Tuesday, December 6, 2011
Open Access versus ‘doing business on corpses’: Is PLoS ONE the choicest journal of the TB community?
Given this, I must congratulate all those authors who have by publishing in ONE in a way dumped the might of the journals that block Open Access to TB research - something like 'doing business on the corpses'. They have for years blocked access to TB works - the situation worsened in high burden countries such as India (where 320000 people died of TB in 2010 alone). Very surprising and painful is the reality that one of these journals, the IJTLD is published by the International Union Against TB and Lung Disease or the Union (www.theunion.org), one of the major champions of the cause of TB. While the Union is doing very laudable efforts in the area of TB control and prevention, I would urge them to consider widening unconditional Open Access to the IJTLD contents by the Indian TB communities (rather than linking access to membership/subscription). Why would someone become a member of the Union just to read an article in need? Currently, the Union makes available the journal through Ingenta Connect who charge about USD 40.00 per view, per article when accessed directly. The cost per view charged thereby is equivalent of the cost of food/ration for one month for a mid size, lower middle class family in India. The same is true with Tuberculosis articles, each accessible at the cost of USD 35.00 levied by Elsevier. The Union receives huge funding and donations from various sources and they should seriously think on converting their journal in to an Open Access, online only journal to better serve the down trodden.
World over, the research on TB is mainly funded by tax payers' money and in no way the TB community should allow these journals to carve business out of this dreaded epidemic. PLoS ONE on the other hand generously waives off cost of article processing for all the authors who request for the same. Each article is available free of cost for unlimited download and distribution with no strings attached. That's why PLoS ONE stands today as one of the choicest journal of the TB researchers.
Thursday, November 10, 2011
German cows get clean chit for the outbreak of Shiga toxin-producing E. coli O104:H4
No evidence of the Shiga toxin-producing E. coli O104:H4 outbreak strain or enteroaggregative E. coli (EAEC) found in cattle faeces in northern Germany, the hotspot of the 2011 HUS outbreak area
Lothar H Wieler, Torsten Semmler, Inga Eichhorn, Esther M Antao, Bianca Kinnemann, Lutz Geue, Helge Karch, Sebastian Guenther and Astrid Bethe Gut Pathogens 2011, 3:17 doi:10.1186/1757-4749-3-17 Published: 3 November 2011
Ruminants, in particular bovines, are the primary reservoir of Shiga toxin-producing E. coli (STEC), but whole genome analyses of the current German ESBL-producing O104:H4 outbreak strain of sequence type (ST) 678 showed this strain to be highly similar to enteroaggregative E. coli (EAEC). Strains of the EAEC pathotype are basically adapted to the human host. To clarify whether in contrast to this paradigm, the O104:H4 out-break strain and/or EAEC may also be able to colonize ruminants, we screened a total of 2.000 colonies from faecal samples of 100 cattle from 34 different farms - all located in the HUS outbreak region of Northern Germany - for genes associated with the O104:H4 HUS outbreak strain (stx2, terD, rfbO104, fliCH4), STEC (stx1, stx2, escV), EAEC (pAA, aggR, astA), and ESBL-production (blaCTX-M, blaTEM, blaSHV). Results: The faecal samples contained neither the HUS outbreak strain nor any EAEC. As the current outbreak strain belongs to ST678 and displays an enteroaggregative and ESBL-producing phenotype, we additionally screened selected strains for ST678 as well as the aggregative adhesion pattern in HEp-2 cells. However, we were unable to find any strains belonging to ST678 or showing an aggregative adhesion pattern. A high percentage of animals (28%) shed STEC, corroborating previous knowledge and thereby proving the validity of our study. One of the STEC also harboured the LEE pathogenicity island. In addition, eleven animals shed ESBL-producing E. coli. Conclusions: While we are aware of the limitations of our survey, our data support the theory, that, in contrast to other Shiga-toxin producing E. coli, cattle are not the reservoir for the O104:H4 outbreak strain or other EAEC, but that the outbreak strain seems to be adapted to humans or might have yet another reservoir, raising new questions about the epidemiology of STEC O104:H4. Access full article free of cost
Wednesday, October 26, 2011
Feast of the Open Access Week: PLoS Won
When Pat Brown, Harold Varmus and I started the Public Library of Science (PLoS) 10 years ago with the goal of making the scientific and medical literature a universally freely available resource, most people in the science publishing industry dismissed us as naive idealists who didn't understand that publishing is a business that has to make money, or derided us as dangerous radicals hellbent on destroying them.
So it has given me considerable pleasure to watch, over the past year or so, as one traditional publisher after another has responded to the smashing success of PLoS One by launching direct ripoffs that seek to capitalize on the business model we have established.
For those of you who don't know, PLoS One, launched in 2006, does things a bit differently than most scientific journals. Every paper submitted to the journal is peer reviewed, but the reviewers and editors consider only the technical merits of the paper in deciding whether or not it should be published – they do not attempt (as virtually all other journals do) to gauge the potential significance or sexiness of the paper. The result is a simple and objective peer review process that gets papers published quickly and, because it is an open access journal, in a place where it is accessible for anyone to find and read. To cover the costs of running the journal and handling the paper, authors of accepted papers pay a fee (currently $1,350 – he money comes from their research grants or institutions, not from their own pockets, and any authors who say they can not pay are granted waivers).
And apparently authors love PLoS One, because they are sending us lots of paper. The journal published 6,700 articles in 2010 and will publish around 12,000 in 2011. This has clearly caught the attention of lots of established publishers, as the past year has seen the launch of a series of PLoS One clones, including:
- The American Society for Microbiology's mBio
- The Genetics Society of America's G3
- BMJ Open
- Company of Biologists Biology Open
- Nature's Scientific Reports
- Cell Press's Cell Reports
- The Royal Society's Open Biology
- SAGE Open
joining already existing offerings from open access publishers BioMed Central, Hindawi and others.
This is, in many ways, exactly what we hoped would happen. In 2001 most publishers lacked both the foresight to see how publishing could better serve the research community, and the incentive to bother figuring it out. Now, PLoS One's volume, and the threat it poses to their existing journals, provides the motivation, and PLoS One's financial success (it is profitable) serves as an inspiration. Our goal was always to see that papers were published in open access journals. If they were PLoS journals – great. But if they were from other publishers – that's great too.
And here, there is a bit of a rub. PLoS and BMC established the standard for open access publishing by adopting the Creative Commons Attribution License (CC-BY), which allows for unrestricted reuse and redistribution subject only to the constraint that the original authors and source be cited. Several of the new journals follow our lead and use CC-BY, including G3, Open Biology and SAGE Open. I fully endorse what these publishers are doing, and have already published one paper in G3.
The others have not been so enlightened, using exclusively (or in one case optionally) licenses that restrict commercial reuse or the generation of derivitive works.
CC-BY-NC – BMJ Open
CC-NC-SA – mBio, Biology Open
CC-BY-NC-ND – Scientific Reports
CC-BY or CC-BY-NC-ND – Cell Reports
This is a very misguided decision on the part of these publishers. The rules governing reuse of content matter a lot if we are ever going to start making more effective use of the published scientific literature. The non-commercial licenses employed by BMJ, Nature, ASM, Company of Biologists, Cell Press and Nature all – rather absurdly – prevent PLoS from reusing their content in tools we are developing to help researchers organize literature in their fields and make the contents of papers they care about more useful. I hope this is a short-lived mistake and that, following Netflix, they realize the error of their ways and switch to a CC-BY license (in the meantime, I urge people who care about open access to continue supporting only those journals that use the CC-BY license).
There is, obviously, still a long way to go before we achieve our original goal of making every paper immediately freely available. Buit it's hard not to see events of the last year as anything but a major victory for PLoS and open access.
Happy Open Access Week!
[UPDATE: I want to clarify that Cell Reports does not view itself as a PLoS One clone, as it will be rejecting papers on the basis of impact/importance. I also want to commend them for offering the CC-BY license to authors, although I think that many will naively choose the NC version].
