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The following new articles have just been published in BMC Medicine

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Insights into physical activity and cardiovascular disease risk in young

Latest Article Alert from BMC Health Services Research

The following new articles have just been published in BMC Health Services Research

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Research article
Clinicians’ views on improving inter-organizational care

Latest Article Alert from BMC Infectious Diseases

The following new articles have just been published in BMC Infectious Diseases

For articles using Author Version-first publication you will see a provisional PDF corresponding to the accepted manuscript. In these instances, the fully formatted Final Version PDF and full text (HTML) versions will follow in due course.

Research article
Fever in the tropics: aetiology and case-fatality – a

In the deep, bioluminescent bacteria bloom bright


Imagine swimming to the bottom of the sea, the water growing impossibly deep and dark the farther you travel. At these depths, beyond the reach of the sun, live strange new sources of light. Fish, jellyfish, and even bacteria light up these midnight waters.

According to new research in PLOS ONE, the light of this deep-sea bioluminescence waxes and wanes with seasonal changes on earth’s surface. In the Mediterranean winter, cold winds cause surface water to cool. As the surface cools, it becomes denser than the water beneath it, and begins to sink. Convection can also cause this layer to expand, potentially extending it to the Mediterranean Sea’s basin floor. When these phenomena occur side by side, as they can in the northwestern part of the Mediterranean Sea, carbon matter from the surface circulates into deeper waters. Think of it as Nature’s way of stirring the pot.

This wintry stir spreads a wave of changing temperatures, water composition and organic matter into the depths of the ocean, which correlates with a burst of bioluminescence activity. Over the course of two and a half years, the researchers recorded two water stirring incidents, followed by periods of bioluminescent activity. In each instance, winter stirring resulted in bioluminescent blooms lasting several weeks in the following spring or summer.

That being said, this phenomenon is likely to change in the coming years. According to the researchers, as climate change continues to affect the sea, convection activity which helps stir the waters and introduce much-needed carbon to the deep sea may decrease by the end of the 21st century. In the meantime, it is important to document deep-sea activity to better understand any actual or forecasted changes.


Citation: Tamburini C, Canals M, Durrieu de Madron X, Houpert L, Lefèvre D, et al. (2013) Deep-Sea Bioluminescence Blooms after Dense Water Formation at the Ocean Surface. PLoS ONE 8(7): e67523. doi:10.1371/journal.pone.0067523

Image: Biolumplate, from Wikimedia Commons.

Evolutionary Applications Publishes issue 6.5

Evolutionary ApplicationsEvolutionary Applications has published a new issue exploring the ways in which evolutionary biology addresses biological questions of health, social and economic relevance.  The issue features an image of a young wood frog on its cover.  Editor-in-Chief: Louis Bernatchez has highlighted the articles below as particularly noteworthy:

purple_lock_open Molecular genetics and genomics generate new insights into invertebrate pest invasions by Heather Kirk, Silvia Dorn and Dominique Mazzi
Summary: This article reviews current applications of molecular genetics and genomics in the study of invertebrate pest invasions and outbreaks, and highlights shortcomings from the current body of research. It also discusses recent conceptual and methodological advances in the areas of molecular genetics/genomics and data analysis and highlights how these advances will enhance our understanding of these areas.

purple_lock_open Evolutionary dynamics of a rapidly receding southern range boundary in the threatened California Red-Legged Frog (Rana draytonii) by Jonathan Q. Richmond, Kelly R. Barr, Adam R. Backlin, Amy G. Vandergast and Robert N. Fisher
Summary: This study reviews the extensive decline in populations of the California red-legged frog (Rana draytonii) since the 1960s due to contemporary disturbance. The authors conclude that while the effects of recent disturbance have left little genetic imprint on these populations, they likely contribute to an extinction debt that will lead to continued range contraction unless management intervenes to stall or reverse the process.

purple_lock_open Genetic and life-history changes associated with fisheries-induced population collapse by Lilian Pukk, Anna Kuparinen, Leili Järv, Riho Gross and Anti Vasemägi
Summary: This article investigates the evolutinary consequences of intensive fishing simultaneously at phenotypic and molecular level in Eurasian perch (Perca fluviatilis L.) population in the Baltic Sea over a 24-year period. This study demonstrates the value of combining genetic and phenotypic analyses in the context of long-term genetic monitoring and suggests that replacement or breakdown of locally adapted gene complexes may play important role in impeding the recovery of fish populations.

In 2013 we have expanded the scope of Evolutionary Applications. As before, we are keen to encourage papers applying concepts from evolutionary biology to address biological questions of health, social and economic relevance across a vast array of applied disciplines. We now also strongly encourage submissions of papers making use of modern molecular and genetic methods to address important questions in an applied evolutionary framework. For more information please visit the aims and scopes page.

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Latest Article Alert from Journal of Occupational Medicine and Toxicology

The following new articles have just been published in Journal of Occupational Medicine and Toxicology

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Reduction of needlestick injuries in

World at Sea

How multitudes of people
can gather to gawk daily
at these magnificent, miserable creatures
being forced through round after round
of revolting Skinnerian circus tricks,
having been brutally wrenched
from their devastated families
to be pitilessly imprisoned
for the rest of their wretched, reduced lives
in holding containers,
tormented day and night
by echoes from their own hopeless sonar cries
while food-deprived and “trained”
to do whatever it takes
to draw delighted cheers
from grinning crowds of humans of all ages…

Did it really require this revealing new movie, Blackfish, to open our eyes to the ugly, shameful fact that this, and all things like this, are wrong, horribly, unforgiveably wrong?

That we provide the mindless market for such heartless abuse, in order to make our children laugh, is as much a condemnation of the sociopathic spectatorship as of the merciless, mercenary management of sadistic sea circuses — and all their land counterparts.

Perhaps the most chilling anomaly is how the “trainers” — of whom some, clearly, “turned,” eventually, after years of having been willing accomplices to the abuse of these helpless animals — were themselves “trained” (by the management along with self-deception) to overlook the obvious in exchange for the fees and the celebrity (“just following orders”? “being professional”?). It seems to have been various blends of venality and sensation-seeking, though some got into it and then got attached to their prisoners and stayed so as to use what little leverage they had to make their fate less worse, rather than abandon them altogether. — Or maybe that was just what they said for the camera? (I hope not.)

But most macabre of all was that some professed to have become Seaworld trainers to fulfill a dream that Seaworld itself had instilled in them as a child.

Tilikum’s punishment for having been kidnapped and abused for decades:

Solitary confinement
to provide sperm
for breeding more orcas
to be wrenched from their mothers
and put into entertainment servitude
for the rest of their miserable lives
to inspire more children
about the wonders of the sea

“Holes in the Tree of Life”: Why and how phylogenetic data must be published

Ross Mounce @rmounce and Joseph W Brown have been tweeting about the lack of data to support published phylogenetic studies. (Readers of this blog will know that Ross and I start work in October to extract trees from published PDFs – an awful statement of how bad the situation is.)

Very simply, phylogenetic data is key to our understanding of the history, ecology and biodiversity of the planet. If we don’t understand species then we shall lose them, and if we don’t understand how species interact we shall lose ecosystems. Look into the details of pollination and often the loss of one species affects others directly. (Though Darwin was wrong about cats->->-> clover ).

Most peer-reviewed phylogenetics is in closed journals (40 USD for a 1 day read). It’s appallingly arrogant to assume that anyone who needs it (academics) can get the info. But worse, almost none of the data are published. Phylogenetic trees are mainly computed using molecular information (DNA of key genes) and are costly. Yet the data are relatively simple. They are well understood (30+ years of sequence / gene repositories) and they are compact (accession numbers are often fine). An uncompressed tree costs perhaps a few Kb and with indexing/compression a complete study could be published in ca 1 Mb. That’s less than the size of many single images!

Here’s what sparked the discussion. I’ll give it in full, and argue that any reasonably literate person could understand it. I have highlighted some parts

Missing data lead to holes in the tree of life.

The fundamental importance of archiving scientific datasets has received increasing attention over the past several years, and failure to properly archive data can adversely affect study reproducibility. However, in plant systematics (or evolutionary biology) there has been no comprehensive review that examines the deposition practices of the underlying phylogenetic datasets and trees that are the foundation of the discipline. Furthermore, there is little understanding of how the deposition rate of DNA sequence alignments and phylogenetic trees has changed over time. In the process of gathering data to build the first tree of life for all ~1.9 million named species (the Open Tree of Life Project), we sifted through over 7200 peer-reviewed phylogenetic studies published between the years 2000 and 2012. Our survey covered over 100 journals and included publications focusing on green plants, animals, fungi, microbial eukaryotes, bacteria, and archaea. This broad survey included 1243 seed plant publications. Overall, we found that only 17% of examined studies made nucleotide alignment data and/or trees available in an accessible repository such as TreeBASE or Dryad. Within seed plants, only 24% of studies from the past 12 years have been archived. Furthermore, most corresponding authors (54% for seed plants) that we contacted for un-deposited datasets and trees did not respond to our repeated (2) requests for data. Thus, most of the trees and alignments produced during the past several decades is essentially lost forever. The plant systematics community needs to significantly improve data deposition practices to ensure that crucial data (trees, alignments) are archived and thus freely available to other interested scientists. Our results illustrate that voluntary data submission policies have not worked, and dictate the urgent need to adopt new policies requiring public archiving of DNA sequence alignments and trees in a routine manner as is done routinely with raw sequence data. These stark findings should encourage the systematic community as well as journal editorials to adopt data sharing policies that require deposition of alignments and resulting phylogenetic trees in established databases prior to publication.

Very simply (this applies to many subjects):

Many/most authors don’t care about making their science available to the world. The final result of their work is a “scholarly article”, not useful, reusable, verifiable science that can be built on, re-used by policy makers and citizens. The authors do not feel that being publicly funded gives them any obligations to the public. The ivory tower only rewards their work in the torrid market of scholarship, not the wider value to the world.

It has worked in some subjects – sequences/genes, crystal structures, galaxies. Here the disciplines have developed cultures where scientists are expected and then mandated to deposit data. The commonest ways are (a) on publishers’s websites (e.g. crystallography) and (b) in domain repositories (e.g. sequences).

Making phylogenetic data available for each study is technically straightforward. The bytecount is insignificant in today’s world. The standards and protocols (e.g. nexml) exist. The problem is 99% a people problem.

The problem is community. In some cases the learned societies are more concerned to generate income than to service science (Where are the publishers that actually make subscription material available to the world within – say – 6 months of publication?) Many are actually making it more difficult. The last 12 months have confirmed that most legacy publishers are part of the problem, not the solution.

So how, if publishers are antagonistic or indifferent to requiring publication data do we manage it? The Universities are totally vapid today – they have shown no leadership. So the only clear path is funders mandates.

And that will work. I’ve seen the pressure in the US that the NSF mandate on data management has applied and I think it’s starting to work. That’s got to happen everywhere. So my message to funders is:

Mandate the deposition of data at time of publication. And if not, chop 10% off the grant.

That works. It’s a lot of work, but it’s a trivial amount compared with the current loss of data (which I estimate as >> 100 Billion USD per year).




#rfringe13 Repositories for scientific data with #animalgarden

We are going to the Repository Fringe this week and are going to present a PechaKucha. What’s that? It’s 20 slides of 20 seconds each that change automatically. So 400 seconds in all. And the first one has to introduce you and that last says thanks. You can see some past ones at has a slot called “Capturing and Publishing Scientific Data”. He’s asked us [#animalgarden] to create the slides


We’re #animalgarden – we make photocomics about openness. Here’s one we made about #openbibliography. It won second prize. (We don’t do it for the prizes, we do it because we like making photocomics).

PMR doesn’t think Institutional repositories work for scientific data (or publications). He thinks we need domain repositories (e.g. proteins, galaxies, phylogenetic trees, molecules, crystal structures, materials, etc. So we’re going to present the issues as a photocomic.

We all take different roles

Here’s Chuff (the OKFN Okapi) advocating open data, clean penguin being a hacker, and OWL (geddit?) representing the Semantic Web. We’re thinking about props and roles (PMR hasn’t worked out the story yet).

Back to work … See you at #rfringe13

MicrobiologyOpen Publishes its 100th Article!

MicrobiologyOpenMicrobiologyOpen has now published its 100th article! The journal published its first papers in January 2012 and since that time has accepted excellent papers across the broad scope of the journal, covering all aspects of Microbial Science. We are delighted by the success of this new open access journal. It was accepted for indexing in MEDLINE within its first year of publication.

The 100th article published in the journal is:

purple_lock_open TusA(YhhP) and IscS are required for molybdenum-cofactor-dependent base-analog detoxification
by Stanislav G. Kozmin, Elena I. Stepchenkova and Roel M. Schaaper
Summary: We show that Escherichia coli mutants deficient in the sulfurtransferase TusA or the cysteine desulfurase IscS are hypersensitive to the toxic effects of the adenine analog 6-N-hydroxylaminopurine (HAP). This sensitivity is similar to and epistatic with the HAP sensitivity of moa mutants, which defective in biosynthesis of the molybdenum cofactor (Moco). Our results suggest that TusA and IscS are critical for the insertion of the dithiolene sulfurs in Moco that coordinate the molybdenum atom.

Visit the journal homepage to see our new landing page celebrating the MicrobiologyOpen 100! This highlights the top downloaded and top cited articles from within the first 100 papers, and also shows the geographical spread of our author base and the subject areas covered by the journal.

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