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PubPeer.com – an online conversation among peers

We have just learned about the website and blog PubPeer:  The Online Journal Club.  Founded in October 2012, the site’s goal is to “create an online community  that uses the publication of scientific results as an opening for fruitful discussion among scientists.”    Scientists may comment on almost any scientific articles published with a DOI or a preprint in the arXiv.

Although not specifically designed for discussion of scientific misconduct, many comments are about image integrity and other ethical issues.  The site now receives 10-50 comments a day.

 PubPeer joins several other sites devoted to conversations about ethical publication.

A Model For Microscopy Labs

On May 22, 2013, the Core Microscopy Facility at the University of Indiana at Bloomington held an all-day workshop on image processing and analysis.  Approximately 120 people from all levels of academic science at the university attended, surely one of the largest events at a university on these issues.  Further, the workshop has several lessons for the science community on how to engage researchers in the major issues of digital image technology and integrity.

In the morning sessions, faculty members first gave presentations and led discussions of key topics in image processing such as principles of image quantification and basic digital image quantification.  See the agenda with links to presentation slides here.  In the afternoon, graduate students gave short research talks involving image process and quantification.  Then the final four hours was a presentation on issues and emerging standards in the integrity of science image data, followed by workshop sessions on basic image processing and basic image quantification.  (The session on image integrity was presented by our own Kirsten Miles, who provided support as well for the workshop sessions.)

The Indiana event has several lessons that can be successfully applied to other workshops and sessions devoted to these increasingly important issues in science.

  • Key was the emphasis on the use of data images in current research on campus, followed by  using appropriate techniques, retaining the appropriate metadata on the capture and manipulation of images, and the importance of understanding wider issues of maintaining the integrity of research images.

  • A second factor was the engagement of researchers at all academic levels, so that graduate students could hear issues from a wide range of fields as they discussed the use of images.

  • Finally, including hands on experience helped to solidify the connections between the issues and the details of conducting research in this environment.

We think that similar seminar-workshops can be  an effective method for other universities, and research institutions, especially including microscopy labs, whether for 120 as at Indiana or in smaller department settings.

Research ethics: Thinking differently across cultures

In an April post to this website, we commented on ORI’s video on common concerns that arise in research labs with international postdocs.  That video illustrated ways that communication issues are often barriers in the international environment of scientific labs.  Along with language issues, cultural perspectives add complexity to conveying information, and the more sensitive the subject, the more difficult the task of conveying ideas and the more likely that misunderstandings will arise.

A resource for thinking about these issues is The Geography of Thought, in which Richard Nisbett discusses studies done on cognitive thinking in various cultures.  Although the book focuses on Western and Eastern cultures and societies, the effort to understand the cognitive process is also useful in understanding differences between all groups.  One reviewer pointed out that the research in the book challenges the assumption that thinking is the same across all cultures.

This book, like the video described in the April post, does not focus specifically on issues of responsible conduct of research or of image integrity.  Nonetheless, it sets in context the complex nature of interactions and ideas across cultures.  We need to understand more than language differences to have clear communication on matters of research and especially ethics.

Just as science is global, so must the reach for research integrity be across cultures.

Images and retractions: A rising trend

John Kruger of the federal Office of Research Integrity tackled tough and important
questions about retractions—and especially retractions involving
data images—in the December 2012 ORI newsletter article. He posed three
questions:
• What is the scope of the retraction problem?
• What factors contribute to the rise in the retraction trend?
• Based on the answers to the first two, are there tangible
measures (beyond talk and exhortation) that various
constituencies can do to combat this trend?
Throughout the article he deals with problems of data images.

He observes that the “most notable shift in allegations of misconduct over
the past decade has been the increase in the number of ORI cases that
involved questioned images” and goes on to discuss what the rise of
retractions in general and those involving images tells us about the
nature of research misconduct.

Link to article http://ori.dhhs.gov/images/ddblock/dec_vol21_no1.pdf

ORI’s new video about international postdocs

The Office of Research Integrity (ORI) has created video scenarios about common concerns that international postdocs and their U.S. colleagues face in working collaboratively in research laboratories.  Some of the videos deal with communications challenges while others deal with everyday problems with visas, finances, and  the details of studying and conducting research in a foreign culture.

Although the series does not directly address research integrity, it is clear that communication issues are often barriers to productive research work.  If problems with culture compromise communication between postdocs and mentors about ordinary work issues, they affect even more the mentor’s ability to convey expectations about the complex issues of research integrity.    In our experience from questions following seminars, and  consultations, cultural differences can easily lead to miscommunication and errors in research ethics, and there are few resources for either party when attempting to resolve the outcomes.  This video is a needed beginning to a long overdue dialog.

The videos are available at http://ori.hhs.gov/mentoring-international-post-docs

 

A four-day conference in April, 2013 Reassessing Research Integrity, co-produced by the Office of Research Integrity and Johns Hopkins University focused on issues of responsible conduct of research (RCR).  Leaders in the field of research integrity examined  the state of and future direction  of RCR, including such questions as what should be measured in the evaluation of the RCR.

This timely conference occurred a month before the Third World Conference on Research Integrity in Montreal,  which “will focus international attention on research integrity, responsible conduct of research, and publication of research.  Attendees will have opportunities to learn the current state of worldwide progress on research integrity, discuss new challenges and emerging topics, and help shape national and international responses.”

 We hope that these conferences will generate insights and concrete suggestions for dealing responsibly with digital images in science research and publication.

How much should a retraction tell us?

Would the science record be better served if we were able to see falsified data images from retracted papers to better understand the errors?   In late November 2012, the U.S. Office of Research Integrity (ORI) sanctioned University of Kentucky researcher Eric Smart, PhD, after determining that he had falsified or fabricated 45 figures in 10 published articles (plus grant proposals). Most were images of Western blots. Thomsen’s Scientific Web of Knowledge reported that “some of [them] were cited more than 100 times.” How does this affect the science record?

Entering the dialog

 

We welcome you to our redesigned website.  We hope you will find these features useful:

  • a moderated comment section
  • articles presented in a shorter format that can be expanded by the reader.
  • icons to distinguish between downloadable files, direct links, presentations, and other options

What does a retraction tell us?

Retraction Watch has been a powerful partner in the examination of falsification in the published record, doing the hard work of gathering retraction notices and categorizing them, generating data from these retractions, highlighting research about retractions, and collecting wide-ranging comments, all in one readily available blog.

ORI’s “The Lab” – Avoiding Research Misconduct

Each university that uses funds from the Public Health Services,  must provide training in the Responsible Conduct of Research (RCR).   The Lab is a new interactive movie developed by the U.S. Office of Research Integrity (ORI), that allows viewers to experience an ethical challenge involving research as one of four characters.  Set in an active lab with a tier of graduate students,  post docs, PIs and a research integrity officer (RIO), the story line follows each character as a case of data-image falsification is discovered and followed through by steering the chosen character through a series of choices and outcomes. 

Analyzing the Blot

Last week we looked at the post processing results in a Biotin Turnover blot, trying to assess the potential for error.   Check the following slide (Figure 1), to which a Gradient Mapping tool in Adobe Photoshop has been applied.  There should be no crisp edges on such a blot.  The absence of soft edges and any background detail of these blots indicates some manipulation, suggesting that further questions should be asked of this image, and the original presented for review.

Whether the missing background detail is considered important or affects the research outcome,  manipulations such as this are usually considered inappropriate, and at the very least  must be documented to allow honest peer review lest they invalidate the data and compromise the researcher, institution, and the research itself.

We include a portion of the original data-image (Figure 2), also with the Gradient Mapping tool applied. Retaining the original offers the researcher, institution and journal the opportunity to make transparency possible, correct and salvage the research.

Figure 1

Figure 2

 

Annual conferences increasingly include topics in digital image integrity.

Microscopy & MicroAnalysis Arizona conference

 August 3-7 at the Connecticut Convention Center in downtown Hartford, CT.

 

 

CSE Annual Meeting

Communicate Science Effectively: The World Depends On It!

May 2-5, 2014

San Antonio, Tx

Links for relevant topics from 2013 will be posted soon:

Links for relevant topics from 2012:

The role of journal editors and publishers in educating authors and reviewers about publication ethics.

 

Demystifying  Scientific Misconduct Issues through the Instructions to Authors

 

Link to Panel Discussions from 2011 relating to Digital Image Integrity

Link to Panel Discussions from 2012 relating to Digital Image Integrity

What is Image Falsification;  A proposed schema:  Falsification Table

“Changing Standards for Manipulation of Digital Images in Biomedical Articles”: Poster presentation of research on author instructions at 446 biomedical journlas.  Presented at 2011Council of Science Editors Annual Meeting.  CSEPoster2011

Four Best Practices in Image Integrity for Journal Editors: From panel discussion at the Council of Science Editor’s annual meeting.    Journal-BestPractices

Data Management for Digital Images: Precis overview of the issues involved in image integrity for researchers in biomedicine; covers publication and data management; appropriate for use in seminars and presentations: Digital Image Data Management

ORI Forensic Tools for Quick Examination of Scientific Images and Plagiarism. Tools developed by the federal Office of Research Integrity for examining digital images. http://ori.hhs.gov/tools/

Books and Publications on Image Data Processing in Biomedical Science.

John Russ:  Books on Digital Image Data Processing

Doug Cromey:  Website, Online Learning Tool,  Ethical Guidelines,

Jerry Sedgewick:  Book on Scientific Imaging in Photoshop

Timeline:  Prominent events in issues digital data- images:  DigitalImageTimeline