Just four weeks ago I wrote a blog post titled How do you read papers? 2010 will be different. Not only have we since seen the announcement of the Apple iPad, but last Monday the free Nature.com iPhone app was launched. The application gives access to the full text of all Nature and Nature News content (through until 30 April 2010, how access is handled afterwards hasn’t been announced yet). A version for the Android platform was promised for April, and the app will work with the just-announced iPad. I included a few screenshots for those without an iPhone or iPod Touch. A free Nature.com personal account is needed to use the app.

The iPhone app doesn’t use HTML or PDF but rather the ePub format. The Nature.com website will soon offer downloads in ePub format (an example article is here). Adobe Digital Editions and Stanza are examples of ePub readers. In contrast to PDF, ePub adapts to the screen size and is therefore a much better format for the iPhone.

References are links in the text, clicking on them opens a new window.

Figures are also links in the text that open in a new window. The figures can be saved to the iPhone Photos application.

The iPhone app also gives access to the full text of Nature News. In contrast to Nature papers, images are rendered within the text.

Nature and Nature News content, as well as PubMed search results can be saved for later reading. This content (or rather the DOI) is also available from the new Nature.com mobile apps page. Because the Nature.com mobile apps page stores only the DOI, a Nature subscription is required to access the fulltext article from there. From the Nature.com mobile apps page you can also export the citation in RIS format.

The Nature.com iPhone app also searches both Nature.com and PubMed. Regular searches can be saved.

PubMed searches will retrieve abstracts, with a link to the fulltext article via the DOI.

Papers for iPhone is another app that allows PubMed searches. You can also search for the latest Nature content, but the fulltext content is available only with a subscription and only as HTML or PDF.

Support for ePub is the most exiting feature for me, as it opens the door for many interesting mobile applications. I hope that more scientific journals will start to use the format (Hindawi was one of the first publishers to support ePub), and that we then start to see mobile apps for more than a single journal.

Bug reports, suggestions and feature requests can be sent to mobile@nature.com. Or add your comments to Henry Gee’s Nature On Your iPhone post.

This weeks’s blog post is a guest post on the Biomedicine on Display blog – I was kindly invited by Thomas Soderqvist from the Medical Museum of the University of Copenhagen.

Following the ScienceOnlien2010 conference, librarian Dorothea Salo wrote on her blog:

This disconnect is the number-one threat to science librarianship today—perhaps to all academic librarianship. How can science libraries persist when scientists haven’t the least notion that libraries or librarians are relevant to their work?

These are serious questions, and of course I don’t have the answers. But I would like to add my thoughts from a researcher perspective. The role of libraries in providing teaching material for students (textbooks, etc.) is another story that I will not touch today.

Flickr image by Radioher

I’m old enough to remember the time (maybe 15 years ago) before literature searches were possible via the internet and scientific papers were available in electronic form. I had to go to the library to use Medline or Current Contents in printed form (and later on CD-ROM), or to flip through the newest issues of the most interesting journals. I would photocopy the papers I would then read at home, and then file away for later use.

PubMed, Scopus, Web of Science, and Google Scholar now allow me to search the literature from my desk at work (or from home). Most researchers (including myself) probably don’t have the skills for sophisticated searches, but these tools more or less get the job done. Electronic publishing means that I can obtain a paper directly from the journal (as long as I access the journal from a computer in the university network), and licensing is handled (almost) transparently by the library.

These developments have dramatically reduced the time researchers spend at a library. This is good, as this saves them a lot time. But interactions between researchers and librarians have also been dramatically reduced. Publishers and other companies (e.g. Thomson Reuters, Mendeley, Faculty of 1000, to name just a few) have used the opportunities to adapt their offerings to the internet (e.g. electronic-only journals), and to create new products that weren’t possible (or even thinkable) before. Although libraries have in many ways adapted to the internet as well, they probably haven’t seized the opportunity to the same degree. The homepage of my university library is a place I visit much less often than PubMed or the pages of my favorite journals. Some ideas of how this could be changed are listed below. Most of them are not new, but maybe at least some libraries haven’t gone all the way to make their pages an attractive destination for the researchers of their institution.¹

Provide and support online reference manager
Institutions should support at least one online reference manager, possible options include (in no particular order) Zotero, Mendeley, Endnote Web, Refworks and CiteULike. RefWorks and Endnote Web are commercial products and require a private (Endnote) and/or institutional license. The institution should either pick a free reference manager as their primary choice, or buy an institutional license in order to allow every researcher and student to use these tools without additional cost.²

As we can’t expect everybody to use the same reference manager, libraries have to help with several products. The easiest way to do so is via an online forum (see next paragraph), as this is more efficient than one-to-one support and allows experienced users to help out. Online reference managers provide additional features (e.g. they can be used from different computers, allow shared folders for groups of users) and should therefore be preferred over standalone applications.

Online user training and support
User support is obviously one of the central functions of science libraries. This has two aspects: helping with a specific problem (e.g. finding scientific literature), but also training users to do this on their own. The required skills include use of PubMed and other databases, and reference managers such as Endnote or Zotero. Skills in evidence-based medicine are critical to find and appreciate the appropriate medical literature, but in my experience many physicans and medical students would benefit from additional training in this area.

Introductory classes, help in person or a phone call are sometimes the best way to do this, but often users require quick help for a specific situation that can best done with online tools. Appropriate tools include email, online forum, Twitter, Yammer (a microblogging tool similar to Twitter but for institutions), SlideShare, FaceBook (and StudiVZ in Germany), FriendFeed, and Wikis. Every institution should make a decision about the services they plan to support, with emphasis on tools that are easy to use.

Institutional bibliographies
A regularly updated listing of all publications of an institution is not only a valuable PR service, but is often also required by administrations to evaluate research output. Librarians are often involved in this, but there is probably a lot of untapped potential. As unique identifiers for researchers become more widespread, there really no longer is a need for researchers to compile publication lists themselves.³

Article deposition in institutional repositories
Most journals allow researchers to post their accepted papers in institutional repositories of their institution. But because this requires technical skills and extra time, many researchers aren’t particularly eager to make use of them. Institutional bibliographies can obviously be nicely integrated with institutional repositories, thus reducing redundant work.

Help authors with article submissions
Article processing charges for authors are often handled by their libraries, and sometimes libraries have membership deals with publishers that give authors a discount. But researchers often are left alone with the article submission process. Most authors submit at most a handful of papers each year, and they have to deal not only with different article formats between journals (most notably different reference styles), but also different article submission systems (e.g. Editorial Manager, eJournal Press, Manuscript Central or BenchPress). The total number of papers submitted by an institution is much larger, and thus at least some recurring problems could be avoided or at least the time required reduced with centralized support from the library.

Help with Web 2.0 tools for scientists
Libraries don’t have to reinvent all the Web 2.0 tools for scientists that are already out there, but they are a good place to help interested researchers get started with some of them (e.g. ResearchGate, Nature Network, or Academia.edu). Ideally, these tools could be integrated into the library webpages via an API.

¹ I would like to be proven wrong by great examples of libraries gone Web 2.0.

² My university picked RefWorks as their primary reference manager.

³ Scopus is already pretty good in this.

Three events from last week inspired me to write this: a blog post by (and short Twitter conversation with) Dorothea Salo (Science Online 2010: Scientists and librarians), a meeting with the other organizers of BibCamp Hannover (“a BarCamp for librarians and other hackers” in May 2010), and a discussion via email with Oliver Obst from the Medical Library, University of Munster.

ScienceOnline2010 just finished a few hours ago, and from what everyone was saying it was yet another wonderful meeting. I attended last year and moderated a session called Providing public health and medical information to all, but unfortunately could not come this year. News about ScienceOnline2010 are all over the place, including from our own Henry Gee.

Flickr picture by missbakersflickr.

Graham Steel has more experience attending ScienceOnline remotely (Science Online ’09 – How was it…. via the internet?), but I did my best to follow the meeting via Twitter, FriendFeed, Flickr, YouTube and of course blogs and media. There was even a ScienceOnline2010 iPhone app. Another ScienceOnline2010 trend was the widespread use of Flip for short videos such as this one:

The overall online coverage far exceeds what I see at my usual science meetings, but following the sessions live (including the ability to ask questions) is far more difficult. For that you need video and microblogging (or the two combined in Second Life). Video of sessions from two rooms was streamed live at Ustream and Second Life, but Ustream didn’t always work for me (didn’t try Second Life, all sessions were recorded and will appear on YouTube next week).

For me and many others FriendFeed is the perfect microblogging tool for conferences (Microblogging the ISMB: A New Approach to Conference Reporting). But the use of FriendFeed in Science 2.0 conferences seems on the decline during the last 12 months because of Twitter, and at ScienceOnline2010 it was no longer possible to follow sessions using FriendFeed. Twitter is wonderful for many things, but makes it very difficult to create a connected discussion around a particular topic such as a conference session. But the Twitter board was cool:

Flickr picture by SignalShare.

After ScienceOnline2010 is before Science Online London 2010. The first planning meeting took place last Friday. We hope to announce the location and date in the coming weeks, but we are aiming for a bigger (with enough room for at least 250 people) and longer (two days) meeting with enough parallel sessions to cover all the topics that we care about.

One personal goal I have for Science Online London 2010 is to provide an even better experience for those unable to attend in person. Second Life worked pretty well for us last year, and we even had one speaker giving his presentation this way. But maybe we can do better. Livestreaming of good quality audio is probably the most important thing, the video quality seems less critical. Alternatively, we can synchronize the audio with the slides from the presentation, something SlideShare calls SlideCast. We might also find better ways to use Twitter for microblogging, e.g. by using separate hashtags for every session and a Twitter board in the sessions.

In November 2008 I wrote a blog post called How do you read papers? The blog post was actually about different strategies to find interesting papers, e.g. browsing journal tables of content (TOC), different search strategies, filtering by papers others read, or filtering by experts (e.g. Faculty of 1000). A paper by Duncan Hull et al. published around that time in PLoS Computational Biology (Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web) also talked about finding strategies and the best tools for this.

In this blog post I want to talk about the actual reading of scientific papers that you found with one of the strategies mentioned above. There are some interesting recent developments, and I think we will see some significant changes in how we read papers in 2010.

Printed journal
Holding the printed journal in your hands is probably still the most satisfying reading experience because of professional typesetting and color reproduction. But unless you have a personal journal subscription, it is not convenient as you would have to go to the library to read the paper. Plus, many journals no longer produce a printed version, or the library has only an electronic subscription.

Photocopy
This used to be the most common way to read papers 20 years ago. But the quality of photocopies is usually worse than a printout of an electronic version, and photocopies are far more inconvenient to obtain. Reading photocopied papers will only be necessary for the small number of journals that produce no electronic version, or for older papers.¹

PDF printout
This is the way most people read scientific papers today, unless they just want to look up small parts of it. Quality color printers have become affordable, and the reading experience is similar to the printed journal with the added convenience of electronic distribution. Most people use PDF printouts for reading, and later discard the paper copy, sometimes even the same day. This is not only more expensive than reading on an electronic device, but also not very friendly to the environment.²

Reading PDFs on a computer
This approach appears to be very common for reading just parts of a paper, e.g. to look up experimental details, a figure or reference. Most people now store papers as PDF (hopefully with an intelligent program such as Papers) and not the PDF printouts. Looking at the PDF on the screen is therefore often the first step, and then the decision is made whether or not to print out the paper to read it in more detail. Reading PDFs on screen is possible, but not really convenient for longer texts. Screen sizes are often too small for the PDF format (A4 or US letter). Many people don’t like the eye strain from looking at a screen for longer periods of time, although this is probably more relevant for reading books rather than reading a scientific paper.

Utopia is a PDF viewer launched in December by the University of Manchester that enhances PDF files of the Semantic Biochemical Journal with interactive content and live linking to web resources. Read more about Utopia at Duncan Hull’s blog.

Reading on a mobile device
Many mobile devices such as the iPhone can open PDFs and Papers for iPhone makes this process convenient. But PDFs in an A4 or US letter format are almost impossible to read on a small screen.

The ePub format is more suitable for smaller screens found on mobile devices. ePub is usually used for e-Books, but the Open Access publisher Hindawi since 2008 provides papers also in that format. Although ePub is more suitable than PDF for mobile devices, it doesn’t solve the problem that figures and tables are simply difficult to show on a small screen. Mobile devices are probably great for reading journal table of contents or the abstract of a paper (and an RSS reader such as NetNewsWire for iPhone is perfect for this), but not fulltext papers.

Reading on an e-Reader
The screen of an e-Reader uses electronic ink which not only means a much longer battery life, but also a very pleasing reading experience, including reading in direct sunlight. Electronic ink is black & white, which is not a problem for fiction books, but limits the use for scholarly papers (and scientific textbooks). Ideally an e-Reader should have a 10" screen, similar in size to A4 or US letter paper.

The Kindle DX from Amazon was announced in May 2009 and is currently the most popular e-Reader. The Kindle uses its own file format, but a recent software update now allows the Kindle to open PDF files. Some journals (e.g. the New England Journal of Medicine) offer Kindle subscriptions, but that doesn’t include early release articles and no subscriber access to the journal website. A number of similar devices were demonstrated this week at the Consumer Electronics Show in Las Vegas. The Kindle is primarily an e-Book reader, and David Crotty over on the Scholarly Kitchen blog is skeptical about dedicated e-readers, because he thinks that market is just too small.

Apple iSlate
Unless you have been on a remote island for the last three months, you will know that Apple will announce a tablet computer later this month. There is wide speculation about the technical details, but it looks like this will be a very interesting device for reading scholarly papers. In contrast to e-Readers it will not use electronic ink. This means a shorter battery life, but allows color documents and many other more traditional computer uses. Based on the iPod and iPhone experience, many people think that the iSlate will change the way we use tablet computers. One of them is Kent Anderson (Game Over, Man – Has the Disruption of Publishing Already Occurred?).

Sports Illustrated did a very nice demo of a fictional tablet computer in December, and it is obvious that many of these concepts can also be applied to scholarly publishing.

Reading Web Pages
Most examples mentioned above try to reproduce the experience of reading something printed on paper on an electronic device. An alternative approach would move beyond the traditional format of a paper and rather takes advantage of the electronic medium. And it looks like the web technologies HTML5 and Flash are best suited for this. Cell Press was experimenting with this approach in 2009, and officially launched their Article of the Future with the first 2010 issue of Cell (all papers will be available without subscription for 60 days, you can provide feedback here). The basic idea of the Article of the Future is to break away from the concept of reading a paper from beginning to end, and to make navigation between the different parts of a paper much easier.

Whereas the Article of the Future tries to make navigation with a paper easier, the PLoS article-level metrics help with navigating to related content: citations, blog posts, reader comments, etc. The Notes feature lets registered users highlight text for specific comments – very much what you would do on a printed paper (but with the added benefit that everybody can see this note).

I’m most excited about projects that enhance the scientific paper instead of recreating an exact electronic version of the traditional paper. And HTML is a more promising format than PDF for these approaches. Michael Clarke (with whom I had the pleasure to do a session at SciFoo 2009) reminded us that Tim Berners-Lee invented the WWW in 1991 to facilitate scientific communication (with HTML and navigation both within and between documents as central concepts), but papers and journals have changed surprisingly little in the last 18 years (Why Hasn’t Scientific Publishing Been Disrupted Already?).

¹ Many journals are scanning their older papers and make them available in electronic form, e.g. Nature. The first issue of Nature from 1869 can be seen here.

² We all know that computers haven’t brought us the paperless office, but that we all use more paper than 10 years ago.

ORCID stands for Open Researcher and Contributor ID and was announced in early December. This blog post tries to summarize some of the problems that have to be solved to develop a unique identifier for scientists.

1. Identify the problem
The Researcher Identification Primer by the Gen2Phen Knowledge Center lists some of the problems that a unique identifier for scientists tries to solve, including

• Disambiguation of author names in the scientific literature and establishing/validating relationships between authors and publications.
• A solid foundation for permitting and tracking online scientific contributions, such as database submissions, scientific blogging, and community curation efforts.
• Knowledge discovery applications using some or all of the above components.

The Gen2Phen workshop co-organized by Gudmundur Thorisson in May 2009 discussed these issues in much more detail. One of several articles talking about the problem of disambiguation of author names (especially Asian author names) appeared in Nature News in February 2008. A December 2009 Nature editorial emphasized that a unique identifier for researchers will be especially valuable to track scientific contributions that are not related to authoring a paper. Phil Bourne and J. Lynne Fink also wrote about this in PLoS Computational Biology in December 2008: I Am Not a Scientist, I Am a Number. A number of tools have tried to solve this problem, but it is not possible to link the researcher identities in the many systems.

2. Define what you want to accomplish
Geoff Bilder gave a very good introduction to the problem at Science Online London in August and STM Innovations in December. Both talks were similar, but the latter is available as video and PDF. He emphasized that ORCID is about Knowledge Discovery and not Access Control, and explained the terminology for subject, identifier, profile, persona and credential. Access Control is a related problem that is sometimes mixed in, but there is no requirement that a unique researcher identifier also has to provide secure access via whatever mechanism (Open ID is one solution to that problem).

3. Win support of stakeholders
Founding members of the ORCID initiative can be found on the ORCID homepage and include publishers, funders, universities, organizations and software companies. A number of important stakeholders are already part of the initiative, support by more funders (besides the Wellcome Trust) and software companies (particularly those that build reference managers or social networking sites for scientists) would be great. Probably the biggest name not on the list is the U.S. National Library of Medicine that runs the PubMed database of biomedical literature (the ORCID members Wellcome Trust and British Library are involved in UK PubMed Central).

4. Make decisions about the general design of the system
Some of the design decisions obviously are not set in stone at this stage. One continuing discussion is centralized vs. federated, and it looks like ORCID will be a centralized system similar to the DOI. Geoff Bilder has some good arguments for a centralized system. Another recurring theme is how much control an individual researcher has over his ORCID record. Although external assertion from publishers or funders will certainly be part of ORCID, the individual researcher will have an important role, not only because of privacy concerns, but also because this is the easiest way to fix errors that even the best automated algorithms for author assignment will produce. And it looks as if ORCID will be an extensible system that will for example allow publishers or social networking sites to add functionality they require. The discussion at the STM Innovations meeting in early December touches some of these issues and is recorded as video (after the talk by David Kochalko).

5. Pick a name
The name Open Researcher and Contributor ID (ORCID) is obviously a combination of ResearcherID (Thomson Reuters) and Contributor ID (CrossRef). I would have preferred a simpler name, but I guess we have to get used to ORCID.

6. Build on available tools
ORCID will be based on the ResearcherID software from Thomson Reuters. From what I’ve seen, the Open ID system will not be a central part of ORCID. But ORCID certainly will be designed to work together with Open ID and other authentication mechanisms. I don’t know what Elsevier and the Scopus Author ID will contribute to ORCID.

7. Form an independent organization
In order to be adopted widely, ORCID must be run by an independent organization, and not by a single publisher, software company, research organization or funder. With the experience of running the DOI system to identify digital objects such as scientific papers, CrossRef would be one obvious candidate, but the ORCID founding members have yet to decide on that.

8. Secure financing
Starting and maintaining ORCID will obviously cost money. In my little survey about author identifiers back in April 2009, the opinions were split about who should pay for this. Journal publishers and database maintainers (referring to such databases as PubMed, Scopus or Web of Science) were the two most common answers. ORCID will make it easier for funding agencies to evaluate scientists and they might therefore also contribute to the system. Individual researchers hopefully will not have to pay for any of this, but their input in time is obviously required.

9. Promote ORCID
A Nature editorial in December was a good start to promote ORCID to a wider audience. A unique identifier for scientists will only become accepted if widely used. That’s why it is important that publishers and funders quickly adopt this service. Software companies that build interesting tools around ORCID are also critical, e.g. integration of ORCID into manuscript submission systems (including the use of ORCID for the peer reviewers) and social networking sites (including of course Nature Network). My experience with the DOI for papers (e.g. the limited support in PubMed) tells me that adoption of ORCID will be a long process.

10. Involve individual researchers
Individual researchers currently have no way to get directly involved in ORCID. But some level of involvement is critical for an author identifier to work. The best place is currently probably the LinkedIn Group Unique Identifiers for Researchers started by Cameron Neylon. But I hope we soon see ORCID discussions on Nature Network and other social networking sitess. The best place on Nature Network to discuss ORCID is currently probably the Scientific Researchers and Web 2.0: Social Not Working? Forum.

Sustainability in science is nothing new. The term sustainability science was probably first used in 2001 (see Wikipedia entry), and the title of this blog post was already used by a 2002 editorial in Science. There are both journals (Sustainability: Science, Practice & Policy, Sustainability Science) and conferences (e.g. here and here) about this topic and you can get a degree in sustainability science. The term sustainability is usually used in the context of climate change and the conservation of natural resources.

Flickr image by Changhua Coast Conservation

Here I want to use sustainability in a broader sense, using the original definition: able to be maintained at a certain rate or level.¹ Examples where the way we currently do science will probably no longer be sustainable in the future include grant applications that have a chance of success as low as 1% (the wait continues for NIH Challenge Grant applicants), the ever-increasing costs for access to scholarly publications (the serials crisis), or the exponential growth of drug development costs without any increase in approval for new drugs in the last 60 years (Drug Companies Since 1950).

Sustainability in science requires the individual researcher to think about his responsibility, i.e. to go beyond research that is personally interesting and is paid for by someone. I do think that increasing sustainability in science is a worthy goal, and I picked six examples.

Make access to research results affordable
For those not working at an academic institution, many subscription-based journals now make their papers available after a 6-12 month embargo period. Immediate full access to an individual paper in these journals can cost anywhere between $10 and $30 ($31.50 Cell, $15.00 Science, $32.00 Nature, $31.50 The Lancet, $10 New England Journal of Medicine). As you can guess from the wide range for these journals alone, these prizes are probably not calculated to cover actual costs. Deep Dyve launched a rental service for scientific content in October. They charge $0.99 per article rental, but currently include only a limited number of journals.

Most researchers have access to subscription-based journals through their institutions. My university library currently has a budget of about 900,000 € for just over 2000 researchers and 2600 students. Even with this money, our institution can’t afford subscriptions to all journals import for my work. And subscription costs are increasing much faster than library budgets. Open Access obviously is one answer to this dilemma, but may not work for all journals. Most of us would probably be happy to pay for journal subscriptions if subscription costs simply remained reasonable. Because a handful of publishers own a large part of scientific journals, this will only happen if someone representing a large group of universities and research institutions sits at the negotiation table.

Reduce the bureaucracy in science funding
We are currently spending too much time trying to obtain research funding compared to the time actually doing research. This is in part because the chances of obtaining a grant are often fairly low and grant applications have to be submitted many times, and because the duration of some grants is to short, e.g. only 2-3 years (sometimes meaning you have to start writing on the extension grant after the first year). Providing funding to excellent researchers for longer periods of time instead of funding projects is one approach to improve this situation. The Howard Hughes Medical Institute has done this for many years with HHMI investigators and the Wellcome Trust last month announced a similar approach with Wellcome Trust Investigator Awards.

Communicate and use research results
A lot of research has practical value, but this practical value has to be explored. One nice example from my area of expertise is an international consortium to improve the outcome of a specific form of acute leukemia in the developing world. The first results were reported at the ASH meeting earlier this month, one of only a handful of abstracts to be picked for the plenary session. But use of research results goes beyond translational research, using them for science education (both in schools and universities) is equally important.

Science blogging could have an important role in communicating research, and this blog post from a few days ago is a wonderful example of how a blog post can enhance a Nature paper. It would be great if more journals would follow the PLoS journals in linking to blogs posts about a paper,² and journals should help their authors to blog, e.g. by asking for a blog post (that could be hosted by the journal) on paper acceptance. Conference blogging is another area where science blogging would be a very welcome addition. It was nice to see official conference blogging at the German Genetics Conference this year, and I hope to see more of that.

Develop and promote technologies that make scholarly research more efficient
Obviously I have written a lot about this topic on this blog, e.g. about the article of the future, reference management, paper submission, validation, formatting and exporting of scholarly content, or researcher identifiers. But I believe that there is still a lot more that can be done, and I expect to see one or more disruptive technologies in the future. Time will tell if Google Wave is one of them, the Open Researcher Contributor Identification Initiative (ORCID) announced earlier this month certainly is a very big step forward.

Preserve research data
Providing and preserving the research data behind a project is becoming increasingly important, and simply writing up a paper is no longer enough] In many areas we lack the infrastructure (nomenclature, databases, etc.) and resources for this, especially for long-term preservation. One ambitious project is Elixir, which is trying to develop an infrastructure for biological information in Europe. The CaBIG project at the U.S. National Cancer Institute is trying to do something similar for cancer research. Examples for digital preservation projects can be found at the British Library and the German Nestor project.

Involve people outside of universities and institutions in research
Many areas of research would profit from this approach. A prominent example of citizen science is Galaxy Zoo, where more than 150,000 people are helping with the classification of astronomy images. Involving people is especially in medical research. PD Online Research is a wonderful community site about research on Parkinson disease that launched in June 2009. Personalized genetics can give the patient or healthy individual a more active role in healthcare decisions.

Whether sustainability will ultimately play a greater role in science will ultimately depend on those paying for research. If universities, institutions and funders continue to look mainly at goals that are both too short-term and only an indirect measure of scientific progress (e.g. the Impact Factor of a journal that a paper is published in), and don’t honor activities such as data annotation, public outreach, etc., this will be very difficult. I wish you a great start into the new year.

¹ The German word for sustainability is Nachhaltigkeit.

² And please, please use the DOI for that.

³ This blog post was one important inspiration for this post, as was the SciFoo meeting in July, and many small things in between, including of course the Science Online London meeting.

Two papers (this and this) and an editorial in the latest issue of Archives of Internal Medicine examine the cancer risks associated with the use of computed tomography (CT) examinations.¹

Ionizing radiation increases the risk for developing cancer. There is direct evidence from atomic bomb survivors in Japan in 1945 and from nuclear accidents such as the one in Chernobyl in 1986. There are no studies directly demonstrating an increased cancer risk from the diagnostic use of X-rays (either conventional radiographs or computed tomography), as this would require long-term follow-up of a very large number of people. This risk can only be estimated, based on the assumption that there is no lower radiation threshold dose for cancer risk and that a linear correlation exists between dose and cancer risk. Similarly, we know very little about the actual radiation doses that patients receive during a diagnostic CT scan.

Flickr image by Решила Вонасах

The paper by Rebecca Smith-Bindman and her coworkers looked at the radiation doses associated with the 11 most common computed tomography examinations in four hospitals in the San Francisco Bay Area. Radiation doses to individual patients were not measured directly, but were estimated using the commonly used “effective dose”. Median effective doses for routine computed tomography of the head, chest and abdomen-pelvis were 2, 8 and 16 mSv. The highest median effective doses (31 mSv) were used for multiphase CTs of the abdomen-pelvis (range 6-90 mSv). The 8 mSv dose for a routine chest CT is equivalent to 119 conventional chest X-rays. Interestingly, there was wide variation of effective doses used both between hospitals and within the same institution (with a mean 13-fold variation between highest and lowest dose for each CT study type).

Based on these doses, the authors then estimated the increased risk for radiation-induced cancer following a CT examination. This risk is higher in younger people and in women. Women have a higher risk to develop lung cancer following radiation exposure and they have the added risk of developing breast cancer. The authors estimated that it would for example require approximately 620 CT scans for ruling out pulmonary embolism in 40-year-old women to induce one cancer.

The second paper by Amy Berrington de Gonzalez and coworkers tried to calculate the total number of CT scans performed in the US in 2007, and estimated the increased risk for cancer related to these CT scans based on examination type, age and sex. They used a similar model to calculate the cancer risk as the first paper. Overall, about 72 million CT scans were performed in the US in 2007. The authors estimated that approximately 29.000 additional cancers will eventually develop, equivalent to approximately 2% of all cancers diagnosed annually in the US.

CT scans have dramatically improved patient care, and the conclusions of these two papers should not preclude their use in patients where the potential benefits clearly outweigh the risks mentioned above. But in order to reduce the cancer risk associated with CT scans, the authors of the two papers and the editorial suggest to optimize and standardize the CT scan procedure (remember the 13-fold difference in dose for the same procedure) and to decrease the number of unnecessary examinations. The latter is most relevant when CT scans are performed as screening procedures.

More blog posts discussing these papers can be found on Nature Blogs and Dr. Len’s Cancer Blog.

¹ All three papers are available as fulltext without a subscription. And none of the papers displays it’s DOI, which makes linking to them unneccessarily difficult.

Smith-Bindman, R., Lipson, J., Marcus, R., Kim, K., Mahesh, M., Gould, R., Berrington de Gonzalez, A., & Miglioretti, D. (2009). Radiation Dose Associated With Common Computed Tomography Examinations and the Associated Lifetime Attributable Risk of Cancer Archives of Internal Medicine, 169 (22), 2078-2086 DOI: 10.1001/archinternmed.2009.427

Berrington de Gonzalez, A., Mahesh, M., Kim, K., Bhargavan, M., Lewis, R., Mettler, F., & Land, C. (2009). Projected Cancer Risks From Computed Tomographic Scans Performed in the United States in 2007 Archives of Internal Medicine, 169 (22), 2071-2077 DOI: 10.1001/archinternmed.2009.440

Redberg, R. (2009). Cancer Risks and Radiation Exposure From Computed Tomographic Scans: How Can We Be Sure That the Benefits Outweigh the Risks? Archives of Internal Medicine, 169 (22), 2049-2050 DOI: 10.1001/archinternmed.2009.453

Earlier this month I gave this talk in my department. It is basically a summary of two blog posts that I wrote in October during Open Access Week (Open Access Week: a researcher’s perspective part I and part II), and I had given a similar talk in November in an Open Access workshop organized by the Helmholtz Association. But because this time my audience (researchers and clinicians in a university hospital) was less knowledgeable about Open Access, I added a few introductory slides in the beginning.

The discussion is usually the most interesting part, and this topic certainly has a lot of material for discussion. Interestingly, we talked mainly about the problem of copyright. Even though anybody who has ever submitted a paper to a (non-Open Access) journal has signed a copyright transfer agreement, the implications of this were not really clear to most people in the audience. Reuse of a figure or table in an academic seminar usually falls under fair use, but many journals still require a (free) permission.¹ And using the same figure in a medical conference can cost several hundred dollars, and it doesn’t really matter that you are one of the authors of the paper (slides 15-17 in the presentation). Some of my colleagues have run into issues with copyright, usually when the talks of a conference were later redistributed on a CD or website.

Unfortunately there wasn’t enough time to discuss some of the other issues raised in the talk, e.g.

• Why can’t our Medical School Library afford an institutional subscription for Cell?
• Why is there no institutional repository at our university?
• Why is it very unlikely that we will have a mandate for Open Access in Germany in the near future?
• Why has the Impact Factor become so important in Medicine?

The seminar was also interesting in that this was one of the rare occasions where I talked publicly in my department about some of the topics that I regularly write about on this blog. I always felt that most of my colleagues don’t really care about these topics, and that they probably think I should rather spend my time working on the next paper or grant. I haven’t gotten much feedback after the talk, but maybe I should reconsider that position.

¹ Many journals use Copyright.com, which makes this process straightforward.

Nature Communications is a new journal that will launch in Spring 2010. The journal will publish papers in all areas of the physical, chemical and biological sciences and is open for submissions.

The Nature Publishing Group publishes one fully open access journal (Molecular Systems Biology) and more than ten journals that offer an open access option for authors (including EMBO Journal). Nature Communications will be the first Nature journal with an open access option for authors. Nature Communications papers where the author has not opted for open access will be available through an institutional subscription, or by purchasing an individual article.

There are many good arguments for open access, but from a journal perspective the publishing model must make business sense. Most open access journals use the author-pays model, and an editorial in the August 2009 issue of Nature Materials talked about some of the difficulties of this publishing model for the Nature journals – the costs that are currently spread among many subscribers would be prohibitely high for an author-pays option. Some high-profile open access journals have article publication charges that are probably not covering all costs (e.g. PLoS Biology) or use a different business model that doesn’t require article publication charges (BMJ). Nature Communications will have an article publication charge of $5000, which is higher than what most journals charge. I interviewed Lesley Anson, the Chief Editor of Nature Communications, to learn more about the journal.