Ulrike Träger – PLOS ECR Community https://blogs.plos.org/thestudentblog Serving students and early career scientists Sat, 04 Apr 2020 06:36:34 +0000 en-US hourly 1 https://wordpress.org/?v=4.9.13 Ten tips to stay on top of your reading during grad school https://blogs.plos.org/thestudentblog/2017/01/12/ten-tips-to-stay-on-top-of-your-reading-during-grad-school/ https://blogs.plos.org/thestudentblog/2017/01/12/ten-tips-to-stay-on-top-of-your-reading-during-grad-school/#comments Thu, 12 Jan 2017 17:00:23 +0000 http://blogs.plos.org/thestudentblog/?p=12090 0000-0002-4493-1136In grad school we tend to focus on experiments: planning, performing, analyzing and interpreting them. While keeping up with relevant literature is equally important, this part of a PhD often fades into the background. I]]>

In grad school we tend to focus on experiments: planning, performing, analyzing and interpreting them. While keeping up with relevant literature is equally important, this part of a PhD often fades into the background. I learned this the hard way – during my PhD I allocated too little time to reading, missed a paper and wasted time on a dead end. In order to avoid this happening again, I’ve optimized my tools to stay on top of the flood of papers – 2.5 million papers are published in 28,100 journals each year. Here’s how you can do the same!

  1. Set up email alerts. Scanning journals and databases such as PubMed for new publications each day or week is a time consuming task. But there are several websites that scan new publications daily and send you email alerts if publications matching your search terms are found. You can set up those alerts directly on PubMed, or use other services such as PubCrawler (my personal favorite), Google Scholar or Web of Science.
  1. Spend time finding the perfect search terms. When you start setting up alerts, it is important to play around with your search terms. There is a fine line between too few hits when your search criteria are too strict, and getting back hundreds of publications per alert because you are too vague. I personally found it most helpful to set up several specific search terms (each getting 5-10 hits per week) instead of one vague one. Boolean operators are also your friend – learn how to use them! The right use of AND and OR can make all the difference. Another useful feature on PubMed and other sites is using truncations in your search terms. For example, I work on macrophage differentiation. By entering differentiat* instead of differentiation my search results will include not just differentiation, but also differentiated, differentiate and differentiating.
  1. Don’t limit yourself to keyword searches. Set up alerts for new publications from the key players – and your competitors (!) – in the field. This way you will never miss a publication from them ever again. You should also set up citation alerts to all of your own publications. Why? People who cite your work will likely publish on topics relevant to you. If you haven’t published yet, you can set up alerts on your PI’s papers. Lastly, setting up citation alerts on key papers in your field will allow you to keep track of new results as well as how findings are received in the field. Are people citing the new theory already or are they avoiding or disproving it?
  1. Keep your search terms updated. Every few months you should check your search terms. Are they still relevant to you or has your focus changed? Should you add a citation alert for a new and important paper? Can you delete or improve a keyword search you set up a year ago? Maintaining your search criteria is as important as setting them up in the first place.
  1. Set up eTOCs and RSS feeds with the journals you frequent most. In addition to specific keyword search email alerts, I also set up alerts with several journals in my field. This strategy allows you to keep a broader overview. Instead of remembering to check the latest issues each week or month, a table of content summary (eTOC) is sent to you automatically. Most journals will also have RSS feeds you can subscribe to – allowing you to also see publications that are in press but not yet listed on PubMed. To subscribe to those, you do need a RSS feed reader – Feedly being the most commonly used one.
  1. Check out new learning software in addition to classical alerts. I recently came across a new generation of reference managers such as ReadCube, CiteULike and PubChase (although more commonly used Mendeley has a similar feature). These programs not only allow you to save and organize your literature, but they also make recommendations for new papers based on your history. Have a look at the options and see which fits you best. My personal favorite is PubChase; its recommendations have been great for me so far and it is completely free to use. PubChase operates on the basis that users can benefit from each other. Assuming that people reading the same papers share interests, the software compares the libraries of its users and makes suggestions based on what other people with similar libraries read.
  1. Use social media. The discussion surrounding scientists using social media is ongoing, but there are many ways you can use social media – particularly Twitter – to your advantage. Follow journals to see what new stories they have coming out. More and more scientists and labs have their own accounts tweeting about their latest research. Automated twitter accounts – called Twitter bots – also scan the literature for certain topics and help you find interesting new papers. @paperfly digests Drosophila papers, while @plantecologyblot tweets about ecological content from plant biology journals and @EcoEvoJournals covers Ecology and Evolution. In addition to being a source for the latest publications, Twitter also allows you to discuss new findings with other scientists and see how the research community reacts to new ideas.
  1. Check out conferences for new reading material. Conferences are a great place to catch the latest developments in a field, as many researchers will either present their new papers or work in progress. In addition to hearing the work and interpretation by the authors themselves, you can also get a feel of how people receive the work. For conferences you cannot attend – check the online abstract book for interesting new stories or players in your field and use social media! Most conferences have hashtags these days allowing you to follow from afar. Follow conference organizers such as Keystone Symposia and Gordon Conferences for conference announcements.
  1. Add a personal touch – use journal clubs and lab mates to share latest research. If you find a paper that your colleague might be interested in, send it to them! They will often return the favor. Are you bored with your traditional journal club? Why not mix things up and use journal club for a literature overview? Simply divide relevant journals up between all participants, and give each person two to three minutes to highlight one or two interesting papers per week. If, like me, you are the only person in your lab working on a given topic, branch out and start a new journal club with people outside your lab. That way you can not only share new papers but also new techniques you are working on – the input will be invaluable.
  1. Set aside fixed time slots to go over new papers. This is probably the most important point. You can have great tools: email alert, social media or learning software – but if you do not invest the time to look over the alerts and recommendations, they will be of no use. Having a defined time slot for literature search is the most efficient way to scan the literature. I have two hours each week allocated in my calendar for literature searches, every Friday. After that, I normally have one to three papers on my reading list. Happy reading!

 

Featured image: Photo by author

 

References

Pubmed  https://www.ncbi.nlm.nih.gov/pubmed?cmd=search

PubCrawler http://pubcrawler.gen.tcd.ie/

GoogleScholar https://scholar.google.de/

Web of Science https://webofknowledge.com/

Feedly https://feedly.com/i/welcome

ReadCube https://www.readcube.com/researchers

CiteULike http://www.citeulike.org/

PubChase https://www.pubchase.com/

Mendeley https://community.mendeley.com/content/05-mendeley-suggest

Tutorial on setting up alerts on PubMed https://www.nlm.nih.gov/bsd/disted/pubmedtutorial/040_015.html

Truncation on PubMed https://www.nlm.nih.gov/bsd/disted/pubmedtutorial/020_460.html

Boolean operators https://www.nlm.nih.gov/bsd/disted/pubmedtutorial/020_355.html

Mark Ware, Michael Mabe (2015) The STM Report – An overview of scientific and scholarly journal publishing

Mary Gearing (2016) Social media for ECRs: Serious scientists can (and do!) use Twitter , PLOS ECR Community blog

Elizabeth Gibney (2014) How to tame the flood of literature , Nature Toolbox

 

 

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Reforming scientific publishing to value integrity https://blogs.plos.org/thestudentblog/2016/08/24/reforming-publishing-to-value-integrity/ https://blogs.plos.org/thestudentblog/2016/08/24/reforming-publishing-to-value-integrity/#comments Wed, 24 Aug 2016 20:46:49 +0000 http://blogs.plos.org/thestudentblog/?p=11667 0000-0002-4493-1136Sometimes working in academia feels like being a gymnast at the Olympics. Not because we’re tumbling through the lab in glittering costumes, but because of the constant pressure to succeed. Gymnasts are tasked to perform]]>

Sometimes working in academia feels like being a gymnast at the Olympics. Not because we’re tumbling through the lab in glittering costumes, but because of the constant pressure to succeed. Gymnasts are tasked to perform more spectacular routines at every competition, while scientists are expected to publish several high impact papers a year. And as seen with French gymnast Samir Ait Said, who broke his leg in a horrific accident at the vault in the 2016 Summer Olympics in Rio, too much pressure can have drastic consequences. While the “publish or perish” culture in science won’t break bones, it does have a negative impact – the prevalence of scientific fraud, leading to an increase in the number of retractions of scientific papers. This is a problem that doesn’t seem to be easing any time soon – the number of papers retracted in 2010 was more than ten times that in 2000.

A study published in PLOS Biology that investigates what factors scientists reputations are judged on gave a clue as to why this problem exists. When comparing a scientist that produces boring, but reproducible studies with a scientist that publishes exciting, but not reproducible studies, the public perceived the boring scientist as “smarter, more ethical, a better scientist, more typical, and more likely to get and keep a job.” Scientists given the same choices agreed that the boring, but certain scientist was smarter, more ethical and the better scientist. But in a departure from the public’s opinion, scientists found the exciting but unreliable scientist to be more likely to get a job and be more celebrated by peers. This is a stark contrast to the public’s view of science, which seems to favor well-done science over flawed science. Worryingly, when scientists were asked which of the two model scientists they would rather be, more said they wanted to be a scientist that produces exciting results, even though the majority knew that publishing reproducible research is better overall. While one survey of 313 researchers does not represent the whole science community, these results paint a surprising picture of scientists’ priorities.

Publish or perish

But it’s hard to lay blame on the scientists – as they are not wrong in their perception that innovative science is more celebrated than replicable science. In our current scientific culture, publishing high impact papers often seem to be all that counts for success. The shortage of tenure-track positions (only about 14%-23% of PhD level biologists, chemists, or physicists hold tenure-track positions after five years) leads to a fierce competition between scientists for those jobs. And the main way scientific success is judged in job or grant applications is the number of high impact publications an investigator has authored.

The pressure to publish one’s work in the top journals is immense, especially for early career scientists who are just starting to make a name for themselves and have few publications. The prospect of a high impact factor publication has even been shown to effect neuronal response and behavior in controlled experimental settings. The results were comparable to reward-based responses normally seen in the context of money, leading the authors to dub impact factors the “currency of science.”

Publishing in high impact journals has disproportional advantages for the authors, compared to publishing the same data in a “lesser” journal. Advantages range from better prospects on the job market and invites to conferences, to better chances on grant applications. This leads some scientists to strive for the perfect, most publishable study. On the way, they may ignore data not fitting their conclusions or leave out negative data. The rush to be the first to publish may also lead to neglect of thorough replication of experiments. The crisis in reproducibility of scientific data is evident, as detailed in a previous post on the PLOS ECR Community Blog. The strong correlation between a journal’s impact factor and the number of papers it retracts, found in a study in 2011, supports the notion that scientists are more likely to take risks and forget scientific vigor in order to publish in high impact journals.

How can we cultivate greater value for sound science?

One common way to assess quality of science is judging the journals in which scientists publish. Impact factors of journals are one popular measure in use. Most scientists agree that impact factors are an imperfect measure of quality, but they are an easy metric. Calculating the average number of citations per article published is easy. By extension, judging careers by a list of publications associated with one number is easy. But when has the easy way ever been the best way? Impact factors are based on citations, but, like all other citation-based metrics in use, it ignores the fact that one in 15 citations is from the authors themselves. Most importantly, however, citation numbers do not account for the type of citations. For example, a paper may be cited 1000+ times but only in publications challenging its findings, meaning the impact factor in this case is not representative of the quality of the research.

Recognizing the shortcomings of impact factors, PLOS instead uses article level metrics (ALMs) to measure the quality of science published in their journals. ALMs measure the quality of a scientific article by not only taking  the number of citations in to account, but also press coverage, shares, and views the article receives. By taking into account social as well as academic factors as soon as the article is published, the influence of the article is charted over time prior to the point where the article is cited in other academic literature. While ALMs can share some drawbacks with the more traditional impact factor (e.g. self-promotion on social media or news coverage of poorly done science), they do provide an advantage over impact factors in getting a faster picture of the influence a paper has on both the scientific and general communities.

A second alternative to impact factor is valuing science based on scrutiny from an open access community. A lot of scientific journals only let paying subscribers view their publications, which limits exposure to research published in these journals. Open access policies allow anyone interested in a study to access the research, without barriers. More importantly, not just the access should be free but also the peer review process. Peer review before publication is a key step in checking the quality of science, however the current peer review system is imperfect. I believe that post-publication peer review should be a key process to improve science integrity. Ideally both pre- and post-publication peer review would be made available alongside the published manuscript for increased transparency in the scientific process. A few publications have introduced open reviews including EMBO, BMJ Open and F100research. Alternatively, you can find online journal clubs like PubPeer where articles are discussed post-publishing, or leave comments on articles post-publication.

Currently, a lot of sound science remains unpublished, as negative or inconclusive data are less likely to be published due to reporting bias. A 2010 study in PLOS ONE showed that 82% of papers published between 2000 and 2007 in the United States included positive results only, in spite of the value of negative data. By publishing negative or null results the scientific literature captures a more complete picture of a particular field, and includes more balanced information. I feel a well-done study with negative results deserves the same recognition as a positive one, as it still expands human knowledge and saves resources for other researchers. For example, publishing what isn’t the cause of a given disease will prevent other scientists from spending time and money looking into the same thing. The PLOS Missing Pieces Collection includes negative, null or inconclusive results, and is a great platform for scientists who conduct an experiment and yield a result of this type. In addition, PLOS ONE is a journal that does publish negative, null, or inconclusive results. Replication studies also receive limited recognition in spite of their importance to advancing the scientific field. They are key in validating scientific findings, but few scientists risk doing them as it is hard to publish them for their “lack of innovation,” – a notion we should start to forget.

Boycotting high impact factor journals

Nobel Prize winner Randy Schekman declared his boycott of top notch journals in 2013, arguing that their policies are damaging to science and cause scientists to cut corners. Schekman’s statement started an important discussion, but it is important to note that despite his controversial stance, the repercussions for him are slight. As a well-established principal investigator and Nobel Prize winner, people will read his papers whether or not they are published in a high impact journal, because his career is celebrated in the scientific community. Early career researchers do not share Schekman’s established professional reputation, and may be hesitant to embrace alternatives to the conventional closed-access, impact factor journals when selecting where to publish their findings. Fortunately, there are plenty of communities devoted to reforming the current scientific publishing system and journals committed to transparency. Some of these include: the OpenCon community, which is a group of ECRs advocating for more open science; and in addition to PLOS journals, eLife, Nature Communications and Cell Reports all publish open access science.

While extreme measures such as completely boycotting high impact journals may not be the best solution for all ECRs, there are initiatives devoted to changing the existing science publishing paradigm. Believing that the “challenges facing early-career researchers because of hypercompetition are damaging the efficiency of science,” the Future of Science initiative is a forum lead by post-docs intended for ECRs to discuss the problems they encounter and possible solutions. I encourage all young scientists to take part in the discussion in order to promote change in the scientific community. We need to shift focus back on the science, and not sacrifice ethics and accountability for career advancement.

Featured Image: Image of a gymnast completing a pass on the vault in the London 2012 Olympic Games. Flickr. License: CCBY 2.0

References

Dwan K, Altman DG, Arnaiz JA, Bloom J, Chan A-W, Cronin E, et al. (2008) Systematic Review of the Empirical Evidence of Study Publication Bias and Outcome Reporting Bias. PLoS ONE 3(8): e3081. doi:10.1371/journal.pone.0003081

Ebersole CR, Axt JR, Nosek BA (2016) Scientists’ Reputations Are Based on Getting It Right, Not Being Right. PLoS Biol 14(5): e1002460. doi:10.1371/journal.pbio.1002460

Fanelli D (2010) Do Pressures to Publish Increase Scientists’ Bias? An Empirical Support from US States Data. PLoS ONE 5(4): e10271. doi:10.1371/journal.pone.0010271

Paulus FM, Rademacher L, Schäfer TAJ, Müller-Pinzler L, Krach S (2015) Journal Impact Factor Shapes Scientists’ Reward Signal in the Prospect of Publication. PLoS ONE 10(11): e0142537. doi:10.1371/journal.pone.0142537

Reich ES (2013) Science publishing: The golden club. Nature 502:291-293 doi:10.1038/502291a

Sauermann H, Roach M (2012) Science PhD Career Preferences: Levels, Changes, and Advisor Encouragement. PLoS ONE 7(5): e36307. doi:10.1371/journal.pone.0036307

Steen RG (2011) Retractions in the scientific literature: is the incidence of research fraud increasing? J Med Ethics 2011;37:249-253 doi:10.1136/jme.2010.040923

Megan Yu (2016) The irreproducibility crisis- An opportunity to make science better PLOS ECR Community Blog

Eva Amsen (2014) What is open peer review? F100 Research Blog

https://pubpeer.com/

http://admin-apps.webofknowledge.com/JCR/help/h_impfact.htm

http://collections.plos.org/missing-pieces

https://www.plos.org/article-level-metrics

https://www.plos.org/open-access

https://www.theguardian.com/commentisfree/2013/dec/09/how-journals-nature-science-cell-damage-science

https://www.theguardian.com/sport/2016/aug/07/fabian-hambuchen-gynastics-injuries-samir-ait-said-andreas-toba

http://www.sciencemag.org/careers/2015/12/people-year-future-researchs-postdoc-activists

http://futureofresearch.org/

http://bmjopen.bmj.com/

http://f1000research.com/

http://emboj.embopress.org/

https://www.plos.org/

https://elifesciences.org/

http://www.nature.com/ncomms/

http://www.cell.com/cell-reports/home

http://www.opencon2016.org/

http://www.vox.com/2016/7/14/12016710/science-challeges-research-funding-peer-review-process#4

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4648225/

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