Today we published the article,Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results, by Wicherts et al. In the manuscript, the authors show that weaker evidence in a psychology paper published in a journal requiring signed agreements to share data is associated with a failure to comply with this signed agreement to share.

Rochelle Tractenberg

In the following opinion piece, Rochelle Tractenberg, the academic editor who handled the peer review of Wicherts et al., discusses the ways in which “research ethics” and the “responsible conduct of research” go beyond human subjects protection, to include data sharing, professional conduct, and the careful, correct and complete reporting of all analyses in published research.  Rochelle is a biostatistician and research methodologist at Georgetown University.

The article by Wicherts et al. describes their study of 1148 “statistically significant results” that were published in 49 different papers within two psychology journals. As it was being reviewed and revised, this paper sparked a vigorous debate among PLoS ONE editors and reviewers for two very different, ethics-oriented, reasons. These reasons were:

1. Disciplines differ in their requirements that data analyzed and published should be made available to any scientist that requests the data. In some cases, the data cannot be properly de-identified, which violates a key feature of human subjects protections that all scientists are supposed to commit to whenever they carry out scientific work involving living persons. The Ethics Committee of the authors’ institution explicitly required them NOT to publicize the authors who refused to share data – and whose work was identified as being weak in terms of evidence and/or quality of results.
2. The readers of published work are totally dependent on the quality and accuracy of the statistical results presented –and described – in any manuscript they wish to utilize as evidence in their own argument or scientific endeavor. The option to re-analyze data is critical to check the reliability of published designs, results, or conclusions. Time is a precious commodity; knowing what work is most likely to require replication prior to its use would limit our reliance on work likely to include mis-analyzed data, misinterpreted results, or both.

These considerations highlight diverse conceptualizations of the “responsible conduct of research”: in the first conceptualization, the protection of human subjects –the authors who did and did not share their data, whose published work was analyzed in this paper – is the sole concern. The second conceptualization involves the responsibility of the authors of the reviewed published papers to fulfill their professional ethical obligations as well as their contractual agreements. Wicherts et al. did obtain permission from their Ethics Committee to provide a list of authors who failed to share data – if specifically requested, but are NOT permitted to identify which authors were compliant and defiant within their paper, nor to place their data file, as is, into a public archive. Wicherts et al. analyzed the contents of published articles, and then requested the data these papers represented. The journals’ and APA ethics policies are public and require data sharing, so neither the requests nor the failures to comply with those requests can be considered privileged. In short, no feature of the data in this manuscript can be considered to be privileged. The responsible conduct of research is much more than protecting study subjects and obtaining informed consent, but the Ethics Committee did not act like it is.

As the editor shepherding this article through the review process, I applaud the effort by Wicherts and colleagues, and disagree with the Ethics Committee decision. I believe that every journal should document requests for data and the failures of authors to provide the requested data as part of the publication record. This compliance information should be accessible to all reviewers for journals and grants, and to scientists who look to the published literature for replicable, reliable, ethically obtained results.

A prior report by Wicherts et al. in 2006 found that, while journals published by the APA all require authors to sign an agreement to share their data, 73% of authors who were contacted for that study failed to do so. These 73% defied their written agreement, and professional obligation (see APA Ethical principle 8.05), to share their data. This is not responsible conduct of research; this is unethical behavior and every scientist is entitled to know whether or not an author is responsible in their conduct –and reporting – of their research. As critical as these features are to responsible conduct of research, the review of manuscripts and grants for “ethical considerations” cannot be limited to the inclusion of women and minorities, balance between male and female subjects, and properly obtaining informed consent.

Wicherts et al. conclude that policies for data archiving should be strengthened/more widespread, even though their 2006 findings that, in defiance of their signed agreements, the journals’ publishing policy, and the professional association policy on data sharing, nearly ¾ of APA published authors refused to share data when contacted. In their current study, the refusal rate was “only” 57%.

A survey of geneticists working at 100 universities in the US led to an estimate of 47% failure to share. The challenge is clearly widespread and has a prevalence rate in the 47-73% range. By contrast, in her survey of the prevalence of “unethical” or “questionable” scientific behavior, Fanelli arrived at far smaller estimates – possibly because of a lack of awareness among her respondents that a failure to share data or research resources constitutes irresponsible –not merely questionable – research practice.

A broader appreciation of how critical transparency and replicability are for good science could support the cultural shift necessary to promote the idea that the “responsible conduct of research” is not limited to properly obtained consent. A mechanism for documenting failures in these key features of responsible conduct of research would also support this shift. Every reviewer should have this information about the likelihood that an applicant or author will violate sharing policies and/or defy contracts they’ve signed and/or professional ethical science standards they should be held to.

The responsible conduct of research includes conscientious protection of human subjects. In the book, “Scientific Integrity”, Macrina  also notes, “(s)haring research materials published in the peer reviewed literature has been a traditional practice that follows from the expectation that scientific research must be amenable to replication” (p. 81) and that “…written communication is an essential part of scientific research.” (p. 83) (see also National Research Council, 1992; Board on Life Sciences, 2003). As such, these should be just as conscientiously executed as other aspects of the research enterprise. Refusals to share data harms science and constitutes violations of our obligations to be responsible conductors of research.

Rochelle Tractenberg has also written a companion piece to this article, which can be found in the comments section of the Wicherts et al. manuscript.  In the second piece, she interprets the association between weak evidence and failures to comply with data sharing requirements in a different way. Instead of supporting mandatory archiving of data, Dr. Tractenberg concludes that readers and reviewers of manuscripts and grant proposals should be notified of the author’s/applicant’s history of compliance with data sharing mandates and policies. She believes that such documentation will do more to change the culture towards one promoting science and data sharing than mandatory data archiving. To read this post, please click here.

References

Board on Life Sciences (2003). Sharing Publication-Related Data and
Materials: Responsibilities of Authorship in the Life Sciences.
Washington, DC: National Academy Press.

Campbell, E. G., Clarridge, B. R., Gokhale, M., Birenbaum, L.,
Hilgartner, S., Holtzman, N. A., et al. (2002). Data withholding in
academic genetics: Evidence from a national survey. Journal of the
American Medical Association, 287, 473–480.

Fanelli D (2009) How Many Scientists Fabricate and Falsify Research? A
Systematic Review and Meta-Analysis of Survey Data. PLoS ONE 4(5):
e5738. doi:10.1371/journal.pone.0005738

Macrina FL. (2005). Scientific Integrity: Text and Cases in
Responsible Conduct of Research, 3E. Washington, DC: American Society
for Microbiology Press.

National Research Council (1992). Responsible Science, Vol 1: Ensuring
the Integrity of the Research Process. Washington, DC: National
Academy Press.

Wicherts JM, Borsboom D, Kats J, Molenaar D (2006) The poor
availability of psychological research data for reanalysis. American
Psychologist 61:726-728.

Wicherts JM, Bakker M, Molenaar D (2011) Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results. PLoS ONE 6(11): e26828. doi: http://dx.plos.org/10.1371/journal.pone.0026828

At PLoS, we’re dedicated to the tenet of Open Access, making academic literature widely available on the web. However, with an ever-growing pool of scientific literature, our goals have to consider not only making content available, but also accessible. With the breadth of articles we aggregate, you need a strong tool to find the specific information you want. Our authors have published on methods to get the most out of search engine queries and even how search engine data can yield its own important results. To help our users navigate the sea of information PLoS publishes daily, we introduced an Advanced Search function with a broad range of filters.

When searching for PLoS articles, the standard search bar at the top of the page will return all results where the term has been mentioned throughout the entire article (see Figure 1). While this is good for very specific searches, a search for a term like “influenza” will yield over 2,000 results across the PLoS journals. This is where the Advanced Search’s filtering system comes in handy.

Figure 1

Advanced Search

Advanced Search provides multiple filters for results by limiting what field you’re searching (Title, Abstract, Author Name, etc). Using the pull-down menu (Figure 2), you can search for your term in the Title or Abstract of the article, which makes it more likely that the article is focused on that subject. You can also search for specific authors, editors or author affiliations. This allows you to find papers published or edited by your colleagues or researchers at a specific institution.

You can make your search more targeted and powerful but using the search box to combine these different searches using the qualifiers AND, OR or NOT, limiting the search results further. For example, you can shorten the results by saying you want articles that mention “influenza” in the abstract, but NOT “vaccine.”

Figure 2

Advanced Filters

Below the search block is a series of filters that allows you to limit your results further: Journal, Subject Category and Article Type (Figure 3). This allows you to filter the search results down to specific PLoS journals, or a subject area you are studying (e.g., Genetics of Disease or Systems Biology) or down to a particular article type, like Research Articles or Editorials.

Figure 3

Sorting Results

After performing the search, you can sort the results using an additional drop-down menu, found at the top of the search results. “Relevance” is the default setting, but you can also sort by Most Viewed, which will yield the most popular article by page views meeting your search criteria, and Date—so you see the newest items that have published since the last time you performed your keyword search.

Related to the sorting types, each search result features links its Views, Citations and Bookmarks. Hovering over these links provides a breakdown of each statistic. Views will be broken down to the number of views in each format (HTML, XML and PDF) and Citations will break down by databases the citations are listed in (e.g., PubMed Central or Web of Science®) (Figure 4).

Figure 4

In addition to publishing the highest quality scientific research, PLoS is dedicated to making our content accessible to our audience. Our team is always working to find new ways to assist the readers of our journals, and we hope that our Advanced Search will get you the information that you seek.

In addition, we also have the same functionality operating at the article level. The widget is able to display tweets about a particular article by looking for the article DOI appearing in an ‘unpacked’ URL. If there are no tweets for a particular article, it will not appear.

The paper, Inner Speech during Silent Reading Reflects the Reader’s Regional Accent, is a nice example of this widget in use.

We should point out that this handy widget has a few limitations.  For one, the widget isn’t able to store tweets for all eternity.  It will only be able to show recent tweets. Also, it isn’t connected to our Article Level Metrics …yet (we’re working on it though).

Otherwise, we think this widget will make a nice new addition to our site and will be a helpful way to see what our community is saying.

These tiny unicellular creatures live in the ocean, where it is easy to imagine that an egg and sperm might have trouble finding each other. To solve this problem, they have evolved a system where pheromones actually orchestrate the whole process, so that egg and sperm are only released on cue, hopefully making it easier for them to connect.

Here’s how it works. The females release their sex pheromone, called ph-1, constantly. Then, when a male is nearby, he senses the pheromone, which triggers him to make and release sperm. At the same time, he also begins to produce his own sex pheromone, called ph-2, which makes the female produce and release her eggs. The researchers suspect that there is yet a third pheromone, called ph-3, that is then released by the eggs to continue attracting the sperm. However, while they detected ph-1 and ph-2 in their experiments, ph-3 was not directly observed.

By relying on these chemical signals, the diatoms make sure that they are only releasing their gametes when a potential partner is nearby, which keeps them from wasting lots of energy. This elegant solution so far appears unique among related organisms.

The researchers also found some other cool elements of the diatom’s reproductive cycle, like “threads” on the sperm that help it move and grab things, and “blobs” on the sperm with unknown function. Check out these movies for a look!

This post was written by Rachel Bernstein, an associate editor at PLoS ONE.

The article, A Computational Analysis of Limb and Body Dimensions inTyrannosaurus rex with Implications for Locomotion, Ontogeny, and Growth, by John R. Hutchinson, Karl T. Bates, Julia Molnar, Vivian Allen,  and Peter Makovicky received coverage from Xinhua, The Christian Science Monitor, and Slashdot.

Fairness Expectations and Altruistic Sharing in 15-Month-Old Human Infants received media coverage from Science 2.0, Scientific American, and WFAA-TV.

News for Your Neurons, Surprising Science and The Thoughtful Animal covered, Use of “Entertainment” Chimpanzees in Commercials Distorts Public Perception Regarding Their Conservation Status.

For more in-depth coverage on news and blog articles about PLoS ONE papers, please visit our Media Tracking Project.

This post is written by Nicholas Ellinwood, who has worked with PLoS ONE since last year. He is a Publications Assistant who focuses on assigning Academic Editors to appropriate manuscripts, managing email queries and handling our new species papers.

A CT and MRI of a red-eared slider are this week’s featured image. These pictures from Figure 1 of the article entitled “Inside Out: ModernImaging Techniques to Reveal Animal Anatomy” show how CT and MRI have different capacities in visualizing vasculature, soft tissue, and skeleton.

The paper by Lauridsen et al. includes many more three-dimensional visualizations of animal anatomy in living specimens including fish, amphibians, reptiles, mammals, and spiders.  The authors encourage other biologists to take advantage of modern imaging modalities like clinical scanners that exist in most current large hospitals.

The abstract reads:

“Animal anatomy has traditionally relied on detailed dissections to produce anatomical illustrations, but modern imaging modalities, such as MRI and CT, now represent an enormous resource that allows for fast non-invasive visualizations of animal anatomy in living animals. These modalities also allow for creation of three-dimensional representations that can be of considerable value in the dissemination of anatomical studies. In this methodological review, we present our experiences using MRI, CT and mCT to create advanced representation of animal anatomy, including bones, inner organs and blood vessels in a variety of animals, including fish, amphibians, reptiles, mammals, and spiders. The images have a similar quality to most traditional anatomical drawings and are presented together with interactive movies of the anatomical structures, where the object can be viewed from different angles. Given that clinical scanners found in the majority of larger hospitals are fully suitable for these purposes, we encourage biologists to take advantage of these imaging techniques in creation of three-dimensional graphical representations of internal structures.”

This particular episode of the conflict involves a paper published in PLoS ONE in Jan. 2010, so we feel at this point it is appropriate for us to comment and express our disapproval of this behavior.

The PLoS ONE study was the first response to an Oct. 2009 article in the journal Science that reported a correlation between CFS and a virus called XMRV. Contrary to the original finding, the PLoS ONE paper reported no evidence of XMRV in CFS patients, and a number of similar studies followed on its heels (see examples here and here), prompting Science to issue an expression of concern.

These later reports generated a very negative response from some individuals at the time of publication – a number of comments on the PLoS ONE paper had to be removed from the website because of inappropriate content – and it appears that the situation has not improved. According to the Observer article, “the militants are now considered to be as dangerous and uncompromising as animal rights extremists.” The article goes on to describe various instances of physical and verbal abuses, including daily death threats addressed to the lead author of the PLoS ONE paper, Professor Myra McClure.

As the debate about CFS continues, we at PLoS would like to take the opportunity to express support for our authors and for their right, and of course everyone else’s right, to enjoy the freedom to debate and investigate scientific topics openly, constructively, and without fear. This situation has emphasized, to us, the importance of civilized discourse in these matters. Those who threaten researchers’ safety above all do themselves a major disservice by dissuading other researchers from entering the field, chasing away the very people who may be able to help them. It is bad both for science and for patients, and should absolutely not be tolerated.

The aim of this project is to collect all pertinent news articles from legitimate media outlets and research blogs covering PLoS ONE articles. So, how does it work? From now on, we’ll attempt to bookmark relevant news articles and blog posts about PLoS ONE articles using Diigo (a collaborative research and social content site). If you would like to see the articles we’ve collected so far, check out our library. On a weekly basis, we’ll collate these bookmarks and list the relevant media coverage in the commenting section of each research article. An example of the media coverage comment can be found on the article: Scientists Want More Children.

We recognize that – despite our best efforts to track media coverage – we will inevitably miss some (and we will not aim to exhaustively list all sources which simply re-print a standard release for any given article).  So, we would encourage you to participate as well.  If you read, write, see or hear media coverage on a PLoS ONE article, please don’t hesitate to link to it in the comments section of the paper. Our suggested format is as follows:

Publication:

Title of article:

Link:

For an excellent example of  an author documenting media coverage, take a look at the article, Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees. Jonathan Eisen, one of the authors of this manuscript,  has meticulously posted links to media coverage in the comments section of his paper.  We appreciate his involvement and encourage authors to follow his lead.

In the meantime, we’ll still post PLoS ONE News and Blog Round-Ups of the most widely covered articles on a regular basis.

This week’s featured image comes from the manuscript, Tradeoff between Stability and Maneuverability during Whole-Body Movements by Drs. Alaa Ahmed and Helen Huang at the University of Colorado Boulder.

In the paper, the authors tested if a person’s maneuverability comes at the expense of his or her stability.  Standing on a balancing board, the subjects were asked to lean forward and use their center of pressure (CoP) to move a cursor toward a target on a computer monitor. The image above (Figure 1) illustrates the set-up and protocol of this experiment.

From the abstract:

Background

Understanding how stability and/or maneuverability affects motor control strategies can provide insight on moving about safely in an unpredictable world. Stability in human movement has been well-studied while maneuverability has not. Further, a tradeoff between stability and maneuverability during movement seems apparent, yet has not been quantified. We proposed that greater maneuverability, the ability to rapidly and purposefully change movement direction and speed, is beneficial in uncertain environments. We also hypothesized that gaining maneuverability comes at the expense of stability and perhaps also corresponds with decreased muscle coactivation.

Materials and Methods

We used a goal-directed forward lean movement task that integrated both stability and maneuverability. Subjects (n = 11) used their center of pressure to control a cursor on a computer monitor to reach a target. We added task uncertainty by shifting the target anterior-posterior position mid-movement. We used a balance board with a narrow beam that reduced the base of support in the medio-lateral direction and defined stability as the probability that subjects could keep the balance board level during the task.

Results

During the uncertainty condition, subjects were able to change direction of their anterior-posterior center of pressure more rapidly, indicating that subjects were more maneuverable. Furthermore, medio-lateral center of pressure excursions also approached the edges of the beam and reduced stability margins, implying that subjects were less stable (i.e. less able to keep the board level). On the narrow beam board, subjects increased muscle coactivation of lateral muscle pairs and had greater muscle activity in the left leg. However, there were no statistically significant differences in muscle activity amplitudes or coactivation with uncertainty.

Conclusions/Significance

These results demonstrate that there is a tradeoff between stability and maneuverability during a goal-directed whole-body movement. Tasks with added uncertainty could help individuals learn to be more maneuverable yet sufficiently stable.

Citation: Huang HJ, Ahmed AA (2011) Tradeoff between Stability and Maneuverability during Whole-Body Movements. PLoS ONE 6(7): e21815. doi:10.1371/journal.pone.0021815

This week’s featured image comes from a paper by Frank DiMaio et al. entitled, Modeling Symmetric Macromolecular Structures in Rosetta3.

Most homomeric protein assemblies are symmetric and the authors of this paper use Rosetta 3 to implement “a general framework for modeling arbitrary symmetric systems.”  The figure above illustrates a variety of symmetry groups found in the Protein Data Bank.

From the abstract:

Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be modeled using Rosetta’s symmetric framework. We then describe how this symmetric framework is efficiently implemented within Rosetta, which restricts the conformational search space by sampling only symmetric degrees of freedom, and explicitly simulates only a subset of the interacting monomers. Finally, we describe structure prediction and design applications that utilize the Rosetta3 symmetric modeling capabilities, and provide a guide to running simulations on symmetric systems.