Category Archives: Research

Standards and Services and PRISMA, Oh My! Systematic Reviews at MLAnet16, Day One

First posted at the MLAnet16 blog: http://www.mlanet.org/blog/standards-and-services-and-prisma,-oh-my!-systematic-reviews-at-mlanet16,-day-one


Toronto Scenery

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.

Dean Giustini asked me what’s new, so let me get right to that.

PRISMA

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.

Priorities for Systematic Review Search Strategy Reporting

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.

MLAnet16 Systematic Review Services

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!

MLAnet16 Systematic Review Services

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.

MLAnet16 Systematic Review Services

From the Arxiv (What Caught My Eye Last Week)

Quantifying the impact of weak, strong, and super ties in scientific careers
Alexander Michael Petersen
PDF: http://arxiv.org/pdf/1509.01804v1.pdf
Soundbite: “We find that super ties contribute to above-average productivity and a 17% citation increase per publication, thus identifying these partnerships – the analog of life partners – as a major factor in science career development.”

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”

Estimating Reproducibility in Genome-Wide Association Studies
Wei Jiang, Jing-Hao Xue, Weichuan Yu
PDF: http://arxiv.org/pdf/1508.06715v1.pdf
Soundbite: “This can be used to generate a list of potentially true associations in the irreproducible findings for further scrutiny.”

Nucleosome positioning: resources and tools online
Vladimir B. Teif
PDF: http://arxiv.org/pdf/1508.06916v4.pdf
About: Gene Regulation Info
Includes: Nucleosome positioning datasets sorted by cell type

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.”

Reduction of Alzheimer’s disease beta-amyloid pathology in the absence of gut microbiota
T. Harach, N. Marungruang, N. Dutilleul, V. Cheatham, K. D. Mc Coy, J. J. Neher, M. Jucker, F. Fåk, T., Lasser, T. Bolmont
PDF: http://arxiv.org/pdf/1509.02273v1.pdf
Soundbite: “Our results indicate a microbial involvement in the development of Alzheimer’s disease pathology, and suggest that microbiota may contribute to the development of neurodegenerative diseases.”

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.”

The Brain Uses Reliability of Stimulus Information when Making Perceptual Decisions
Sebastian Bitzer, Stefan J. Kiebel
PDF: http://arxiv.org/pdf/1509.01972v1.pdf
Soundbite: “Our analysis suggests that the brain estimates the reliability of the stimulus on a short time scale of at most a few hundred milliseconds.”

Brain Model of Information Based Exchange
James Kozloski
PDF: http://arxiv.org/pdf/1509.02580v1.pdf
Coolness: IBM Neural Tissue Simulator (about NTS | NTS slides | 1st article)

Interplay between the local information based behavioral responses and the epidemic spreading in complex networks
Can Liu, Jia-Rong Xie, Han-Shuang Chen, Hai-Feng Zhang, Ming Tang
PDF: http://arxiv.org/pdf/1509.01321v1.pdf
Soundbite: “The spreading of an infectious disease can trigger human behavior responses to the disease, which in turn plays a crucial role on the spreading of epidemic…. Our finding indicates that, with the increasing of the response rate, the epidemic threshold is enhanced and the prevalence of epidemic is reduced.”

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.”

Researchpalooza 2015!

Researchpalooza 2015Researchpalooza 2015 at a Glance

Researchpalooza! A place for the bold! The bright! The blue!

Researchpalooza is a big festival for people all around the University of Michigan campuses who are engaged with, supportive of, or otherwise a part of life sciences research. From the service side to the production side, people come out, play games and eat ice cream, and talk about the services they provide and the discoveries they’ve supported. They talk about resources, people, and places. They make new connections and foster new collaborations. People discover opportunities they weren’t aware of, get excited, and share their own passions. Basically, this is a pretty awesome event. I took a lot of pictures, and collected pictures and tweets into a portrait of the event. You can explore below, or go directly to the Researchpalooza 2015 Storify and find more.

UofM Student Research on 3D Everything (Except Printing)

#mlibres Students on #3d

Last week there was another of the wonderful Emergent Research Series of lectures sponsored by the University of Michigan Libraries Research Unit (2014 archive, 2013 archive).

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.

What Patients Think about Clinical Trial Engagement (#patientchat)

At the Doctor's Office

I had really wanted to participate in this Twitter chat today (#patientchat), on how patients find clinical trials, decide to engage with them, what resources they use, their expectations, and their concerns. I missed the chat, but it is archived in Symplur, so I was able to scroll through, search, dig, prowl around, and find my favorite bits. Since I went through all of that, I thought I’d share it. I’d recommend reading more deeply in the transcript for anyone in clinical trial research or recruitment, patients with basically any kind of diagnosis (as Mighty Casey eloquently said), people interested in translational medicine (where patients play a crucial role), as well as clinicians. Evidently, patients consider clinical trial recommendation from the primary care clinicians to be an obligation, not an optional part of providing care. Who knew? I bet we could automate relevant clinical trial notifications in EHR and as part of clinic visit prep. Why not? Explore below and see what other surprises and creative nuggets appear.

Ann McKee on Boxing, Football, and the Brain (Leiter Lecture) [#mlanet15]

Part 4 of a series of blogposts I wrote for the recent Annual Meeting of the Medical Library Association.


Was it just yesterday? I was sitting in the Leiter Lecture listening to the incredible Dr. Ann McKee present about past, present, and future trends in concussion research. I had been reading about her work in the indie-published award-winning book from 2014, Conquering Concussion, and was very interested in learning more. By the end of the talk, I wasn’t the only person who had tweeted out that I had tears in my eyes.

The story she told that touched me the most was of the athlete who had been diagnosed with ALS, but who phoned her, suspecting that what he really had was, “what you’re studying, Doc.” That would be Chronic Traumatic Encephalopathy (CTE). Basically, CTE is what happens when you bounce someone’s brain around on a regular basis, and they never really have a chance to heal. Some folk with that history develop CTE, some don’t, and Dr. McKee would really like to know why. To do this research, people or families donate their brains after they die. This athlete had met with her a few times, and there was a relationship, a sense of trust between them. Then the call came (I’m paraphrasing here, working from memory), “Hey, Doc, we’re having a big party! All my family and friends, a big blast. I’ve decided to go off respiratory support, and my docs don’t think I’ll make it through the weekend.” He died the next day. Someone went to pick up his brain, and when they ran the tests, he was right — he did have CTE.

I shared that story later that day in the airport waiting room with a man whose wife and son both had a history of severe concussions. I also shared that Dr. McKee’s insights on a possible genetic connection (for why some folk never develop CTE) and what people can do NOW to help prevent the long term:

* EXERCISE
* Diet (rich in antioxidants)
* Sleep
* Avoid conditions or triggers that cause inflammation in your body

Dr. McKee is also working on finding biomarkers so CTE can be diagnosed before people die, and needs donations of NORMAL brains to be able to identify the differences. A friend of mine asked me on Twitter what qualifies as ‘normal,’ and for this, let’s just say it would be someone who doesn’t have a history of multiple concussions, or subconcussions. There was a lot more, but I’ll limit myself to sharing the Concussion Checklist she recommended, and the Storify, if you want more. There are several interviews with her and other articles about her, if you want to dig in a little more deeply.

Molecular Biology & Genomics SIG Meeting #mlanet15

Part 1 of a series of blogposts I wrote for the recent Annual Meeting of the Medical Library Association.


MolBio & Genomics SIG #mlanet15

I’m trying to track what’s going on with emerging technologies, new tools, new-to-me tools, and so forth. I’m not an official member of the MolBioGen SIG, but I wish I was (especially since personal genomics is one of my hobbies). I learned so much at their meeting Monday morning. The best part was the Round Table, where they each talked about who they are, what they do, what’s new at their place. Now, this was exciting! They talked about many tools they seemed to all know and take for granted, and I’ll share some of those later. They also had so many exciting and creative ideas for how to engage their target audiences, types of classes that are most effective, crowdsourcing instruction from within the audience, strategic partnerships that make a difference, strategies for point-of-care genomics, and so much more.

Here are the tools that I found most interesting.

PhenoTips
PhenoTips

Reactome
Reactome

Online Bioinformatics Resource Collection
Bioinformatics MOOCs Example

Galaxy Project
Galaxy

Open Helix
OpenHelix
(Note: These folk are in the Exhibit Hall, if you haven’t seen them yet.)

BioStars
BioStars

GenePool
GenePool

Data Carpentry
Data Carpentry

Project Hydra
Hydra

Fedora
Fedora

NCBI: Gene Expression Omnibus (GEO)
GEO (Gene Expression Omnibus)

Complete Genome: Public Genome Data
Complete Genomics Public Data

NYU Data Catalog
NYU Data Catalog

Want more? Check out the Storify!

Informed Consent in a New Era

Informed Consent copy

I’m a big fan of John Wilbanks’ work in the area of open personal health data and informed consent, and have blogged about that here before. Briefly, my awareness of John’s work began with “We Consent” which has now transformed into Sage’s “Participant Centered Consent Toolkit.”

Cool Toys Pic of the day - We Consent
Sage: Participant-Centered Consent Toolkit (E-Consent)

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!

Can Broad Consent be Informed Consent?

Broad consent is informed consent

Broad consent versus dynamic consent in biobank research: Is passive participation an ethical problem?

Broad Consent Versus Dynamic Consent: Pros And Cons For Biobankers To Consider

Broad Consent in Biobanking: Reflections on Seemingly Insurmountable Dilemmas

Should donors be allowed to give broad consent to future biobank research?

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

Fair Use & Figures: When Is It OK? (Part Two: Fair Use)

Fair Use?

Point 2: Is it fair use?

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:

“Note: an image or figure would commonly be considered a work in and of itself, weighing against fair use; or could summarize the key point of an article, also weighing against fair use.” Reuse of figures, images, and other content in theses http://libraries.mit.edu/scholarly/publishing/copyright-publishing-guide-for-students/reuse-of-figures-images-and-other-content-in-theses/

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).

“Redrawing a figure does not change the Fair Use analysis; the figure cannot be used without permission just because it is redrawn.” ACM Guidance for Authors on Fair Use http://www.acm.org/publications/guidance-for-authors-on-fair-use

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.

“When Shelley Batts wrote up a report on an article about antioxidants in fruits, she never expected to get contacted by the copyright police, but that’s exactly what happened.” Munger, Dave. Is reprinting a figure fair use? http://scienceblogs.com/cognitivedaily/2007/04/26/is-reprinting-a-figure-fair-us/

In Shelley’s words:

“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.

On Validating Search Strategies

validation

This question came up because of this:

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:

(validated OR validation OR “quality control” OR “quality assessment”) search strategy review http://www.ncbi.nlm.nih.gov/pubmed/?term=(validated+OR+validation+OR+%22quality+control%22+OR+%22quality+assessment%22)+search+strategy+review