I’ve recently begun to write a few posts for the Michigan IT Newsletter, and will be reposting those here once they are released. This is part of my grand scheme to force myself back into blogging! Life’s crazy, so things are running late. Here’s the first piece I did for them, which was posted at https://michigan.it.umich.edu/news/2017/12/04/cool-toys/
The Cool Toys Conversation group started out as one of the many spaces on campus where people share cool tech they’ve discovered for education, research, clinical care, outreach, and productivity. Since then, it’s evolved to become more of a community of practice around emerging trends and technologies, but without ever completely giving up the original sharing of cool toys. Some of this happens in monthly meetings, usually at noon on the last Tuesday of the month (moving to BlueJeans only in January 2018), some in our email group cooltoysconversations@umich.edu (you may request to be added even if you aren’t part of UMich), and some on social media with the hashtag #cooltoysu. The scope of the resources shared is broad, as fits the scope and range of activities and interests across the university, with some of them focusing on pretty hard core tech and others focusing on links or apps or tech to do something interesting in another topic.
Here are just a few interesting things selected from the hashtag. Highlights include: augmented reality, virtual reality, artificial intelligence, mobile apps, games, and productivity tools.
Seeing AI is a free app that narrates the world around you. Designed for the low vision community, this research project harnesses the power of AI to describe people, text, and objects.
A fun little “photo” app, Mirage allows you to create 3D audio/video/emojis/doodles augmented reality content with your phone. You can also browse other people’s content, but right now, since it’s fairly new, you may not find a lot of content where you are. Here’s a nice introduction to augmented reality from Hackernoon.
The Evolution of Trust is a clever online game/interactive simulation that explores the mathematics of trust, distrust, and miscommunication through various character types.
This online checklist tool helps you choose where to publish your research. In their words: “Sharing research results with the world is key to the progress of your discipline and career. But with so many publications, how can you be sure you can trust a particular journal? Follow this check list to make sure you choose trusted journals for your research.”
Index touts itself as an alternative to Evernote, or as a one-stop-shop organizational tool. In their words: “Index is the easiest way to capture your ideas. #tag links, notes, files and anything from anywhere, and Index will organize everything into searchable, shareable #collections. Just promise you’ll use it for good and not evil.”
Wow, wow, wow! What an AMAZING day! I’m at the Medical Library Association Annual Meeting, and trying to get to as many of the systematic review events as I can. Today is the first full day of the conference, and it was a jackpot — PRISMA for searches, a session on EBM/EBHC training, and a session on systematic review services. Lots of posters, too, but I haven’t had a chance to go look at those yet.
I tweeted a screenshot of the special session on systematic reviews this afternoon.
I saw an event in the program, something about PRISMA standards, so I thought I’d poke my head in. When I poked my head back out later, I could not stop talking about it. The gist of it is that PRISMA, whom most medical librarians and journal editors know of as providing standards and guidelines for how systematic review data should be reported, are branching out. Me, I’ve been watching with excitement the various PRISMA extensions that have been being added recently. Thsee include standards for reporting protocols, meta-analyses, patient data, abstracts, and more. Well, it turns out there is a pretty substantial team working on developing PRISMA guidelines for reporting search strategies. This is pretty exciting for me! And somehow, I had missed it until today. The group today was opening the results from the original team to a broader audience and asking for reactions. They had come up with 123 guidelines, which they narrowed down to 53, and then we broke into four subgroups (search strategy, grey literature, documenting results, database characteristics) brainstorming about how to narrow down even further, into truly actionable points. I tell you, this is a group to watch.
Some of my favorite lines:
“I did this review according to PRISMA standards.” “You can’t. PRISMA is a ‘reporting’ standard, not a ‘doing.'” (Margaret Foster)
“The faculty are asking individual students to do something that is essentially a team sport.” (Ana Patricia Ayala)
“Cochrane says, ‘You will not limit by language.’ PRISMA says, ‘You will report any limits.'” (Margaret Sampson)
Here is just one of the flip boards from the conversation to whet the appetite of the systematic review methods nerds.
SYSTEMATIC REVIEW SERVICES
Later in the day, there was a complete session devoted to systematic review services in medical libraries. Yes, this is the same one from the tweet earlier in this post. I was dashing in late from the poster session, so I missed the beginning of the presentation on training needs by Catherine Boden and Hellsten. I was disappointed, because they were citing many wonderful articles I wanted to look into later. I’m sure glad the slides are in the online MLA system, because I’ll have to go find them! Being late also means I didn’t get any photos from their talk. The most provocative concept I pulled from their talk was the idea that systematic reviews are actually “a constellation of related methods rather than a single methodology.” So elegantly put, and so true. It’s a helpful way to reframe how we think about what we do, and is supported by the same drive that is motivating the various PRISMA extensions mentioned above.
Sarah Vistinini presented for her team on scoping reviews, their similarities to and differences from systematic reviews, and the value of being included in the ENTIRE process (which she cleverly described as giving a “better appreciation of all the moving parts.”). Sarah showed some very cool evidence mapping (see pic above), dot prioritization, and more. There were glowing recommendations of the 2005 Arksey and O’Malley article on scoping review methodologies and a wonderful link to all the references: bit.ly/visin-2016.
Kate Krause presented for a team primarily from the Texas Medical Center Library about their efforts to launch a new systematic review service, and the resulting “opportunities” (wink, wink, nudge, nudge, we all know what THAT means). The moderator described their presentation as a “collective therapy session,” which generated considerable amusement among the audience. The most important parts of her talk were, of course, the solutions! They require systematic review requests to come through an online request form, which gives them solid statistics and allows them to manage workflow better. They are using a memorandum of understanding (MOU) with faculty to facilitate a discussion of the duties, timeline, and expectations. They are providing different levels of service, with some interesting requirements for the highest level of service (like, if I understood correctly, mandatory five face-to-face meetings with the project lead). One curious nugget for which they are seeking the citation was heard at a prior MLA meeting — the more face-to-face meetings you have with a systematic review researcher, the more likely they are to actually publish on the project. They have a wonderful-sounding information packet given to new SR researchers, but I didn’t catch everything in it. I did catch bits (Cochrane timeline? list of other review types?) that make me want to know more!
Lynn Kysh and Robert E. Johnson presented a talk with the awesome title: “Blinded Ambition, misperceptions & misconceptions of systematic reviews.” They discussed some of the challenges to co-authorship and publication being assumed as an automatic good for librarians working on systematic review teams. Lynn described constraints to completing publication, and described times when librarians there removed their name from articles being submitted for publication because of methodological concerns. Very very interesting content. Well, and then there were the forest plot kittenz.
Last but not least, Maylene Kefeng Qiu represented a team that did the bulk of the work for a rapid review in … three weeks. Intense! Much of the challenge centered around timing, expertise available, staffing, workflow, and management coordination. The librarians on this team actually did the critical appraisal of the articles before giving the final dataset to the faculty member writing the review. My favorite line from her talk was, “Stick to your inclusion/exclusion criteria.” Their slide deck had so many wonderful images illustrating parallels and differences between systematic reviews and rapid reviews. I hope it’s ok if I share just one.
Why Ada Lovelace Day matters, asks the Guardian today. Usually people celebrate by highlighting famous women scientists. I asked myself, what about right here, right now? What are women scientists and inventors doing at the University of Michigan?
I figured the best way to find out was to go through the UM Tech Transfer database of Available Technologies for licensing. I skimmed the most recently deposited 100 inventions, looking for women. I found inventions in education and healthcare (even new cell lines!). I also found women inventing new batteries and biosensors, researchers working in engineering and code and physics, and even, yes, gamma rays! Some were prolific with MANY inventions listed recently. Most had one or two. They are ALL fabulous. And I am proud to say I know some of them personally. Take a look. See what cool smart women are inventing here. And remember: The sky is the limit!
There has been a lot of science communication (#SciComm) action on Twitter recently centering around what does life look like for real scientists. I have a head start on this because when I was a little tyke, my dad dragged me into the lab with him and told me things like to watch the door of the High Wind Velocity Testing Lab so that the tornado didn’t get out while he was working on his mass spectrometer lithium sample testing. What can I say? I was gullible. So all those fun lifestyle pithy tweets will come in a later post, but for today, here is proof of presence of laboratories on Twitter. For the record, there are a lot more of these in each category, because Twitter’s search limits don’t return complete results for matches to the search criteria. Basically, that means I found a lot of these by browsing, when I should have been able to find them through search. I hope this is a useful resource. Enjoy!
Do we need another coffee house? The amenity space and the evolution of neighborhoods
César A. Hidalgo, Elisa E. Castañer
PDF: http://arxiv.org/pdf/1509.02868v1.pdf
Soundbite: “Neighborhoods populated by amenities, such as restaurants, cafes, and libraries, are considered to be a key property of desirable cities. … Finally, we use the Amenity Space to build a recommender system that identifies the amenities that are missing in a neighborhood given its current pattern of specialization.”
Liberating language research from dogmas of the 20th century
Ramon Ferrer-i-Cancho, Carlos Gómez-Rodríguez
PDF: http://arxiv.org/pdf/1509.03295v1.pdf
Soundbite: ” Those tenets can be summarized as a belief in the existence of word order constraints that cannot be explained by evolutionary processes or requirements of performance or learning, and instead require either (a) heavy assumptions that compromise the parsimony of linguistic theory as a whole or (b) explanations based on internal constraints of obscure nature.”
Interesting: “We submitted our commentary to PNAS but it was rejected. We hope that the availability of our submission helps to liberate language research from dogmas of the 20th century”
Combining exome and gene expression datasets in one graphical model of disease to empower the discovery of disease mechanisms
Aziz M. Mezlini, Fabio Fuligni, Adam Shlien, Anna Goldenberg
PDF: http://arxiv.org/pdf/1508.07527v1.pdf
Soundbite: “It is not unusual to observe a significant gene expression change in thousands of genes, the majority being a downstream, rather than the driver, effect (e.g. inflammation, drug response, etc) Additionally, and more importantly, there is a large heterogeneity in gene expression in cancer: many patients within the same subtype will appear to have an abberant expression. These variations are of unknown cause.”
Using Genetic Distance to Infer the Accuracy of Genomic Prediction
Marco Scutari, Ian Mackay, David Balding
PDF: http://arxiv.org/pdf/1509.00415v2.pdf
Soundbite: ” In human genetics, decay curves could be used study to what extent predictions are accurate and thus to improve the performance of medical diagnostics for the general population. In plant and animal breeding, on the other hand, it is common to incorporate distantly related individuals in selection programs to maintain a sufficient level of genetic variability.”
Population genomics of intrapatient HIV-1 evolution
Fabio Zanini, Johanna Brodin, Lina Thebo, Christa Lanz, Göran Bratt, Jan Albert, Richard A. Neher
PDF: http://arxiv.org/pdf/1509.02483v1.pdf
Soundbite: “In most patients, the virus populations was initially homogeneous and diversified over the years, as expected for an infection with a single or small number of similar founder viruses (Keele et al., 2008). In two patients, p3 and p10, the first sample displayed diversity consistent with the transmission of several variants from the same donor.”
Soundbite: “Our reasoning proceeds as follows. Figure 6B indicates that diversity accumulates over a time frame of 2-4 years, i.e., about 1,000 days. Recombination at a rate of 10−5/bp/day hits a genome on average every 100 bps in 1000 days. Mutations further apart than 100bps are hence often separated by recombination and retain little linkage consistent with the observed decay length in Figure 7.”
Inadequate experimental methods and erroneous epilepsy diagnostic criteria result in confounding acquired focal epilepsy with genetic absence epilepsy
Raimondo D’Ambrosio, Clifford L. Eastman, John W. Miller
PDF: http://arxiv.org/pdf/1509.01206v1.pdf
Soundbite: “Because the authors could not induce focal seizures by FPI, they ended up comparing absence epilepsy in their controls with absence epilepsy in FPI rats, and concluded that they look similar. They also used inappropriate epilepsy diagnostic criteria that cannot distinguish between focal non-convulsive seizures and genetic absence epilepsy. Moreover, the authors failed to consider all literature conflicting with their conclusion, and surmised similarities between the absence epilepsy in their rats with the focal seizures we induce by rpFPI.”
Fractal Fluctuations in Human Walking: Comparison of Auditory and Visually Guided Stepping
Philippe Terrier
PDF: http://arxiv.org/pdf/1509.01913v1.pdf
Soundbite: “[B]ecause it can be assumed that AC and VC mobilize the same motor pathways, they can probably be used alternatively in gait rehabilitation. The efficiency of VC to enhance walking abilities in patients with neurological gait disorders needs further studies. However, the high gait variability induced by VC might have detrimental effects, for instance, a lower dynamic balance. This should be taken into account in the development of VC rehabilitation methods.”
Identification and modeling of discoverers in online social systems
Matus Medo, Manuel S. Mariani, An Zeng, Yi-Cheng Zhang
PDF: http://arxiv.org/pdf/1509.01477v1.pdf
Soundbite: “We develop an analytical time-aware framework which shows that when individuals make choices — which item to buy, for example — in online social systems, a small fraction of them is consistently successful in discovering popular items long before they actually become popular. We argue that these users, whom we refer to as discoverers, are fundamentally different from the previously known opinion leaders, influentials, and innovators.”
Time-aware Analysis and Ranking of Lurkers in Social Networks
Andrea Tagarelli, Roberto Interdonato
PDF: http://arxiv.org/pdf/1509.02030v1.pdf
Soundbite: “Our goal in this work is to push forward research in lurker mining in a twofold manner: (i) to provide an in-depth analysis of temporal aspects that aims to unveil the behavior of lurkers and their relations with other users, and (ii) to enhance existing methods for ranking lurkers by integrating different time-aware properties concerning information-production and information-consumption actions.”
Main topics covered were spatial tracking, 3d virtual reality, optical motion capture, holography, optical tracking, acoustic motion tracking. During the Q&A, a major diversion (at least for me) was “Sim-sickness”, in which 3d immersive virtual reality (think of Oculus Rift & Google Cardboard) make folk nauseous, some to the point of actually tossing their cookies. There are videos in Youtube. I don’t need to find them for you. Fun topics mentioned included virtual augmented reality, Hololens, holography for teaching anatomy, biomechanics, cultural preservation, robotics, aerospace engineering, body slicing with the Kinect, body tracking, and DIY arduino acoustic sensors and automated echolocation. There were lots of tips and tricks, what works and what doesn’t. Many interesting links in the Storify below.
Within minutes after the previous post went live, I was contacted on Twitter by another patient advocate, Willow, also known as Serious Skeptic. She* expressed another wide area of patient concerns about clinical trials, ones that were new to me, and which deserve representation in this post, even if they aren’t from the official public #PatientChat event. Because Willow has a locked account, and I respect that, I asked her permission to share the links and the essence of some of her private tweets. The following is posted with her consent, but represents my words and distillation of what I learned from her.
Willow was concerned about ethical breaches in clinical trials, especially:
– trials that are designed specifically to promote use of a drug (marketing);
– trials that suppress undesired findings or which fail to publish or share negative findings;
– trials that don’t share their data;
– trials that don’t make relevant or useful findings available to all trial participants.
I had the impression she’d kind of like the research studies to also notify trial participants of publications that do result from their participation. I know, I do, myself, and being a medical librarian, I take notes on my research participation, the names of studies, the names of the PI, and I stalk their publications for years until I see the research in which I participated. I often ask to be alerted, and usually received some sort of polite demurral, and nothing else. I wish they had an email list I could just subscribe to for alerts from their lab.
Anyway, when Willow described clinical trials that are actually marketing ruses, my reaction was, “Whoa! Not really? Doesn’t the IRB process protect against that?” Evidently not. The concept she was describing most is called seeding trials. Here are some links she shared with me, or quotes and/or resources from those articles.
A physician is invited by a pharmaceutical company to take part in a study involving an FDA-approved drug. The physician’s responsibilities entail prescribing the drug for patients and then completing three questionnaires about each patient’s experience with the drug. The questionnaires are quite short and will take about 20 minutes each to complete. The sponsor will pay $1,500 for each completed questionnaire. The physician is very interested in participating because it looks like a great way to increase practice revenues.
The public has lacked convincing documentary evidence of a long-suspected drug company practice: promoting a new drug by sponsoring a randomized trial in which participating physicians use the drug as they follow the trial protocol. This practice—a seeding trial—is marketing in the guise of science. The apparent purpose is to test a hypothesis. The true purpose is to get physicians in the habit of prescribing a new drug.
Seeding trials are designed to appear as if they answer a scientific question but primarily fulfill marketing objectives. Kessler and colleagues (3) portrayed seeding trials as “attempts to entice doctors to prescribe a new drug being marketed by the company” while the company puts its product in the hands of practicing physicians, hoping that the experience of treating patients with the study drug and a pleasant, even profitable, interaction with the company will result in more loyal physicians who prescribe the drug (4).
“Merck’s marketing division handled both the scientific and the marketing data, including collection, analysis, and dissemination; and Merck hid the marketing nature of the trial from participants, physician investigators, and institutional review board members.”
The maker of Neurontin disguised an effort to promote the anti-seizure drug to physicians as a clinical trial and failed to inform involved physicians and patients, according to a new analysis published Monday in the Archives of Internal Medicine journal.
Seeding trials are an unethical, dangerous way to market a product. The IRB needs to become a better-equipped committee that can identify seeding trial practices from honest clinical trials, and the FDA needs to demand more transparency from companies sponsoring clinical trials, to better protect public health and the integrity of clinical research.
Because of the risks and distrust generated by the practice of seeding trials, Willow suggested that it might be wiser to wait to test new meds on your own body until they’ve been out for a few years, unless you are so ill that you have no alternatives. Now, of course, if everyone does that, then there are NO NEW DRUGS because we can’t test them! And that is a situation in which we all lose.
My own choices? I take risks that I won’t ask others to take. I try to be informed about the risks I take. When I participate in a research study, I ask a lot of questions, and I pay very close attention to my body. If my canary-in-the-mine body complains, I withdraw from the study. Well, I would. So far, I’ve never actually needed to withdraw from a research study, but I have ceased taking actual FDA-approved meds prescribed for me that my body couldn’t handle. I’m hoping that the #bioethx chat group will pick up on this topic next, and hoping they can find an invited speaker to talk about what IRB committees have done and are doing to try to address this, to build confidence in medical research.
* I am assuming Willow is a she because I interpret the name Willow as a female name. I have no knowledge or confirmation of that, and it isn’t any of my business anyway. I am using the female pronoun to describe her simply for convenience, and intend no disrespect.
ADDENDUM TWO, June 13
A few clarifications and corrections from the ever thoughtful Willow.
Willow feels my concern about limiting drug discovery isn’t valid, since seeding trial occur for drugs that are already patented. My concern is that fear of seeding trials will scare some participants off of drug trials entirely. Drug discovery trials are legitimate, but the problem remains that it can be difficult to distinguish discovery trials from seeding trials, since the physicians and patients are both kept in the dark by the drug manufacturers.
Recently someone asked me a question about “online informed consent.” I think they were remembering my having mentioned John Wilkin’s stuff, a.k.a “portable legal consent” or “portable informed consent.” These and “online informed consent” are … related concepts, but perhaps not as closely related as some might think. Just to complicate matters, people are also using jargon like “dynamic consent” and “broad consent” to mean things related to both of these, but which are not quite the same. There are also people trying to get the phrase “informed consent” converted to “educated consent” as possibly being more meaningful. In this post, I will try to sort some of this out, but I’m no kind of expert in consent, and this is complicated, really REALLY complicated.
First, the short-short explanation. Portable informed consent (PIC) usually is part of online informed consent, but online informed consent (OIC) is rarely portable. Riiiight. OK, a step backwards.
PORTABLE CONSENT
The idea of portable informed consent is (in my mind, at least) analogous to Creative Commons licensing for your own creative works, except that it applies to your own health data. Actually, the idea of this really came from people wanting to share genomic data. You walk through an online informed consent process, agree to which version of a license you are comfortable with, and then when you share your data in a secure repository, that license or consent agreement is attached. People who want to use your data, must agree to follow those predetermined restrictions. Researchers who don’t agree, aren’t allowed to see your data, only data from other folk who agree to whatever guidelines they need for their project. Researchers who don’t follow the rules will be denied access to all of the data.
Personal Genomics
Genomics is basically mapping the genome. Personal genomics is doing this for a person in particular, rather than a species or condition or other collective group. Some people get involved in exploring personal genomics because of simple curiosity, but many are driven by long standing medical challenges without any easily identifiable solution. Some people are terrified at the idea of what they might find out. Others are concerned that the data will result in problems with jobs or insurance. Those urgently seeking help for health problems often want to share and find others who might have insights into their problem. OpenSNP and the Personal Genome Project are two examples of places where people share their genomic data. By making their data public and consenting to its use by researchers, they are hoping to support solutions not only for themselves but for others like them. Making sure that consent is LEGAL is essential for supporting future research. One great example of this is Jay Lake, who contributed his whole DNA sequencing data and that of his tumor, making possible research on new treatments that came too late for him. It’s a powerful story.
ONLINE INFORMED CONSENT
Online informed consent is a great deal simpler, in that it mostly takes the usual informed consent process (reading forms, signing forms, filing forms) and puts it all into an online web-based interface in a secure system. But, PIC gets more buzz in the popular press and media, while OIC gets more attention from within the hallways of day-to-day research communities. PIC grew out of work with personal genomics and is designed to make data sharing simpler, research more open, and problem solving more dynamic, all while still being responsive to issues of privacy and ethics. OIC is a tool designed to make the IRB management simpler for researchers.
DYNAMIC CONSENT
Dynamic consent is closer to portable consent, but grew more out of tissue and biobanking contexts, rather than data or genomics. Dynamic consent has a lot of nitpicky little options, and allows you to change your mind over time. That’s why it’s dynamic — things keep changing. Right now, dynamic consent is used primarily for what happens to parts of your body that are removed from your body while you are alive, and used for various medical purposes. Sometimes those purposes involved throwing what wasn’t used in the nearest incinerator, but sometimes there is something interesting and the doctors or researchers want to keep a sample for future use.
Biobanking
Now, remember, I’m drastically oversimplifying here. There are many more situations and options that come into play. Healthcare researchers have come to realize that we often don’t know where the next interesting possibility will come from, which is part of why biobanking is becoming more important. A biobank is sort of a library of tissues (meaning parts of human or animals or plants). Biobanks are often focused on a certain type of tissue or condition. Many biobanks collect tissues for a particular kind of cancer, or conditions like Parkinson’s, Alzheimer, autism, etc. Others may focus on a particular organ, like brains, breast tissue, lungs, or genome. In book and journal libraries, the librarians have traditionally spent a lot of time trying to select just the most important material on their special topics, but over generations, we’ve found the most desired content is as often as not the parts that were considered cheap and unimportant at the time, which are now expensive and hard to find, because no one kept them. Some of the same issues are coming up with biobanking, but complicated by the challenge of each and every sample being unique (although there might be copies of cell lines). At least with books, if one library lost theirs, another library might have a copy. Part of the idea of all these different kinds of consent is to try to maximise the number and diversity of samples that can be preserved and made accessible to future researchers.
PRESUMED CONSENT
Presumed consent also related to tissues, actually organ donation, but after you are no longer alive or aware enough to give or change your consent. Where I live, you have to register as an organ donor. If you don’t, and are in a fatal accident, no one is allowed to use your organs as transplants to save the lives of other folk who need new organs to survive. That isn’t how it works in all countries, though. In some countries they have “presumed consent,” where the assumption is that organ donation is fine with you as long as you don’t say NO beforehand. So, opt-in vs. opt-out. That’s the main difference. Sounds simple, doesn’t it? But people have incredibly strong feelings about both of these options.
BROAD CONSENT
Broad consent is probably the messiest of all of these. Just look at these article titles!
You can just feel the tensions rising as you read through the list. It is obvious that this is not an area of consensus. And what can it possibly mean to consent mean when there isn’t an agreement about what consent is?
“Broad consents are not open nor are blanket consents. To give a broad consent means consenting to a framework for future research of certain types.” Steinsbekk KS, Myskja BK, Solberg B. Broad consent versus dynamic consent in biobank research: Is passive participation an ethical problem? European Journal of Human Genetics (2013) 21:897–902.
Broad consent attempts to make a best guess of what might be needed by the researcher of the future, and to try to get the individual to agree to a flexible use and reuse of tissues, samples, or data. As you can tell from the titles above, “broad consent” tends to refer to tissues rather than data, but when you get down to brass tacks, all of these could theoretically apply to a wide variety of donated content.
CLOSING THOUGHTS
The idea behind all of these myriad forms of consent is knotted into the dynamic between the rights of the individual and the needs of the community. Without research, we stagnate and die, literally, since solutions cannot be discovered for the aches and pains and problems that lead to increased mortality and reduced longevity. As a community, as a species, we don’t make progress without sharing. At the same time, the goal is to reduce harm to individuals, and forcing people to ‘consent’ against their will causes harm. I’ve known people who practically had a nervous breakdown at the idea of becoming an organ donor, the idea of part of them living on in someone else distressed them that deeply. I know others who fear what could happen to them if their genetic data fell into the “wrong hands.” I’m not one of them. I’m a registered organ donor, and I donated my genomic data to OpenSNP. But I still respect the emotional pain that would be caused by forcing consent. It’s an ethical dilemma which our society is obviously still working to solve. While looking at background material for this post I stumbled across two phrases that seemed to express some of the challenges well: “From Informed Consent to No Consent?” “Open Consent for Closed Minds.”
“I’m proposing … that we reach into our bodies and we grab the genotype, and we reach into the medical system and we grab our records, and we use it to build something together.” “I hate [the] word ‘patient.’ I don’t like being patient when … health care is broken.” John Wilbanks
In part one of this post on using research tables and figures in social media, the focus was on, “Let’s find something that isn’t copyrighted, and just use that, because we know that will be safe” (sort of). But sometimes what you want is new, not old, and from a copyrighted publication, not something open access. When that happens, what do you do? Can you still use it?
It started with Andrew’s question, but he sure isn’t the only person asking!
The answer is (again) it depends. And, to be honest about it, the “it depends” is a whole lot messier. The idea of “fair use” makes the idea of “copyright” look like child’s play. As usual, I am not a lawyer (IANAL), so take the information here at your own peril, and don’t go quoting me to your own lawyers. That said, I’ll be giving references to a lot of information that IS from lawyers, so refer people to the original sources whenever possible!
This is a question that comes up a lot. Even more often, I suspect, it doesn’t come up at all when it ought to, because someone assumed it was alright and didn’t think about it more deeply. I may have even done that myself (and I’m afraid to go back and look too closely at my blogposts).
WHY ARE FIGURES DIFFERENT?
The shortest version I’ve found explaining why “fair use” for research figures from articles are DIFFERENT from other images is this snippet from Scholarly Publishing @ MIT Libraries:
That’s the gist of it. Applying “fair use” to reusing content from a larger work depends on four factors:
1. The purpose and character of the use, including whether such use is of commercial nature or is for nonprofit educational purposes
2. The nature of the copyrighted work
3. The amount and substantiality of the portion used in relation to the copyrighted work as a whole
4. The effect of the use upon the potential market for, or value of, the copyrighted work
US Copyright Office: Copyright: Fair Use: http://www.copyright.gov/fls/fl102.html
The point from MIT regards the 3rd factor, “amount and substantiality.” If the image is considered a work independent of the article, then copying it is copying a complete work instead of a percentage, and that is not OK. If the figure is considered a fair distillation of the complete article, then that could be considered equivalent to copying the whole article. To be allowed to use something under “Fair Use” claims, it is recommended to meet all FOUR of the four factors: no money, factual or data-focused content, a tiny bit of it (insignificant amount), and little to no impact on sales of the original. If any of those are iffy, you’ve got a problem.
In a recently published article in the research journal CIRCULATION, the editors of the journal attempted a randomized controlled trial to test the success or failure of social media in promoting readership of articles. How did they do this? Well, they posted randomly selected articles to Facebook and Twitter, but a bit part of how they posted included (you guessed it!) FIGURES. For exactly the same reasons we are NOT supposed to use them, technically speaking.
“However, our social media postings were comprehensive in that they focused on the main message of the article and included a key figure from the article. Thus, it is possible that social media users did not find it necessary to access the full article and therefore experienced increased awareness of the article but not online access of the primary source. This raises the possible concern that social media could reduce the potential reach of original published research as demonstrated by altmetrics.” Fox CS, Bonaca MA, Ryan JJ, Massaro JM, Barry K, Loscalzo J. A Randomized Trial of Social Media From Circulation. Circulation 2015; 131: 28-33. http://circ.ahajournals.org/content/131/1/28.full
In that test, it was the editors of the journal posting the figures, and even then, they questioned the utility and benefit. A big part of the question, which they highlight in that snippet, was whether it is better to have awareness of the article and its findings, or actual readers. This assumes that people who click through to the article actually read it, which is itself questionable.
So, that’s the short view. Just to round it out, here are a few more pieces relating to this topic.
WHAT IF I DRAW MY OWN FIGURE?
A common recommendation is to redraw the figure. Annoying, time-consuming, but supposedly legal, most of the time, as long as the content is primarily data (since data can’t be copyrighted). Indeed, this is recommended by many experts as THE solution to this problem.
Q: I want to use a figure from another thesis or dissertation from my group. Do I need to ask permission?
A: “Usually. The student who wrote the thesis or dissertation owns the copyright and must be asked for permission. Figures are generally considered works in and of themselves and do not usually constitute a small portion of the work. See “How to Use Copyrighted Materials” for more information. If, however, the figure is a simple representation of data, you may not need permission. Data cannot be copyrighted, so non-creative ways of representing the data are generally considered fair use.” Copyright Frequently Asked Questions | Michigan Tech Graduate School http://www.mtu.edu/gradschool/administration/academics/thesis-dissertation/copyright/faq/
It depends on who you ask, though. I don’t know the court law on this, but I’ve found recommendations on both sides. Overwhelmingly, what I’ve found it people recommending to redraw the figure. And then I found this, from the Association for Computing Machinery (ACM).
WHAT IF I JUST GO AHEAD AND USE IT? NO ONE WILL CARE, RIGHT?
Another common approach (probably the one I am most guilty of myself) is to assume that you aren’t important enough to bother with, or that no one will notice you did it, or that if they do notice all that will happen is they ask you to take it out. I haven’t even attempted to figure out how often this happens. The gist of the idea is that, while it may not be strictly legal, it IS fairly common practice, and can be a win-win for each side (as long as you are saying nice things, anyway).
The “Win-Win” Argument:
“Most authors will probably be happy that their results are disseminated, and reuse is likely to lead to more people reading the full paper and citing the work.”
Martin Fenner. Why can’t I reuse these tables and figures? Gobbledygook (PLoS Blogs) 2010. http://blogs.plos.org/mfenner/2010/09/30/why-cant-i-reuse-these-tables-and-figures/
The “Standard Practice” Argument:
“Posting figures from papers “was something we all did, all the science blogs, and I had been doing it since I started the blog. I always thought I was doing a public service, I wasn’t plagiarizing or claiming it was my own data.”” Andrea Gawrylewski. For blogger: A threat, then an apology. The Scientist May 2, 2007. http://www.the-scientist.com/?articles.view/articleNo/25066/title/For-blogger–A-threat–then-an-apology/
So, it’s fine, right? Uh, not so much. If you are doing this on a work related blog or for your organization, it is awfully risky, since they can be held liable, which is a real can of worms. If you are only doing this on your personal blog, and it is made clear that these are your words and actions and not to reflect on your employer, … it’s your decision.
WHAT IF THEY PULL OUT THE BIG GUNS?
There are publishers who have (or will) pull out the big guns. Yes, usually, even if they notice, they’ll just ask you to take it down, to “cease and desist,” but there is no guarantee. The best known case in science blogging of use of a figure gone wrong actually centered around a PhD student here at the University of Michigan, Shelley Batts, back in 2007.
“In short, I was threatened with legal action if I didn’t take it down immediately. I used a panel a figure, and a chart, from over 10+ figures in the paper. I cited and reported everything straight forwardly. I would think they’d be happy to get the press. But alas, no.” Batts, Shelley. When Fair Use Isn’t Fair. http://scienceblogs.com/retrospectacle/2007/04/25/when-fair-use-isnt-fair-1/
The blogosphere went WILD. Some of the issues brought up included that this was government funded research paid for by taxes; the “amount used” argument (since it was such a small fraction, not even a complete image); the stifling impact on science discourse; the chilling of public awareness and policy discussions; and heavily, the critical distinction between “fair use” and being granted permission.
“First, the blogger Batts did not go through the usual process to request permissions to use published material in advance. It is not clear that had this been done that she would have been refused and indeed permission may eventually be extended. … Of course, once the appropriately senior person at Wiley was involved, the situation was resolved. This is not a “win”. This is a “loss” …” DrugMonkey. “This figure is reproduced with permission of the publisher.” https://drugmonkey.wordpress.com/2007/04/26/this-figure-is-reproduced-with-permission-of-the-publisher/
It is easy to find posts about this, but the one that seems to have really tipped the balance was when BoingBoing stepped in.
“This is, of course, bullshit. Reproducing part of a figure in a critical, scholarly essay is so obviously fair use that it hardly bears discussion. Wiley’s lawyers know this. You and I know it too.” Doctorow, Cory. Wiley threatens scientists with copyright law – UPDATED. http://boingboing.net/2007/04/26/wiley-threatens-scie.html
Eventually, it all calmed down, when Shelley was “granted permission” to use the image by the publisher. Many expressed concern that this ended up muddying the waters, that this was and should have been respected as fair use, that the publisher should have acknowledged this was fair use, and that granting permission implies that permission was theirs to grant (permission that is irrelevant in the case of fair use). Shelley was happy – she wasn’t getting sued, and her original blogpost was able to stay (although I can’t find it now, and I don’t know why).
“I was so surprised that anyone would think I was doing science a disservice. Science blogs bring pedantic ‘ivory tower’ knowledge to a completely new audience that would probably never hear about it otherwise. But in the end, I’m glad it happened — and that the entire blogosphere howled.”
Moments in Medicine at Michigan, Summer 2007. http://medicineatmichigan.org/magazine/2007/summer/moments
But the University of Michigan lawyers stated that she had done nothing wrong to begin with. So. Clear as mud, eh?
“Maybe if we weren’t so worried about copyright, we’d be able to report on more research.” Dave Munger, op cit.
Varela-Lema L, Punal-Riobóo J, Acción BC, Ruano-Ravina A, García ML. Making processes reliable: a validated pubmed search strategy for identifying new or emerging technologies. Int J Technol Assess Health Care. 2012 Oct;28(4):452-9. http://www.ncbi.nlm.nih.gov/pubmed/22995101
What did they mean when they said “a validated PubMed search strategy”? Our MLA systematic review team that is working on search strategies for emerging technologies identification was, shall we say, curious. For this article, it meant that they tested the search results against the next best method previously used (handsearching). The topic was emerging technologies, and what they did was select influential journals and scanned the TOCs manually (which actually means by using their own eyeballs). The journals they scanned were: Science, JAMA, Lancet, Annals of Internal Medicine, Archives of Internal Medicine, BMJ, Annals of Surgery, Am J Transplantation, Endoscopy, J Neurology Neurosurgery Psych, Archives of Surgery, Annals of Surgical Oncology, British Journal of Surgery, and Am J Surg Path. Of the 35 articles that qualified from these journals, the search strategy accounted for 29. The ‘missing’ articles lacked appropriate title words relating to the novelty of the concept, OR used text words that had been removed from the search strategy to improve specificity (reduce total numbers retrieved).
Is that an appropriate way to validate a search strategy? Probably a pretty fair approach for this one, IMHO, especially since they did such a good job of reporting the specific calculations and details of the actual findings of the searches. Is that how most search strategies are validated? Well, perhaps not.
What I’ve been doing to validate search strategies for systematic reviews is to test and compare the search results to a defined set of sentinel articles. The sentinel articles are selected by the team’s subject experts as being good examples of articles that should be retrieved by a search on the defined question. The requirements beyond topic are that each of the sentinel articles should be older than two years, newer than 1990 (this can be flexible, depending on the topic), and must meet all of the defined inclusion criteria for the review. I usually recommend that the pool of selected sentinel articles include no fewer than 3 and no more than 10 citations. This is to make it possible to achieve complete success, as with each added citation, inclusion of all of them becomes more difficult. I also emphasize that the articles do not need to be excellent or required articles on the topic (ie. “gold standard” articles), but that it is, in my opinion, actually more effective for testing if the articles are a selection of relevant, but not necessarily the best ever written on the topic.
Draft versions of the search are tested against this set of articles, and if any “drop out” (are not included) we need to then figure out why, and determine whether to revise the search to include them, or justify the exclusion, or request NLM to correct the coding error in that article’s record. In these last two cases, the exclusion must be reported in the methods. Ideally, one would also describe the strengths, weaknesses, and/or limitations of the search strategy.
Here are some citations to other ways in which searches are validated.
Hausner E, Waffenschmidt S, Kaiser T, Simon M. Routine development of objectively derived search strategies. Systematic Reviews 2012 1:19. http://www.systematicreviewsjournal.com/content/1/1/19 NOTE: This is basically the same “sentinel articles” approach described above.
Hausner E, Guddat C, Hermanns T, Lampert U, Waffenschmidt S. Development of search strategies for systematic reviews: validation showed the noninferiority of the objective approach. J Clin Epid Feb 2015 68(2):191-199. http://www.sciencedirect.com/science/article/pii/S0895435614003874 NOTE: Interesting article tests the reproducibility of Cochrane reviews and their reported search strategies. The emphasis is on the need for objective and reproducible search strategies in systematic review publications.
Van Walraven C, Bennett C, Forster AJ. Derivation and validation of a MEDLINE search strategy for research studies that use administrative data. Health Serv Res. 2010 Dec;45(6 Pt 1):1836-45. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026961/ NOTE: Compared to handsearching.
Walsh ES, Peterson JJ, Judkins DZ. Searching for disability in electronic databases of published literature. Disability and Health Journal Jan 2014 7(1):114-118. http://www.sciencedirect.com/science/article/pii/S1936657413001647 NOTE: Very interesting two part test to manage the quality control of the search strategy. First, they used the method described above (compared to sentinel articles), then, because the search excluded specific topic terms in favor of broad keyword searching, they validated by comparing retrieval to the results of a known topic search.
Hempel S, Rubenstein LV, Shanman RM, Foy R, Golder S, Danz M, Shekelle PG. Identifying quality improvement intervention publications–a comparison of electronic search strategies. Implement Sci. 2011 Aug 1;6:85. doi: 10.1186/1748-5908-6-85. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170235/ NOTE: Compared relevance and quality of search strategies by results being reviewed for relevance by independent experts. My personal misgivings about this method for validating a search is that it cannot test for what is missed that you don’t know about.
Tanon AA, Champagne F, Contandriopoulos AP, Pomey MP, Vadeboncoeur A, Nguyen H. Patient safety and systematic reviews: finding papers indexed in MEDLINE, EMBASE and CINAHL. Qual Saf Health Care. 2010 Oct;19(5):452-61. http://www.ncbi.nlm.nih.gov/pubmed/20457733 NOTE: Compared sensitivity & specificity for new search strategies in comparison to previously published search strategies on the same topic. Validated by comparing to a large selection of sentinel articles. Very difficult to achieve, and am ambitious strategy!
Brown L, Carne A, Bywood P, McIntyre E, Damarell R, Lawrence M, Tieman J. Facilitating access to evidence: Primary Health Care Search Filter. Health Info Libr J. 2014 Dec;31(4):293-302. http://www.ncbi.nlm.nih.gov/pubmed/25411047 NOTE: Interesting strategy that first created and validated a search strategy in OVID for quality control over the search development process, and then converted the strategy to PUBMED and validated it again. The validation was again through the selection of a set of sentinel citations, but they explicitly selected for the best quality articles in the topic and referred to the set as the “gold standard.”
Damarell RA, Tieman JJ, Sladek RM. OvidSP Medline-to-PubMed search filter translation: a methodology for extending search filter range to include PubMed’s unique content. BMC Med Res Methodol. 2013 Jul 2;13:86. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3700762/ NOTE: Same strategy as the article by Brown, Carne…Tieman above, but a different topic.
You can find more articles on this topic by exploring the following search results:
Emerging Technologies Librarian 