Scholar Medical Publication DIY by Harvard Medical Students

If, as F. Scott Fitzgerald is reported to have said, action is character, then the current crop of Harvard medical students are impressive characters. Amid all the din about who controls publication, open access and shortening the loop between academia  and public dissemination, a small group of determined individuals have just come out with their premiere issue of Harvard Medical Student Review. Considerable forethought, extensive deliberations with HMS leadership and creative talent have produced what is likely to become an authoritative voice for medical students and those interested in medical education and science.  In the words of the student publishers themselves:

Today we are introducing the Harvard Medical Student Review, an online journal that will serve as a forum for students to participate in the conversations on healthcare and medicine. Our classmates here and around the world come from innumerable backgrounds, rich in thought-provoking experiences; we have much to share. Topics may range from research to reflections on training and experiences with patients. We hope that through writing and reflection, we can spark productive debate, generate innovation, and learn from one another at the beginning of our professional education and careers.

As members of the medical community, we have a duty to review the facts and communicate the truth with clarity, precision, and humanity. In his address at the 2012 Harvard Medical School commencement ceremony, Dr. Don Berwick called upon new physicians to wield their voices proudly in carrying out this duty, as each voice “can be loud, and forceful, and confident, and will be trusted.” [2] The Harvard Medical Student Review is a space for students, trainees, and professionals to answer that call.

We hope you will join us.

Ghost stories for scientists

This report in Scientific American, just in time for the Halloween season, demonstrates that incorporeal beings take great interest in obesity, adipokines and leading laboratories at Harvard University. Perhaps they tired of the irreproducibility of their paranormal experiments.

Hat tip: Rachel Ramoni

A thoughtful and useful report on the Aaron Swartz tragedy

This (http://swartz-report.mit.edu/docs/report-to-the-president.pdf) is a report that Professor Abelson helped author on the behalf of MIT. It is chock full of lessons for education institutions, libraries and the larger academic ecosystem, including the ancillary industries. Although section V is focused on questions for MIT, many of those same questions will find wider resonance.

Getting Big About Mapping Dengue

Here's a very nice application of lightly used data sources about Dengue, a scourge of underdeveloped countries. As in so many areas of public health, this huge health burden is woefully under-documented. In the absence of a vetted vaccine, understanding where it is endemic is essential for the application of scarce preventive resources. This group of investigators have cleverly used a number of public but under-used data sources, including the published literature, to create a predictive map of where 390 million infections per year are occurring.

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Take this ontology and shove it. Or, why classification matters.

I was recently called out by one of my colleagues for saying that ontologies were boring, this despite my own doctoral work on knowledge representation. Motivating my glib comment was an image of a group of pasty-faced individuals gathered around a large boardroom table and discussing which angel fit on which pin. Events from this past weekend are a reminder why such glibness is not helpful.

The American Psychiatric Association has just approved a set of updates, revisions and changes to the reference manual (DSM5) used to diagnose mental disorders. Among the changes are those redefining the inclusion and exclusion criteria for autistic disorders. By changing which children are classified as having an autistic disorder, parents will be made to feel more or less comfortable having a child carrying the diagnosis. Just as importantly, insurance companies and school programs might shift their criteria that determine which child and family gets what kind of support and at what cost. In the near term, clinical trials for the treatment of autism may not include the same patients as they would have prior to this retaxonomization.

So, are ontologies boring? Perhaps. But they certainly belong to the class of hugely important societal constructs.

Hat tip: David Osterbur.

No Publication Without Taxation?

I recently obtained a copy of a presentation by Elsevier representatives describing how they price their publications for different academic (i.e. university) customers. They describe how they place each institution into one of a small number of pricing tiers. How do they decide this categorization? A major component of the decision is the research intensity of the institution to which they were selling access to their publications. What was the measure of research intensity? Publication volume as measured by the SCOPUS database (an Elsevier product).

To better understand this policy, I contacted Elsevier and spoke by phone with a very cordial and clear executive. I asked why it seemed that the more we published, the more we were going to be charged by Elsevier to read these publications?

He explained that research intensity served as a proxy for the value that institutions might place on these publications. After all, if we value these publications, then we are more likely to download/use them. And pricing should reflect value.

I then asked why they were not simply measuring the download rate for each journal to directly charge for usage rather than using a proxy measure. The executive explained that their advisory board had recommended not to use the download rate as that might reduce usage thereby impeding scholarship.

So solicitous of the publisher. I knew it would be futile to bring up the effect on scholarship of inflation rates of publication prices that would make the rate of medical care inflation appear flat by comparison. A continual record of inflation that reduces every year the fraction of their own scholarly output made available to scholars throughout the world's academic institutions.

Yet Another Healthcare Research Steeplechase Barrier

I was recently informed that I have to take an on-line course about conflict of interest and then document all commercial activities. I was then informed of the same duty three more times. Because I am engaged in research at multiple universities, hospitals and medical schools, these education and reporting activities have to be done multiple times and of course the forms and "educational" syllabi are all different.

Like all large, heavily funded (and rewarded) organized activities, healthcare research has acquired over time some practices that originally made sense but have evolved into anti-productive structures. There have been a number of highly publicized examples of truly egregious behavior by researchers who have hidden their conflicts of interest. Individuals who used the podium of academia and the cachet of their presumed impartiality to declaim, opine, publish regarding a device, therapy, or diagnostic procedure where they stood to gain financially. For decades, it was made abundantly clear to all investigators that any such conflict was to be disclosed in grant applications, in publications and presentations. Yet. it was left up the the investigator to decide whether or not there was indeed a conflict. This ultimately became an all too carefully parsed taxonomical challenge and rather than waste time in such parsing, several of us went the route of full transparency. For example, I have listed on the web all my commercial activities so that my colleagues and the public can decide whether or not there is indeed a conflict.

Presumably because not everyone has traversed this route of transparency, there are now a host of new regulations for annual disclosure. Some of them appear obvious (e.g. disclosure of equity ownership or payment for speaking), others less so (e.g reimbursement for cab fare to attend a commercial conference where there are no speaking fees). In the end these disclosures are important and yet are each of the healthcare research institutions so different as to require different reporting and educational mechanisms? It seems there is an opportunity for an enterprising company or apparatchik to create a single, authoritative form and set of educational materials. Let's just hope they keep it simple.

Copyright + book = disappearing act?

Many of us worry that the last three decades of scholarship will be lost to posterity because we have yet to provide an institutionalized set of mechanisms for preserving the digital output of academia that are as durable and accessible as our accreted analog/paper-based records. Now here comes word of an equally worrisome trend, the empirical evidence that worries about the effect of copyright on the access to important cultural, literary and scientific works, may be well-founded. A recent article in the Atlantic Monthly describes a yawning gulf in the sale of new books from recent decades such that there are more new books sold by Amazon from 1850, than there are from 1950. In their analyses, the investigators provide intriguing circumstantial evidence suggesting that the copyright laws may be responsible. More detail in this lecture by Paul Heald.

Hat tip: David Osterbur

Genesis of citations

I was just reminded of an excellent review of the various forms of transmission of authoritativeness and outright falsehoods through citations by Steve Greenberg when I saw this all too accurate portrayal of citogenesis.

You are not the boss of me!

This assertion, made by millions of children with respect to their siblings, has its echos in many contemporary conversations about scholarship and authoritativeness. Whether it is the dominance of genetic or environmental effects in child development, or the value of a prostate specific antigen test, or the meaning of a genetic mutation, one group's truth is another's discredited hypothesis or outdated approximation. Of course, there some facts whose authoritativeness are beyond doubt, such as the speed of light. Well, maybe. Certainly, until that eschatological moment when we will all know the absolute truth, those of us who are entrusted with the curation and dissemination of knowledge, in its various guises, will have to provide tools to manage the growing multiplicity of perspectives.

In that spirit, I have unearthed a piece I wrote with Russ Altman over a decade ago about authoritativeness in the peer review process and how it could be managed ecumenically. We'll see if our futurology was authoritative.

Take two aspirin and an algorithm and call me in the morning.

This note from the American Medical Association nicely summarizes the recent approval of certification in Clinical Informatics by the American Board of Medical Specialties. It represent the closest encounter between clinical training and librarianship to date. We'll see what it portends for relative compensation.

Bibliography of Clinical Genomics

Recently, we held a summit on the topic of clinical grade reporting of full genomic sequence. Given the growth in the number of papers (likely to grow hyperexponentially in the near future) David Osterbur has followed up with a very nice bibliographic guide to this emerging literature. Feel free to contact him if you would like other such articles added to the guide.

Stuffed full of information

That bird rendered by taxidermy in a museum is not only of visual interest. This report by an enterprising undergraduate points to some unexpected public health insights gleaned from the feathers of these museum specimens about the trajectory over centuries of mercury contamination in seabirds. Perhaps needless to say, this could not be done with a purely virtual collection.

Write the Future

A very creative approach to impactful scholarship. Worth the try even if if fails.

Hat tip: Christopher Erdmann

Hall or House of Mirrors? The citation perspective.

Kudos to the analysts at SCImago. They have provided an outstanding, entertaining and educational perspective on worldwide academic publishing. I'll focus here on only one aspect: citations. Although the United States is the leader in citations at 87M citations, it is a surprising laggard in self-citation (32% citations are self-citations). The leaders are China (62%), Lithuania (38%), and Iran (37%). However, in the domain of medicine, authors in the United States are considerably less reticent and rack up a self-citation rate of 47%, earning them second place. The map below of the subject areas of the USA publications indicates where the action is.

Hat tip: Peter Park

We, the librarians

As Harvard University reorganizes its extensive library system, it is worth reconsidering where library activity occurs and who drives it. This effort in Finland (hat tip David Osterbur) is a reminder that although professionally trained librarians with a mission and institutional memory are central to the curation, preservation and dissemination of scholarly materials, there is no sharp demarcation as to where expertise, time and effort can be found in our collective efforts. If individual scholars do not curate their own, increasingly electronic, notes, their messages, and other residua of the scholarly process, there will be very little for institutional librarians to work wit and a gaping hole in the scholarly record. But first, academic institutions will have to provide them with a easy to use process that can last their entire careers. This is a first class opportunity for entrepreneurial, techno-librarians who can think at the scale of the Internet. Conversely, libraries must reach out the to network of distributed expertise in all areas of academic endeavors which is populated by experts often well outside the walls of organized academe. Literally tens of thousands of precious modern and ancient scholarly archives remain in the dark, queued up, waiting for an overworked archivist to provide even the most cursory cataloguing. Shotgun mass annotation, leveraging external expertise will have to become the norm and, again, there is a large opportunity for those who are able to provide such capabilities at scale and with the appropriate legal and institutional framework.

Should your email be archived?

Who will make sure that the pearls of your scholarship, scattered throughout your email and other electronic files will survive and be studied? Or should such digital ephemera be allowed to be composted in the big electronic bit bucket in the sky? These and other questions will be addressed June 9th at the Harvard Digital Scholarship Summit.

No iTunes-equivalent for Google

Google and the Authors Guild and the Association of American Publishers had hoped to create a one-stop shop for a wide array of published works. The Department of Justice has just ruled that the current proposal does not pass muster. Whether or not this helps or hinders dissemination or scholarship appears to be a matter of some controversy.

When is obesity as infectious as tuberculosis (or even more)?

As part of our Notable Books series, Nicholas Christakis will be reviewing the interesting relationship between our social networks and disease burden (and related phenomena). This is in context of his recently published book:Connected: The Surprising Power of Our Social Networks and How They Shape Our Lives. Time: December 10th, 4pm. Place: Countway Library of Medicine, 5th floor, Ballard auditorium.

Normality, expertise and fairness.

Who is more knowledgeable? The physician who remembers more diagnostic tests than any other physician or the physician who is the quickest and most savvy at online searching for the relevant tests? Who is the most technically expert surgeon? The one who has the most nimble fingers and the sharpest eyes or the one who can make herself most comfortable with robotically assisted micromanipulators? This story taken from athletics suggests that we are going to be uncomfortable with some of the answers to these questions for many years to come.