quarta-feira, 20 de fevereiro de 2013

Porque as revistas pagas devem acabar

A discussão sobre revistas de acesso aberto (open access) x revistas de acesso fechado (as disponíveis somente para quem faz assinatura de conteúdo) está em voga. Neste blog, temos apresentado alguns argumentos a favor do acesso aberto. Esses argumentos, no entanto, vem sendo apresentados por pesquisadores, em sua maioria. No entanto, ontem me deparei com este post, publicado no The student blog (PLOS Blogs). No post, Jack Andraka, aluno de high school, explica porque, na opinião dele, a divulgação científica (os artigos publicados) devem ser de livre acesso, para todos e não só para quem está na universidade. Veja a história:

After a close family friend died from pancreatic cancer, I turned to the Internet to help me understand more about this disease that had killed him so quickly. I was 14 and didn’t even know I had a pancreas but I soon educated myself about what it was and started learning about how it was diagnosed. I was shocked to discover that the current way of detecting pancreatic cancer was older than my dad and wasn’t very sensitive or accurate. I figured there had to be a better way!

I soon learned that many of the papers I was interested in reading were hidden behind expensive pay walls. I convinced my mom to use her credit card for a few but was discouraged when some of them turned out to be expensive but not useful to me. She became much less willing to pay when she found some in the recycle bin! One of the best journal articles was called Carbon Nanotubes: the route towards applications.

This was the [paywall to the] article I smuggled into biology class the day my teacher was explaining antibodies and how they worked. I was not able to access very many more articles directly. I was 14 and didn’t drive and it seemed impossible to go to a University and request access to journals.

Some adults have told me I should have done that but, as a 14 year old, it was intimidating. It was also hard to get my parents to drive me to a University library since they didn’t really believe in my project and were trying to convince me to change projects! So there are a lot of barriers for kids to learn more and educate themselves. Open access would help people like me who may not drive or have access to a University library.

Luckily I was able to convince my mom to finance some more articles I needed and I learned to try different ways of circumventing the pay walls. I emailed one author with some questions though and he was able to provide me with a copy. Writing authors directly is a good way to get articles without paying but I didn’t figure this out right away.

I was persistent enough to be able to get access or at least the abstracts to enough journals to help me write my proposal which I then used the Internet to find and email over 200 local professors who were working on pancreatic cancer. Of course, most didn’t take me seriously or were too busy or just not interested in helping but I finally did get into a lab. Of course when I did get into a lab, then the University had access to so many articles because they subscribed to them. However, even universities are feeling that the subscriptions are expensive.

I was on a panel with Luis A. Ubiñas , head of the Ford Foundation, and heard him describe how running times at the Olympics plummeted after African countries started participating. I was thinking that if kids around the world could get connected to the internet and journals and each other, that even more creativity would be harnessed to solve the world’s problems.

Open access would be an important first step. I would love to see research that is publicly funded by taxes to be publicly available through neighborhood libraries and public school libraries.

 It would make it so much easier for people like me to find the information they need.  If I can create a sensor to detect cancer using the Internet, imagine what you can do.

segunda-feira, 11 de fevereiro de 2013

Muito além do peso

Aproveito o feriado de carnaval, quando temos algum tempo a mais, para apresentar este vídeo, a respeito da obesidade infantil. É longo mas vale assistir. 

"Não há nada que fazemos mais vezes no nosso dia do que comer. Nós não fazemos contas tantas vezes por dia, nós não lemos tantas vezes por dia, nós não escrevemos tantas vezes por dia. Mas nós comemos. E por que não se ensina o que se deve comer (educação nutricional) assim como se ensina a ler, a escrever e a fazer contas?"

sexta-feira, 8 de fevereiro de 2013

Neutrófilos e Células Dendríticas

O grupo de Fabienne Tacchini-Cottier acaba de publicar uma ótima revisão a respeito do cross-talk (comunicação?) entre neutrófilos e células dendríticas, tema no qual o grupo tem experiência.
A revisão traz um resumo das informações sobre as condições em que neutrófilos induzem a ativação de células dendríticas versus as condições em que isso não acontece, em diferentes modelos.


Neutrophils are massively and rapidly recruited following infection. They migrate to the site of acute infection and also transiently to dLNs. In addition to their well-established role as microbial killers, accumulating evidence shows that neutrophils can play an immunoregulatory role. Neutrophils were recently shown to influence the activation of different leukocyte types including NK cells, B cells, and DCs. DCs are professional APCs playing a key role to the launching and regulation of the immune response; thus, crosstalk between neutrophils and resident or newly recruited DCs may have a direct impact on the development of the antigen-specific immune response and thereby, on the outcome of infection. Neutrophils may regulate DC recruitment and/or activation. We will review here recent progress in the field, including those presented during the first international symposium on "Neutrophil in Immunity", held in Québec, Canada, in June 2012, and discuss how neutrophil regulatory action on DCs may differ depending on the type of invading microorganism and local host factors.

ResearchBlogging.orgSchuster S, Hurrell B, & Tacchini-Cottier F (2012). Crosstalk between neutrophils and dendritic cells: a context-dependent process. Journal of leukocyte biology PMID: 23250891

quarta-feira, 6 de fevereiro de 2013

Another brick in the wall

Não, não vamos falar de Pink Floyd mas, sim, de open access publishing. Com o provocante título (" Hiding your research behind a paywall is immoral"), Mike Taylor, reforça a necessidade de publicarmos nossos resultados em revistas Open Access. O que eu mais gostei foi a maneira como os argumentos foram apresentados, como forma de resposta às perguntas e comentários mais comuns. Veja abaixo: 

Publishing science behind paywalls is immoral. There, I said it.
I know, I know. It's an easy trap to fall into – I've done it myself. To my shame, several of my own early papers, and even a recent one, are behind paywalls. I'm not speaking as a righteous man to sinners, but as a sinner who has repented. Having started my scientific life from rather a conventional stance, it took me a while to come around to this position. 

If you are a scientist, your job is to bring new knowledge into the world. And if you bring new knowledge into the world, it's immoral to hide it. I heartily wish I'd never done it, and I won't do it again.
But aren't there special cases?

I really need to publish in Science/Nature/Cell for my career …

No. Michael Eisen, cofounder of the Public Library of Science (PLOS), doesn't believe this is true and makes a strong case that we're confusing correlation with causation. He notes that fewer than half of biology hires at Berkeley in the last decade have published in Science, Nature or Cell. Berkeley!
We know that important administrative assessments such as the UK's Research Excellence Framework (REF) explicitly disclaim the use of impact factors (surrogates for measuring journal prestige) in assessing research. We know that important funders such as the Wellcome Trust explicitly state that "it is the intrinsic merit of the work, and not the title of the journal in which an author's work is published" that determines who gets grants.
And if you really and truly believe in your heart that your work will be judged by the journal it appears in rather than by its merit (perhaps because you work in France, where assessment policies do depend on impact factors) then there are highly regarded open-access outlets such as PLOS Biology (rated number one for biology in the Journal Citation Reports) and eLife (which is too young to have an impact factor but was established precisely to compete in the Science 'n' Nature space.)

But I can't afford article processing charges (APCs) …

No. First of all, more than half of open-access journals don't charge a fee at all. Among those that do, the average fee is $906 (£563) – a tiny proportion of most research grants. PeerJ, which launches this month, charges a one-off fee of $299 for a lifetime's publications. Most fee-charging open-access journals offer waivers - for example, the no-questions-asked waiver at PLOS, where the philosophy is explicitly that no one should be prevented from publishing by lack of funds.
Tim Gowers, who is leading a boycott against the publisher Elsevier and is starting the new Forum of Mathematics journal says it "will not under any circumstances expect authors to meet APCs out of their own pockets, and I would refuse to be an editor if it did".

But this paywalled journal's subscription fees fund its scholarly society …

No. This is the tail wagging the dog. The purpose of a scholarly society is to promote scholarship, which is best done by making that scholarship available. A society that cares more about preserving its own budget than about the field it supposedly supports has lost its way. Societies need to find other ways to fund their activities. And yes, I am talking to you, Society of Vertebrate Paleontology (my own field's society). You cannot support the science of vertebrate palaeontology by taking science and hiding it where most people can't see it.

But my co-authors want to publish in this paywalled journal …

No. They have no more legitimate reason to lock their work away from readers than you do.

But this paper is a rebuttal, and we want to submit to the same journal, because …

No. I and my colleagues fell into this trap with our neck-selection paper: we sent it to the Journal of Zoology because that's where the original paper claiming sauropod necks were sexually selected had been published. What the heck were we thinking? The scientific conversation doesn't happen within the pages of any given journal, it happens across all journals.

But, but, but …

No, no, no. Dammit, we're scientists. Our job is to make knowledge. If we make it, then brick it up behind a wall, we're wasting our time and our funders' money – which ultimately means we're squandering the world's wealth.
Publishing behind paywalls is immoral. More than that, it's oxymoronic: if it's behind a paywall, it hasn't been published. We have to stop doing it, now and for always.

Voltaremos a esse tema em posts subsequentes. O assunto é importante, deve ser discutido pela comunidade, tanto por pesquisadores quanto pelas agências de fomento. Afinal, se nosso recurso para pesquisa é  público, o resultado que obtemos também não deve ser?

segunda-feira, 4 de fevereiro de 2013

O poder das cores e formas...

Para transmitir informações. Na cola do post de Tiago Mineo No SBlogI e da sugestão dada por Bernardo Franklin, segue o vídeo do HHMI feito para ilustrar ciclo de vida do plasmódio.
Esse post vai em homenagem ao estudante Vitor Rosa, doutorando do Prof Barral, que está na Amazônia, coletando dados para a sua tese em malária.

sexta-feira, 1 de fevereiro de 2013

Susceptibilidade a Leishmaniose Visceral: novos alelos identificados

Os consórcios LeishGEN e Wellcome Trust Case Control publicaram um trabalho na Nature Genetics no qual identificam alelos de HLA classe II associados com o desenvolvimento de Leishmaniose Visceral. O trabalho foi realizado em famílias na Índia e no Brasil. 

ResearchBlogging.orgTo identify susceptibility loci for visceral leishmaniasis, we undertook genome-wide association studies in two populations: 989 cases and 1,089 controls from India and 357 cases in 308 Brazilian families (1,970 individuals). The HLA-DRB1HLA-DQA1 locus was the only region to show strong evidence of association in both populations. Replication at this region was undertaken in a second Indian population comprising 941 cases and 990 controls, and combined analysis across the three cohorts for rs9271858 at this locus showed Pcombined = 2.76 × 10−17 and odds ratio (OR) = 1.41, 95% confidence interval (CI) = 1.30–1.52. A conditional analysis provided evidence for multiple associations within the HLA-DRB1HLA-DQA1 region, and a model in which risk differed between three groups of haplotypes better explained the signal and was significant in the Indian discovery and replication cohorts. In conclusion, the HLA-DRB1HLA-DQA1 HLA class II region contributes to visceral leishmaniasis susceptibility in India and Brazil, suggesting shared genetic risk factors for visceral leishmaniasis that cross the epidemiological divides of geography and parasite species.

LeishGEN Consortium, Wellcome Trust Case Control Consortium 2, Fakiola M, Strange A, Cordell HJ, Miller EN, Pirinen M, Su Z, Mishra A, Mehrotra S, Monteiro GR, Band G, Bellenguez C, Dronov S, Edkins S, Freeman C, Giannoulatou E, Gray E, Hunt SE, Lacerda HG, Langford C, Pearson R, Pontes NN, Rai M, Singh SP, Smith L, Sousa O, Vukcevic D, Bramon E, Brown MA, Casas JP, Corvin A, Duncanson A, Jankowski J, Markus HS, Mathew CG, Palmer CN, Plomin R, Rautanen A, Sawcer SJ, Trembath RC, Viswanathan AC, Wood NW, Wilson ME, Deloukas P, Peltonen L, Christiansen F, Witt C, Jeronimo SM, Sundar S, Spencer CC, Blackwell JM, & Donnelly P (2013). Common variants in the HLA-DRB1-HLA-DQA1 HLA class II region are associated with susceptibility to visceral leishmaniasis. Nature genetics PMID: 23291585