How Newbie Sailors Earn Their Sea Legs

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With America’s Cup sailors training for the upcoming races right across from the PLOS San Francisco office, we can’t resist watching the boats zip by once in a while and thinking about what it’s like to be out on the bay. Those of us who’ve spent time on boats are likely familiar with the transition our bodies experience as we go from land to sea, commonly referred to as “getting your sea legs.”  For some, this transition can happen quickly, but for others, it can take days to feel stable relative to the moving surface of the water.

In a recent scientific study on getting your sea legs, researchers investigated this process by measuring novice sailors’ leg positioning, body sway, and posture, both before embarking on a ship and for several days into the voyage. They also evaluated similar studies with experienced mariners to compare how newbies and professionals adapted to life at sea. Sailing novices, who received no guidance on techniques for gaining stability at sea, naturally adopted a widened stance, maintained the angle of their feet and started to use the horizon line to stabilize themselves on the ship soon after boarding. These are the same techniques employed by experienced sailors in similar studies. The research also suggested that body sway tendencies on land and at sea have the potential to predict individual seasickness and mal de debarquement (land sickness experienced after disembarkment) syndrome susceptibility.

Life at sea is probably second nature to the sailors racing by here in San Francisco, but this study’s results suggest that the rest of us may also find stability on moving surfaces by widening our stances and focusing on the horizon. Keep these techniques in mind the next time you find yourself out on the open ocean!

 

Citation: Stoffregen TA, Chen F-C, Varlet M, Alcantara C, Bardy BG (2013) Getting Your Sea Legs. PLoS ONE 8(6): e66949. doi:10.1371/journal.pone.0066949

Image: Sailing From Sardinia to Sicily by Patrick Nouhailler

Malaria, tuberculosis caused death on the ancient Nile

 

Nile

Southwest of Cairo, the Nile branches into a network of canals that feed Fayum, a fertile agricultural basin that was a center of civilization and royal pyramid-building for several centuries. The unusual geology responsible for Fayum’s rich terrain may have also led to the prevalence of malaria and tuberculosis in the region during these ancient times.

Ancient DNA (aDNA) from sixteen mummified heads recovered from the region reveals that at least four of these individuals suffered both these infections simultaneously. Many of the others showed signs of infection with either malaria or tuberculosis, as scientists report in a recent PLOS ONE study.

DNA extracted from muscle tissue samples was tested for the presence of two genes specific to Plasmodium falciparum, the malarial parasite, and another gene specific to Mycobacteria, which cause tuberculosis. Two samples tested positive for DNA specific to Plasmodium, one tested positive for the mycobacterial gene, and four individuals tested positive for DNA from both infectious agents, suggesting they suffered both infections together while alive. A previous study suggests that both malaria and tuberculosis were rampant in the Fayum region in the early 19th century, but the age of these mummified samples extends evidence of these diseases in Lower Egypt as far back as approximately 800 B.C.

The World Health Organization estimates that malaria is almost non-existent in the Fayum basin and the rest of Egypt now, but before its eradication, high levels of infection were seen in certain parts of the country, and were strongly linked to certain geological features. The lakes and canals that made the Fayum region so fertile also served as breeding grounds for the mosquito that carries the malarial parasite.

The heads tested here (all were missing bodies) were recovered from a village cemetery on the west bank of the lower Nile, and date from about 1064 BC to 300 AD, a period marked by an agricultural boom and dense crowding in the region, especially under the rule of the Ptolemies. These conditions may have increased the chances of tuberculosis incidence and spread of the disease. As the aDNA from these mummified heads attests, these living conditions and the unique irrigation of the Fayum basin likely created a harbor for both malaria and tuberculosis in ancient populations of this region.

Citation: Lalremruata A, Ball M, Bianucci R, Welte B, Nerlich AG, et al. (2013) Molecular Identification of Falciparum Malaria and Human Tuberculosis Co-Infections in Mummies from the Fayum Depression (Lower Egypt). PLoS ONE 8(4): e60307. doi:10.1371/journal.pone.0060307

Image: Sailing on the Nile by David Corcoran

Physiological Reports Publishes Inaugural Issue

Physiological ReportsEverything about Physiological Reports is different. A collaboration between The Physiological Society and the American Physiological Society, the journal offers the highest quality peer review and is proudly open access. Now, here’s your chance to see where it’s taken us, who’s submitted, and the incredible research that we’ve been able to publish so far.

Here are some of the high quality papers which we have published so far:
purple_lock_open Elevated pulmonary arterial pressure and altered expression of Ddah1 and Arg1 in mice lacking cavin-1/PTRF
Karl Swärd, Mardjaneh K. Sadegh, Michiko Mori, Jonas S. Erjefält and Catarina Rippe
Summary: Mutations in caveolin-1 give rise to a heritable form of pulmonary arterial hypertension (PAH). Novel caveolae proteins have been identified in recent years. Here, we demonstrate that mice lacking cavin-1 develop PAH accompanied by reciprocal changes in Ddah1 and Arg1.

purple_lock_open Enhanced force production in old age is not a far stretch: an investigation of residual force enhancement and muscle architecture
Geoffrey A. Power, Demetri P. Makrakos, Charles L. Rice and Anthony A. Vandervoort
Summary: Ultrasound images from a representative older adult at LONG muscle length showing fascicle length (FL) and angle of pennation (?) measurement at rest, during the isometric reference MVC, and during the isometric steady-state following lengthening.

purple_lock_open Interlimb interactions during bilateral voluntary elbow flexion tasks in chronic hemiparetic stroke
Shuo-Hsiu Chang, Ana Durand-Sanchez, Craig DiTommaso and Sheng Li
Summary: This study found that there existed activation level dependent interactions between the impaired and nonimpaired limbs during bilateral force production tasks with progressive increase of contribution from the impaired side. Motor overflow to the contralateral side was greater on the impaired limb and increased proportionally with the level of activation. These novel findings indicated that, among other compensatory mechanisms, ipsilateral corticospinal projections from the nonlesioned hemisphere play an important role in interlimb interactions in chronic stroke, in addition to unbalanced interhemispheric inhibition.

PR-etoc

We would like you to submit your article to Physiological Reports. Authors benefit from:

  • Compliance with open access mandates – articles publish under Creative Commons Attribution (CC BY) License
  • Rapid publication
  • Article publication fee waived for first 100 papers
  • High standard, rigorous peer review

If you’re looking for a home for your top quality original research focused on any area of basic, translational, and clinical physiology and allied disciplines:

Submit here

Moms and babies respond to childbirth with different stress hormones

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A quick internet search reveals that many women rank giving birth as one of the most painful human experiences. Though pain can be hard to quantify objectively, the physiological stress of childbirth is clinically assessed by measuring blood levels of the stress hormone cortisol.

Cortisol is currently used to estimate the stress experienced by both mother and child during the process of giving birth, but recently published PLOS ONE research suggests that a different stress hormone, corticosterone, may be a more accurate way to measure the stress experienced by healthy, full-term babies.

For their study, researchers tested fetal levels of cortisol and corticosterone in 265 samples of umbilical cord blood from healthy deliveries. Though the total levels of cortisol detected were higher than corticosterone levels, fetuses produced the latter at a greater rate in response to the stress of labor and delivery. Newborns secreted more corticosterone when a Caesarian section was performed due to complications during labor than they did after a normal C-section. Fetal corticosterone levels were also higher after passage through the birth canal. These differences were not seen in levels of cortisol production. Based on these data, the authors suggest that the full-term fetus is more likely to secrete corticosterone than cortisol in response to stress and hence, corticosterone may be a more accurate clinical biomarker to assess fetal stress.

Corticosterone isn’t unheard of in the adult world, as adults continue to make the hormone throughout our lives, though in a much smaller proportion relative to cortisol. When babies switch to producing more cortisol rather than corticosterone isn’t yet clear, but the developmental changes involved may help track or diagnose adrenal gland functions in newborns.

Citation: Wynne-Edwards KE, Edwards HE, Hancock TM (2013) The Human Fetus Preferentially Secretes Corticosterone, Rather than Cortisol, in Response to Intra-Partum Stressors. PLoS ONE 8(6): e63684. doi:10.1371/journal.pone.0063684

Image: stress by topgold

The Springer sub-prime scholarly publishing deal?

Reuters recently announced that a group called BC Partners will buy Springer for 3.3 billion euros. Of this, 2.5 billion is debt – backed by Barclays, Credit Suisse, Goldman Sachs, JP Morgan, Nomura and UBS. This debt is described as “covenant lite,” a structure that offers little or no protection for lenders via financial tests”.

This makes no sense at all from a financial perspective. Why buy a company whose traditional high profits are based on an outmoded model that currently enjoys revenues at 4-5 times higher than what is necessary for normal profits  in an emerging open access environment for scholarly publishing that is just beginning to open up to competition – including competition on price? Even if it made sense to buy the company, how could it possibly make sense to load the company with debt? If you’re going to take risks like this, wouldn’t it make sense to look for more rather than less guarantees? 

On the surface this looks a lot like the sub-prime mortgage situation – go ahead and lend money even though this obviously makes no sense at all – and appears to involve some of the same companies. Am I missing something here?

OpenScience comes of age

In 1998, Open Science seemed like a pretty obvious projection of basic scientific principles into the digital age.  I didn’t think the ideas would meet much, if any, resistance from the scientific community.   And in October 1999, Brookhaven National Lab sponsored a meeting called Open Source / Open Science that, in retrospect, was a pretty utopian gathering.  There were a lot of the current OpenScience community members present at the meeting (notably Brian Glanz and Greg Wilson).   It felt like everyone would be convinced to do Open Source & Open Data science in short order.

The past 14 years have been instructive in just how long it can take to make cultural changes in the scientific community.

So, it was an amazing experience to be present when the Office of Science and Technology Policy (OSTP) announced the Champions of Change for Open Science.  These are 13 incredible individuals and organizations with great stories about sharing their science.  It feels like we’ve made significant motion on implementing policies that are friendly to Open Science.   I should note that we’re particularly happy to see OSTP use the phrase Open Science, and not the more narrow terms: Open Data or Open Access.  I’m hopeful that Open Source will also be part of science policy going forward.

openscipostersThere was a second group who got the opportunity to present at this event at a poster session later that day.  I haven’t seen the list publicized elsewhere, but these are some sharp folks who deserve recognition for their work.  I’m going to highlight some of these in the coming week.  Here’s the list of posters:

  1. Richard Judson & Ann Richard from the National Center for Computational Toxicology presented on “ACToR & DSSTox: EPA Open Information Tools for Chemicals in the Environment”
  2. Tom Bleier, Clark Dunson & Michael Lencioni from the QuakeFinder project presented on “Electromagnetic Earthquake Forecasting Research”
  3. David C. Van Essen from WUSTL presented on the “Human Connectome Project
  4. Heather Piwowar & Jason Priem presented a poster on “ImpactStory: Open Carrots for Open Science”
  5. Jean-Claude Bradley (Drexel) and Andrew Lang (Oral Roberts University) presented a poster on “Open Notebook Science“.
  6. Dan Gezelter (that’s me) presented on “The OpenScience Project“.
  7. John Wilbanks from Sage Bionetworks presented on “Portable Legal Consent – Let Patients Donate Data to Science
  8. Matt Martin from the National Center for Computational Toxicology presented on “ToxRefDB & ToxCastDB: High-Throughput Toxicology Resources”
  9. Brian Athey and Christoph Brockel presented on “The tranSMART Platform: Accelerating Open Science, Data Analytics and Data Sharing”
  10. Alexander Wait Zaranek, Ward Vandewege & Jonathan Sheffi from Clinical Future, Inc. presented on “Transparent Informatics: A Foundation for Precision Medicine

It was an intense day, and I’m delighted that Open Science has finally come of age.

Pristine Fossil Reveals Unlikely Pair

Fernandez_Fig1 mediumThe small but sharp-toothed Thrinaxodon probably spent much of its time dining on its Triassic cohabitants, but a study published today reports a pristine fossil of the meat-eater apparently peacefully sharing its burrow with a small amphibian – until they were both buried in a flood.

The researchers uncovered the odd couple through non-destructive imaging 0f a burrow cast from South Africa, where the animals appeared to have died together. In the image of the cast itself, along with the ghostly outlinescast of the animal skeletons you can see that layer 1 is the original bed of the burrow, and layers 2 and 3 correspond to subsequent “pulses” of the flooding event.

The two skeletons are remarkably complete and well-preserved (in the image above Thrinaxodon is shown in brown, and the amphibian in grey), and the artifact provides an excellent opportunity to study the interactions between two different species. Given Thrinaxodon‘s carnivorous ways, it may at first seem most likely that the amphibian was about to be eaten for lunch, but its undisturbed skeleton and lack of expected bite marks rule out this possibility, the authors write. They also conclude that the flood responsible for burying the animals couldn’t have randomly washed the amphibian into the burrow once the animals were already dead because the burrow’s opening was too small.

To find the most likely answer, the researchers turned to modern creatures for insight. They note that animals today will live in a burrow built by another species if it is abandoned, if they can chase away the host, or if the host tolerates their presence. The Thrinaxodon was still in the den, so neither of the first two possibilities seem to apply in this case, leaving the last option as the most likely. As strange as it may seem, it appears that for whatever reason the Thrinaxodon graciously tolerated its amphibian partner’s presence.

If you want to see more, this video shows how the authors virtually dissected the burrow using synchrotron scanning to create an exquisitely detailed reconstruction of the burrow’s contents without cracking it open.

Citation: Fernandez V, Abdala F, Carlson KJ, Cook DC, Rubidge BS, et al. (2013) Synchrotron Reveals Early Triassic Odd Couple: Injured Amphibian and Aestivating Therapsid Share Burrow. PLoS ONE 8(6): e64978. doi:10.1371/journal.pone.0064978 

Fools Gold From Emerald

Rebecca Marsh, Director of External Relations and Services, Emerald Group Publishing Limited & Tony Roche, Publishing Director of Emerald Group Publishing Limited have posted their defence of the Emerald policy changes reported by Richard Poynder: “Open Access: Emerald’s Green Starts to Fade“.

First, a paraphrase of what Marsh & Roche wrote:

(1) All Emerald authors may do immediate, unembargoed Open Access self-archiving if they wish, but (2) not if they must. If they must self-archive, they must wait 24 months or ask individually for permission.

The sensible Emerald author will self-archive immediately, and ignore clause (2) completely. It is empty, unverifiable, unenforceable, pseudo-legal FUD that has been added as a perverse effect of the folly of the UK Finch Committee recommendations.

The Emerald policy tweak is obviously to cash in on the money that the UK has decided to squander on pre-emptive “Fools Gold” OA, as well as to try to fend off universal Green OA as long as is humanly possible.

Below I reproduce the Emerald representatives’ posting’s text, cutting out the empty verbiage, to make the double-talk clearly visible and comprehensible.

Emerald:
“…Emerald has had a Green Open Access [OA] policy for over a decade. [All Emerald] authors who personally wish to self-archive the pre- or post-print version of their article on their own website or in a repository… can do this immediately upon official publication of their paper. This principle continues to underpin our Green OA policy and remains unchanged….

“…[Emerald] has provided an alternative route to OA for researchers who are mandated to make their papers Open Access immediately, or after a specified period. We also set the Article Processing Charge (APC) at a relatively low level to assist authors…

“Emerald has… requested that authors wait 24 months before depositing their post-prints if a mandate is in place. Where a mandate exists for deposit immediately on publication or with a shorter mandate but no APC fund is provided, we invite all authors to contact us…”

Plans by universities and research funders to pay the costs of Gold OA pre-emptively today are premature.

Funds are short; 80% of journals (including virtually all the top journals) are still subscription-based, tying up the potential funds to pay for Gold OA. Hence, for institutions, paying pre-emptively for Gold OA today means double-paying — subscriptions for their incoming articles plus APCs for their outgoing articles– and in the case of “hybrid Gold,” when both sums are paid to the very same journal, it also means double-dipping by publishers.

Even apart from double-paying and double-dipping, the asking APC price per article for Gold OA today (whether “pure” or “hybrid”) is still inflated; and there is concern that paying to publish may also inflate acceptance rates as well as lower quality standards to maximize revenue in the case of “pure Gold” OA.

What is needed now is for all universities and funders worldwide to mandate OA self-archiving (of authors’ final peer-reviewed drafts, immediately upon acceptance for publication) (“Green OA”).

That will provide immediate OA; and if and when universal Green OA goes on to make subscriptions unsustainable (because users are satisfied with just the Green OA versions) that will in turn induce journals to cut costs (phasing out the print edition and online edition, offloading access-provision and archiving onto the worldwide network of Green OA Institutional Repositories), downsize to just providing the service of peer review, and convert to the Gold OA cost-recovery model; meanwhile, the subscription cancellations will have released the funds to pay this residual service cost.

The natural way to charge for the service of peer review then will be on a “no-fault basis,” with the author’s institution or funder paying for each round of refereeing, regardless of outcome (acceptance, revision/re-refereeing, or rejection). This will minimize cost while protecting against inflated acceptance rates and decline in quality standards.

This is the difference between today’s pre-emptive pre-Green double-paid, double-dipped over-priced pre-Green “Fools Gold” and tomorrow’s affordable, sustainable, post-Green Fair Gold.

Harnad, S. (2010) No-Fault Peer Review Charges: The Price of Selectivity Need Not Be Access Denied or Delayed. D-Lib Magazine 16 (7/8).

Houghton, J. & Swan, A. (2013) Planting the Green Seeds for a Golden Harvest: Comments and Clarifications on “Going for Gold”. D-Lib Magazine 19 (1/2)