can review what others are writing and ensure that his or her text does not inadvertently repeat the work of another author. As science progresses and becomes more competitive, the writing of scientists will come under greater scrutiny.

You have just completed manuscript submission process for your target journal. The next steps would be initial review by the editor followed by the peer review by the invited experts. During these steps, you wait for the decision.  However, in some cases, you may want to withdraw your manuscript. For instance, you may want to add or revise important points or you may want to correct some errors discovered after the manuscript submission. In these cases, it ends with your manuscript “withdrawn” from the peer-review process, and typically, its ID number deleted from the journal system.

Another common reason to withdraw your submission after acceptance and before publication is that authors suspect or discover a glaring error, possibly when checking the proofs. This error may require removing existing data, performing some experiments again. It may also require doing supplementary analysis. This may seem additional work, but it can help researchers avoids any future retractions

In addition, when authors do not want to make all research data available to the journal (sometimes required by the journals) for copyright or commercial reasons or when they realize that they have made submission to a potential predatory journal, authors can withdraw their paper. There are unethical reasons for a withdrawal though, such as being “unaware of the publication fees”, or just wanting to submit to a higher-impact journal.

A final reason for withdrawal is impatience with peer review. This is not a black or white issue. Nevertheless, at some journals, the editor may not have yet sent your paper for peer review, even after 1-3 months or a peer reviewer has failed to submit his or her report even after ~4-6 months.  This seems unreasonable.

Tips for Manuscript Withdrawal

Timing and publication ethics-these two considerations should guide your action in making a manuscript withdrawal. The quicker you act, the better the outcome for everyone. At the scholarly journal a handling editor, if already assigned to your manuscript, will have to judge the merit of your request. For this to go smoothly providing facts are helpful for clear communication.

First, try the easiest way to withdraw the manuscript: doing it online via the journal submission system. In it, some journal publishers may have a tab, “withdrawing the paper”, or similar. However, this option may not work for many journals. For example, it seems that the widely used ScholarOne Manuscripts system does not offer this option for an online manuscript withdrawal.

If that does not work, immediately contact the editor handling your submission or the editorial office of the journal. Write a clear and concise letter, signed by all authors, explaining the situation surrounding the manuscript, and the reason(s) for its withdrawal. Often, through the online manuscript submission process, there is a tab or link to directly “contact the editor”, or you can look up his/her email from the website. At some journals, however, it may not be always necessary to give a full, in-depth explanation for the manuscript withdrawal.

There is a big difference between asking for manuscript withdrawal within 1 week of submission and during or after peer review, say in 1-6 months. In the former case, it should not be a problem. However, in the latter case, it is trickier, if not impossible because the journal may forbid it, and you should clearly argue your case on scientific reasons to resolve any misconduct.

Hopefully, you should receive an acknowledgment letter. This may acknowledge the withdrawal, or ask you for more information to adjudicate the issue on more scientific grounds. For the latter, it is important to cooperate and respond in time.

Possible Consequences

Ensure not to simultaneously submit your paper to more than one scholarly journal. This is a standard code of publication ethics. It is unethical to withdraw a manuscript, just because it was accepted sooner elsewhere. Nevertheless, what if you do not get a reply even after multiple requests. Write to the editor-in-chief this time indicating your plans to revise the manuscript, and eventually go ahead with a new submission at another journal after the acknowledgment.

Most journals are not keen on withdrawing your submission. It wastes their resources and the author may incur a penalty for manuscript withdrawal. This penalty could range from 200 to 1000 USD, depending on the journal. This information, however, should be transparent and clearly stated on the journal’s policy webpage. If authors withdraw manuscript on unethical grounds, journals may also blacklist the author and co-authors for future publications.

Some Parting Advice

Be courteous and keep records of all email correspondence with the journal publisher, when planning for manuscript withdrawal. To avoid such situations and any penalties, take extra time to check over your work before the manuscript submission.

Traditionally, both informal and formal peer review happens before a paper is published in a journal (or a book). However, the peer review process is struggling to do its job properly. One key task of peer review is to identify flaws and bad science before publication.

With an emerging alternative,  post-publication peer review the scientific community can engage in discussion and comment on shared research papers on relevant platforms. One such web-based platform is PubPeer. This should strengthen the self-correcting practice in science and improve its overall published quality^.

PubPeer 2.0 is here!

 Founded in 2012, PubPeer, an online, moderated platform for discussing scientific publications, which originally begun as a “spare-time” project, has since cemented its presence as a platform for post-publication peer review. Starting in early 2013, its users could comment anonymously as so-called “Peers”. This factual and verifiable feedback has led to many editorial corrections, and even retractions because of discovered research misconduct.

Now, PubPeer has given itself an upgrade and new look. This PubPeer 2.0 is effectively a rewrite of the platform from the bottom up PubPeer has made changes and added new features for its users and readers.

How is PubPeer Better Used?

One big change is how users can identify themselves.  A signed account is still available and it is not anonymous to the readers who can access the website’s contents. However, choosing anonymity becomes now more secure and guaranteed. In addition, using the “tree of life” to assign pseudonyms, PubPeer users can now obtain an account with just a code (safeguarded by the user). The authenticity of your grey listed account requires vetting before approval. Therefore, it will be near impossible for anyone to know your real identity.

Another big change involves the improved reading and formatting of the peers’ comments. Since it began, PubPeer users had to follow certain guidelines. All the comments go through moderation (for facts and truth). Now, these comments related to either methods, images or more will be more professional and academic.  In addition, mathematicians and physicists might become more involved in PubPeer and its mission, because PubPeer 2.0 platform now supports LaTeX equations.

One new and thoughtful feature for users is the pre-viewing of comments (to detect any spelling and grammatical error). This should improve the quality of comments visible to the readers and the public. The comments now appear in a chronological order to the readers with embedded links.

PubPeer: Pros & Cons

For-profit subscription journals generally remain uninterested in the post-publication peer review process.  as it may cast doubt on the quality of their journal content. With PubPeer 2.0, it is possible to help correct and weed out the low-quality-yet-already-published science. Such platforms also offer an alternative to the traditional peer review landscape dominated by the academic journal publishers.

Moreover, PubPeer 2.0 centralizes the post-publication peer review process. This makes it easy to search from anywhere by anyone.  With the help of this detailed peer review via a 3^rd-party platform, scientists might become encouraged to take more care in the design, execution, and reporting of their research before publication.

A drawback still persists. By allowing post-publication peer review develop along a Facebook or Twitter model may make it difficult to share objective reviews on flaws and merits. This will not be fair to those qualified researchers trying to do sound science.

Finally, does the enhanced anonymity of the peers become a good or bad thing? Depends on who you ask. Certainly, it helps junior researchers participate in peer review without reservations when reviewing the work of their peers or experienced researchers. When coupled to an open post-publication peer review process, it can also mitigate any potential conflicts of interests. These conflicts can sometimes arise between peer reviewers assigned by the journals and authors of the paper.

Peering Ahead…

With PubPeer 2.0, the online platform for post-publication peer review has improved. A key pillar of PubPeer is strong anonymity in peer review. However, this might rub the open access promoters the wrong way. Therefore, it is likely poised to grow in influence and to get much busier.

What are your views on this model of post-publication peer review? Is it bound to find more support? Share your thoughts in the comments section!

The open access model has garnered support from scientific communities over the years.  OA allows members of the public to access the content without permission and paywall barriers. OA journals make it easier for scientists to share their data with a wide audience. Most research done in public institutions use government research grants. These public institutions also pay journal subscription fees to allow their staff and students to read these journals. This means that public funds help in supporting and accessing research. This is one of the reasons that governments and funding agencies support OA journals.

Types of Open Access Journals

The open access model has evolved into many variants.

• Megajournals: In this model, journals offer full open access for a relatively low article processing fee and high volume. These megajournals have an objective peer review. They also tend to offer rapid publication. PLOS One, BMJ Open, and Scientific Reports are examples of megajournals.
• Delayed: These journals involve an initial embargo period. The journal chooses a time duration during which all their articles are behind the paywall. After that period, the articles are freely accessible. Let us say you choose to publish in a delayed open access journal in January 2017. If the journal has a 12-month embargo period, your article will remain behind the paywall until January 2018. As of 2018, your article will become fully open access. Some OA journals also allow self-archiving or green open access. In this model, the published version of the article exists behind the paywall. The journal allows you to deposit a copy of your paper in a public place. This could be your website or your institution’s repository. The version can be pre-print or post-print based on journal copyright policies.
• Hybrid: These open access journals still offer a subscription service. They give authors the option to make their articles open access. If you decide to publish your article as open access, you have to pay an article processing fee.
• Flipped: These subscription-based journals have now changed into OA. For example, Nucleic Acid Research and Nature Communications.

Choosing an Open Access Journal

How do you find an open access journal to publish in? You can use following platforms to find OA journals:

• DOAJ: You can find a list of open access journals in the Directory of Open Access Journals. The DOAJ also makes it possible for you to access content in OA journals.
• ROAD: You can also use ROAD (Director of Open Access Scholarly Resources). ROAD identifies open access resources which have been given ISSN numbers. The corresponding ISSN records are updated. ISSN records are matched with coverage lists provided by indexing databases, registries, and journal indicators. This process creates bibliographic records of open access content.
• SciELO: The Scientific Electronic Library Online (SciELO) is another option. It is a digital library of open access journals. SciELO is used for electronic publishing in developing countries. It was launched in Brazil in 1997. It hosts more than 1,161 OA journals and more than 500,000 open access articles.
• Ulrich’s Knowledgebase: It has information on more than 300,000 periodicals. This list includes OA journals. Ulrich’s can be searched which makes discovery of open access journals easy. The database also includes links to full-text and other content.
• BASE: Bielefeld Academic Search Engine is one of the most voluminous search engines especially for academic web resources available through open access.

Most of the work published today is interdisciplinary and international, involving authors from different research areas and locations. In recent years, the cloud-based authoring tool, Overleaf has made sharing and publishing documents in an international environment much easier and effective.

The online platform allows real-time collaboration between different authors of a file and automatically generates a structured and fully typeset output in the background as they type. This means that authors can directly see a preview of their projects while they are working on them. Overleaf LaTeX can be used to create a range of documents including journal articles, slides, books, conference posters, and CVs.

Collaborative Writing

With this online tool, academics can collaboratively write and/or edit documents in Rich Text or LaTeX anywhere, anytime. The service allows them to share and invite colleagues to co-author, check, edit, or comment on a file without having to pass a manuscript around or deal with several versions of a document. It also minimizes errors and helps prevent long email discussions.

A basic version of Overleaf, which offers a storage space of up to 1GB and allows up to 60 files per project, can be used for free. However, if users require more storage or additional features, they can purchase the Pro or Pro + Teach versions. The service offers several benefits to authors, institutions, and publishers.

Overleaf for Authors

Thanks to its many interesting features, many institutions offer the Pro version to their members for free. Moreover, some publishers have partnered with Overleaf to simplify the submission process. For a number of journals, authors can use the readily available Overleaf LaTeX templates and submit directly from Overleaf to the journal’s editorial office.

Some of the main features of the online tool are intended to help authors write, edit, and submit documents faster and more efficiently.  The following list showcases the important features of Overleaf:

• You can start working and collaborating online right away without having to install a software program.
• You can see and edit your projects—or check the changes made by your colleagues—in real time from remote locations.
• You can send a sharable secret link (assigned to every project) to your colleagues to start a collaboration. Only authorized users can have access to the corresponding file.
• You always access the latest version. All the changes made by you or your co-authors are synchronized.
• You can communicate with your co-authors by adding comments and/or notes to the files.
• You can edit in Rich Text or LaTeX and easily switch between the two modes.
• You can quickly rectify any error based on the alerts received. You can use various templates and features to create tables, prepare great presentations, draft journal manuscripts, compile theses, or create bibliographies.
• You can create protected projects for enhanced privacy with the Pro version. You can also add and remove collaborators at any time.
• You can use journal-provided manuscript templates and make direct submissions to journals from several publishers or to repositories instantly through an integrated feature.
• You can incorporate reference managers such as Mendeley or Zotero when drafting your manuscripts.
• Overleaf has launched a new LaTeX validation service, the details of which are available here.

Using Overleaf

Do you think that Overleaf could help you communicate your research better? Are you interested in learning more about this service? In the next part of this series, we will provide a user guide with information on how to sign up and work with different templates. You can also find more information in this short introductory video.

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If you are already an Overleaf user, we would love to hear about your experience with this exciting tool. Does it make your work with colleagues more effective? Is it easy to use? Which features do you like most? Please feel free to share your thoughts with us by commenting in the section below.

Citation methods vary by academic discipline.  Science and medicine has its own preferred style. Vancouver referencing and citation  style is a numbered referencing system that follows the rules established by the International Committee of Medical Journal Editors (ICMJE). Read on to learn how to cite your sources correctly using this style.

Vancouver Referencing Basics

You should always use an in-text citation when you are paraphrasing or directly quoting someone else’s work. In Vancouver style referencing and citation, in-text citations are indicated by Arabic numerals (1,2, 3, 4, 5,6,7,8,9). Each reference should be given a unique number that corresponds to the order in which it is cited. When the same work is referenced more than once, use the same number each time.

The placement of the number within the text is up to the individual author or journal. Numbers can be placed within the text, or at the end before or after the period. Brackets or parentheses are both fine. Superscripts can also be used. Just make sure you remain consistent throughout your paper.

Let’s look at several examples, all of which are correct.

• Recent research (1) indicates that calorie counting is an effective way to maintain long-term weight loss.
• Recent research¹ indicates that calorie counting is an effective way to maintain long-term weight loss.
• Recent research indicates that calorie counting is an effective way to maintain long-term weight loss (1).

If you use the author’s name in the text, you should still include the citation number.

Blakely (2) notes that previous researchers failed to take age difference into account.

When quoting directly from a print source, you should use single quotation marks and include the page number that you are citing. The page number should follow the quote.

According to Schumann [4], ‘long-term weight loss is sustained through a variety of behavior modification techniques (p.17).’

Note that when you cite different publications by the same author in the same year, each publication should get its own unique reference number.

Multiple Author and Multiple-Source Citations

If a work has more than one author, and you wish to include the name of the author(s) in the text, you should use the last name of the first author followed by “et al.” For a work written by Simon, Blakely, and Faust, the in-text citation would be as follows:

Simon et al. [3] found that mice who were fed a diet high in sugar ate more on average than mice who were not.

When citing multiple sources in a sentence, include the reference numbers for each source in the citation. The numbers should be separated by commas with no space in between.

Previous research [3,7,10] also confirms that diets high in sugar contribute to a decrease in the production of the ‘satiety’ hormone ghrelin.

Consecutive numbers should be separated by a dash.

Decreased ghrelin is associated with increased appetite and weight gain (7-9, 14).

Keep in mind is that in-text citations do not vary according to the type of publication that is being cited. No matter whether you are citing a journal article, book, DOI, URL (weblink), report, or other type of publication, the in-text citation is a number.

The exception to this is the items that are unpublished (correspondence, interviews, emails, and so on). Here, you should cite the name of the person and date of communication in parentheses in the text. For example:

Patient-physician confidentiality plays the important role of building trust and increasing the likelihood a patient will follow their physician’s advice, (Jake Smith, December 13, 2007) which can save lives (8).

Do not include this citation in your reference list.

Composing Your Reference List

The final page of your work should be titled “References” and list all of your sources in the order they are cited in the text. A complete list of guidelines can be found here. For now, some key items to keep in mind are:

• Books and journal names should not be italicized or placed in quotation marks. Journal titles are abbreviated. You can find a guide to these abbreviations in the NLM Catalog.
• The symbol “&” should never be used between author names.
• You should only use a capital letter for the first word of a sentence and words that are usually capitalized.
• Page numbers should be abbreviated to “p”. For example, pages 12-37 would be written as p. 12-37.
• In the reference list, “et al” should only be used when there are more than six authors. In this case, list the first three authors followed by “et al”. So, a publication written by Dewey, Cheatham, Howe, Macklin, Ryan, and Choi, would be written in the reference list as “Dewey, Cheatham, Howe et al.”

Let’s look at several examples of different types of publications as they should be written on a Vancouver style reference list.

Book: Armitage P, Berry G, Matthews JN. Statistical methods in medical research. John Wiley & Sons; 2008 Apr 15.

Journal Article: Powell C. The Delphi technique: myths and realities. Journal of advanced nursing. 2003 Feb 1;41(4):376-82.

Electronic Journal Article: Aho M, Irshad B, Ackerman SJ, Lewis M, Leddy R, Pope T, et al. Correlation of sonographic features of invasive ductal mammary carcinoma with age, tumor grade, and hormone-receptor status. J Clin Ultrasound [Internet]. 2013 Jan [cited 2015 Apr 27];41(1):10-7. Available from: http://onlinelibrary.wiley.com/doi/10.1002/jcu.21990/full DOI: 10.1002/jcu.21990

Did this article help you with your Vancouver style citations and references? What are some other challenges you have in using citations? Let us know in the comments!