This is one of the most famous fossil fields in the world where many species of the earliest animals were beautifully preserved. These fossils tell us about the very beginnings of the evolution of animal body plans. With so many ecological niches wide open to be invaded, animals experimented wildly, adopting a large variety of new anatomies, physiologies and behaviors. This is the time when first (relatively) large predators evolved. This period, known as Cambrian Explosion, was a time of much evolutionary experimentation. Some species were luckier than others, some were perhaps better fitted to the environment than others or were more successful at breeding in large numbers. They are the ancestors of all the body plans and all the animal phyla we have had on Earth since then. The others? The others went extinct and their fossils are sometimes so strange, they look more like space aliens than anything we are familiar with today.

The fossils of Burgess Shale became more widely known in 2000 when Stephen Jay Gould published a book about them – The Wonderful Life. This best-seller introduced words like Opabinia, Hallucinogenia and Anomalocaris into the day-to-day language (OK, OK, I know, not everyone is as geeky as I am). But since the book was written science did not stop. The Shale is still been diligently explored, fossils are reinterpreted and new fossil species are discovered all the time, each such finding helping us refine our understanding of early animal evolution, the principles of speciation, the early ecology and behavior of animals, and the phylogenetic relationships between the phyla.

A number of the strangest fossils from the Shale are so difficult to classify using current animal classification, they were given designation Problematica until more information is uncovered. One such new fossil that helps move some members of Problematica into a more specific group, was recently discovered. This fossil, Herpetogaster collinsi , was described last week in PLoS ONE by Jean-Bernard Caron of the Royal Ontario Museum, Simon Conway Morris from University of Cambridge and Degan Shu from the Northwest University in China in the article Tentaculate Fossils from the Cambrian of Canada (British Columbia) and China (Yunnan) Interpreted as Primitive Deuterostomes:

Molecular and morphological evidence unite the hemichordates and echinoderms as the Ambulacraria, but their earliest history remains almost entirely conjectural. This is on account of the morphological disparity of the ambulacrarians and a paucity of obvious stem-groups. We describe here a new taxon Herpetogaster collinsi gen. et sp. nov. from the Burgess Shale (Middle Cambrian) Lagerstätte. This soft-bodied vermiform animal has a pair of elongate dendritic oral tentacles, a flexible stolon with an attachment disc, and a re-curved trunk with at least 13 segments that is directed dextrally. A differentiated but un-looped gut is enclosed in a sac suspended by mesenteries. It consists of a short pharynx, a conspicuous lenticular stomach, followed by a narrow intestine sub-equal in length. This new taxon, together with the Lower Cambrian Phlogites and more intriguingly the hitherto enigmatic discoidal eldoniids (Cambrian-Devonian), form a distinctive clade (herein the cambroernids). Although one hypothesis of their relationships would look to the lophotrochozoans (specifically the entoprocts), we suggest that the evidence is more consistent with their being primitive deuterostomes, with specific comparisons being made to the pterobranch hemichordates and pre-radial echinoderms. On this basis some of the earliest ambulacrarians are interpreted as soft-bodied animals with a muscular stalk, and possessing prominent tentacles.

Even if the new classification is not 100% certain yet, one cannot help but gasp at the amazing quality of preservation of the fossil over 500 million years, and the strange beauty of this ancient, long-extinct animal:

Morbid Obesity as a Risk Factor for Hospitalization and Death Due to 2009 Pandemic Influenza A(H1N1) Disease by Morgan et al, was covered by CIDRAP, Times of India, Tech Eye, HealthNews and eMaxHealth.

Coverage of Concordant Association of Insulin Degrading Enzyme Gene (IDE) Variants with IDE mRNA, Aß, and Alzheimer’s Disease by Carrasquillo et al, was carried by Benzinga, dBusinessNews Minneapolis, Jacksonville Business Journal and R & D Magazine.

Evolutionary Divergence in Brain Size between Migratory and Resident Birds by Sol et al was discussed by EcoTone and NeuroDojo.

Tentaculate Fossils from the Cambrian of Canada (British Columbia) and China (Yunnan) Interpreted as Primitive Deuterostomes by Caron, Conway Morris and Shu was blogged by Brian Switek of Laelaps.

The Alzheimer’s Disease-Associated Amyloid β-Protein Is an Antimicrobial Peptide was covered by Derek Lowe at In the Pipeline.

Prevalence of Livestock-Associated MRSA in Communities with High Pig-Densities in The Netherlands by van Cleef et al, was reported in Emerging Health Threats Forum.

A Cluster Randomized Trial of Routine HIV-1 Viral Load Monitoring in Zambia: Study Design, Implementation, and Baseline Cohort Characteristics by Koethe et al, was noted in Birmingham Science News Examiner.

Human Prion Diseases in the United States by Holman et al, was described by CJD Blogger.

As you may be aware, as part of our ongoing article-level metrics program, we provide a downloadable Excel file for the entire dataset (3 Mb zipped, but 35 Mb when unzipped). The first such file was created when we launched the usage data (in September 2009) and we have just updated it with the latest data (with data correct up to January 31st 2010). Going forwards, we plan to update this spreadsheet every other month, starting in April.

The main changes with this latest version (other than containing a more recent dataset) are:

• The addition of the ‘missing’ usage data for all our articles.
  • We now have a complete usage dataset for all articles, going back to day of publication (previously some articles missed the usage data for their early years)
• The addition of data from researchblogging.org. Researchblogging.org are a blog aggregating service and we now include their data as part of the article-level metrics data set (as described in an earlier post)
• An update to the various  journal level summary tables

Some people have already started analysing our data and we encourage anyone who is interested to take this dataset and do their own analysis. Also be aware that the ‘live’ data for each article can be accessed by clicking on the link: “Download raw Metrics data as XML” which can be found at the bottom of each article’s Metrics tab.

The Alzheimer’s Disease-Associated Amyloid β-Protein Is an Antimicrobial Peptide by Soscia et al, was covered by New York Times Health Feed, Business Week, Suite101, Scientist Live, Alzheimer’s Reading Room and Neurophilosophy.

Beer Consumption Increases Human Attractiveness to Malaria Mosquitoes by Lefèvre et al, was covered by DNA India, Birmingham Science News Examiner, Smithsonian.com, Discoblog, Scientificblogging.com and Not Exactly Rocket Science.

Declining Death Rates Reflect Progress against Cancer by Jemal, Ward and Thun was reported in Xinhuanet, U.S. News & World Report, Ovarian Cancer National Alliance, Ars Technica and Fight Aging.

A New Horned Crocodile from the Plio-Pleistocene Hominid Sites at Olduvai Gorge, Tanzania by Brochu, Njau, Blumenschine and Densmore was covered by Discovery News and Newswise.

Open space loss and land inequality in United States’ cities, 1990–2000 by McDonald, Forman and Karieva was written up in the Conservation magazine, Global Change and Conservation Maven

Network Analytical Tool for Monitoring Global Food Safety Highlights China by Nepusz, Petróczi and Naughton, was covered by Food Safety News, bjhc & im and Flesh & Stone.

A Demonstration of the Transition from Ready-to-Hand to Unready-to-Hand by Dotov, Nie and Chemero, a rare scientific article that cites philosopher Martin Heidegger, was covered by Wired Science and Softpedia.

Winter Active Bumblebees (Bombus terrestris) Achieve High Foraging Rates in Urban Britain by Stelzer, Chittka, Carlton and Ings was described in PlanetEarth and DNA India.

Is it easy to be urban? Convergent success in urban habitats among lineages of a widespread native ant by Menke, Booth, Dunn, Schal, Vargo and Silverman was covered by Science News

Using Imputation to Provide Location Information for Nongeocoded Addresses by Curriero, Kulldorff, Boscoe and Klassen was described at HealthCanal.

Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults by Larsen et al. was covered by FoodConsumer.org, PRLog and Health Freedom Alliance

pH-Dependent Metal Ion Toxicity Influences the Antibacterial Activity of Two Natural Mineral Mixtures by Cunningham, Jennifer, Summers and Haydel was covered by R&D Magazine and Green Agenda.

Female Scent Signals Enhance the Resistance of Male Mice to Influenza by Litvinova et al, was explained by Ed Yong of Not Exactly Rocket Science.

Female Field Crickets Incur Increased Parasitism Risk When Near Preferred Song by Martin and Wagner was explained by Phased.

Some of our older articles received additional coverage recently:

Could Work Be a Source of Behavioural Disorders? A Study in Horses by Hausberger et al, was presented in TheHorse.com

Altruism in Forest Chimpanzees: The Case of Adoption by Boesch et al was discussed at Big Think.

Athlete Atypicity on the Edge of Human Achievement: Performances Stagnate after the Last Peak, in 1988 by Berthelot et al was discussed in Finding Dulcinea.

Neural substrates of spontaneous musical performance: an FMRI study of jazz improvisation by Limb and Braun was discussed on The Posit Science Blog.

Persistent Cell Motion in the Absence of External Signals: A Search Strategy for Eukaryotic Cells by Li et al was described by BenjaminTseng

Several people blogged about the meeting, and Brian Glanz provided an excellent running commentary for the entire day.

Courtesy of Microsoft Research, the full video coverage of all the talks are now online as follows: Session 1 (Microsoft Research; Cameron Neylon; Jean-Claude Bradley); Session 2 (Antony Williams; Peter Murray-Rust); Session 3 (Heather Joseph; Stephen Friend); and Session 4 (starring myself, in a warm up role for the keynote by John Wilbanks).You will need to install Silverlight to view the videos.

This was an excellent meeting, for which Microsoft and Science Commons deserve a lot of praise – I recommend the video coverage for anyone who couldnt be there.

Pubget is a search engine for life-sciences PDFs. If Pubget have found a PDF which is freely available then you will now be able to access it via our site with just one click. Their database contains 3 million free PDFs, plus tens of millions of subscription only PDFs (naturally we wish that everything was freely available but sadly that is still not the case).

Now, when you look at citations to any article as recorded by CrossRef (which are accessed via the ‘CrossRef’ link in the ‘Cited in’ section of any article’s Metrics tab), a PDF icon will appear if it is freely available via Pubget. Clicking on the icon will take you directly to the PDF. We’ve created a 3 minute screen shot video (with audio commentary) to explain how this works.

As you would expect, we’re just linking to the free PDFs on Pubget. For those citations without a freely available PDF you have two options. The CrossRef link will take you to the publishers site (as it always did). Or, if you work for any of the 170 institutions in Pubget’s network (for example, MIT, and UCSF), you can use the citation to get to the subscription PDFs right away on Pubget.com. If you want to add your institution to the Pubget network, just tell your library – Pubget is free.

On launching this new functionality, Pete Binfield, Publisher of PLoS ONE and the Community Journals said:

“Any service, like Pubget, that makes it easier for authors to quickly find the information they need is a welcome addition to our articles. We like how Pubget helps to break down content walls in science, letting users get instantly to the article-level detail that they seek.”

Dr Ramy Arnaout, Pubget founder said:

“We’ve been long term fans of PLoS because they share our passion for advancing science and information access. We’re excited to take this first step in working together to make science that much faster for everyone who reads articles as part of their research.”

We hope that this new functionality makes it a little bit easier to reach the information that you need.

The title of this post is really a mis-nomer – this should be a bi-weekly round-up as I was at AAAS meeting last week and did not have the time and opportunity to post a round-up last Monday. So today, you will get a double dose:

Article Optimal Waist-to-Hip Ratios in Women Activate Neural Reward Centers in Men by Steven M. Platek and Devendra Singh was irresistible to the media. It was covered widely, including by Herald Sun, Times of India, Telegraph, New York Daily News, The Sun (warning: NSFW, it’s Page 3!), Atlanta Journal Constitution, FOXNews, TheMedGuru, CalorieLab Calorie Counter News, Sideways News, Metro, PhysOrg.com, TopNews, Softpedia, Asylum and ZME Science.

The article Analysis of the Putative Remains of a European Patron Saint–St. Birgitta unveiled that these relics are not what they are thought to be – genetic analysis revealed the remains of what were supposed to be a mother and a daughter to actually be uneraleted to each other. This finding was reported by Register, Gene Expression, Monsters and Critics, A Very Remote Period Indeed, ScienceBlog and, interestingly, by the article’s Academic Editor Bjoern Brembs who describes the incredible thoroughness of the peer-review of this article.

Avian Magnetoreception: Elaborate Iron Mineral Containing Dendrites in the Upper Beak Seem to Be a Common Feature of Birds, an article from the Fleissner lab, attracted a very international coverage, including in Informationsdienst Wissenschaft, Mail.Ru, Ornithomedia, Proplanta and A DC Birding Blog.

A Global Analysis of the Effectiveness of Marine Protected Areas in Preventing Coral Loss by Selig and Bruno shows that establishment of protected areas of the ocean does have some positive effects on the health of coral reefs and that this effect gets greater as the area remains preserved longer. This study was reported in Anthozoa, EcoTone, Newswise, BusinessWeek, Die Welt, Hawaii 24/7 and NPR Science Friday podcast.

The discovery of A New Horned Crocodile from the Plio-Pleistocene Hominid Sites at Olduvai Gorge, Tanzania by Brochu, Njau, Blumenschine and Densmore was covered by Laelaps, National Geographic, New Scientist, FOXNews
OneIndia and Softpedia.

An Investigation into the Cognition Behind Spontaneous String Pulling in New Caledonian Crows by Taylor et al, puts into question the notion that corvid birds demonstrate ‘insight’. The study was reported by A DC Birding Blog
Ars Technica and Wired News.

Human Ovarian Reserve from Conception to the Menopause by W. Hamish B. Wallace and Thomas W. Kelsey experienced a ressurection in the media when Washington Post decided to report on it. True/Slant, Tapped and Washington City Paper followed.

The paper Positive Carotenoid Balance Correlates with Greater Reproductive Performance in a Wild Bird by Safran et al. was covered by CU Boulder News & Events, Daily Camera, IndyPosted, ScienceBlog, Arizona State University News, Laboratory Equipment and Summit Daily News.

This month’s winner is Princess Ojiaku from the Science with Moxie blog, for her post Musical Emotions: Chills Edition that explained the article The rewarding aspects of music listening are related to degree of emotional arousal by Valorie N. Salimpoor, Mitchel Benovoy, Gregory Longo, Jeremy R. Cooperstock and Robert J. Zatorre, all from Montreal. From the Abstract:

Background

Listening to music is amongst the most rewarding experiences for humans. Music has no functional resemblance to other rewarding stimuli, and has no demonstrated biological value, yet individuals continue listening to music for pleasure. It has been suggested that the pleasurable aspects of music listening are related to a change in emotional arousal, although this link has not been directly investigated. In this study, using methods of high temporal sensitivity we investigated whether there is a systematic relationship between dynamic increases in pleasure states and physiological indicators of emotional arousal, including changes in heart rate, respiration, electrodermal activity, body temperature, and blood volume pulse.

Methodology

Twenty-six participants listened to self-selected intensely pleasurable music and “neutral” music that was individually selected for them based on low pleasure ratings they provided on other participants’ music. The “chills” phenomenon was used to index intensely pleasurable responses to music. During music listening, continuous real-time recordings of subjective pleasure states and simultaneous recordings of sympathetic nervous system activity, an objective measure of emotional arousal, were obtained.

Principal Findings

Results revealed a strong positive correlation between ratings of pleasure and emotional arousal. Importantly, a dissociation was revealed as individuals who did not experience pleasure also showed no significant increases in emotional arousal.

Conclusions/Significance

These results have broader implications by demonstrating that strongly felt emotions could be rewarding in themselves in the absence of a physically tangible reward or a specific functional goal.

In her blog post, Princess Ojiaku wrote:

When we get chills or feel intense pleasure when listening to music we enjoy, there is an actual range of bodily responses that go along with that! This seems like common sense, but this is important scientifically because having an actual, quantitative measure of the changes our bodies go through when experiencing good music opens doors to scientists thinking about other questions like, “why is music so unique that it causes actual emotional and physical arousal?”

Usually emotional responses have a definite function, such as joy from eating good food serves to keep us alive, or bonding with friends keeps us happy and connected to our fellow humans. Feeling these emotions helps us by making sure we keep doing the things that are good for our survival and well-being. But music is one of the only things that makes us happy without having a clear beneficial function to our survival as human beings. I think that makes it pretty special and interesting, and that makes me content to consume and play it.

Congratulations to Princess and the authors of the article. I have contacted them and wonderful T-shirts from the PLoS Store will be on their way to them shortly.

Runners-up in this month’s contest were Brian Switek for his coverage of the horned man-eating crocodile fossil and Grrrlscientist for her blog post on the discovery of speed-gene in racehorses.

Previous winners:

March 2009: Ed Yong
April 2009: Eric Michael Johnson
May 2009: Christie Wilcox
June 2009: Iddo Friedberg
July 2009: Toaster Sunshine and Hermitage
August 2009: Bjoern Brembs
September 2009: Alun Salt
October 2009: Andrew Farke
November 2009: John Beetham
December 2009: SciCurious
January 2010 – Anne-Marie Hodge

We’ve had a reprint service for a while but to use it, folks had to add all the article information to the order themselves which made it time consuming and difficult to use. Now, we’re proud to introduce EzReprint, the next generation of print on demand, designed for people who want to generate 25 or more high quality reprints of most of our articles.

You can find the link to this service in the top right of almost every PLoS article.

It is near the option to print it using your desktop printer (which is, of course, still your best bet if you need some copies for any purpose, available to you at no charge thanks to open access). To do this, simply download the PDF and send it to your printer.

In the new system, all the article information is pre-filled on the order landing page, and so all you have to do is make a few simple choices and you are nearly done. If you want a quick guided tour, simply watch this three minute video. This new service is available on most but not all articles, if you do not see the EzReprint logo you will be directed to the original system.

There are a number of different payment options to suit the needs of our largely academic audience. You can enter a purchase order to create an invoice, wire your payment or pay by credit card. Your reprints are dispatched straight to your door and proof of delivery comes as standard on every order.

Although anyone is free to make their own copies of any PLoS article using their desktop printer, we do appreciate that many people want a ‘professional quality’ reprint (high grade paper, high resolution prints, saddle stitching, and the option of custom covers) and for those people we offer what we believe is a fair pricing model for this service. Specifically, we offer a non-commercial rate for those people who want to order low quantities (25-500) – we make a small margin on this to help support our cause. And we also have a commercial rate for organizations who want higher quantities – this price is competitive with other publishers.

Our printing vendor for this service is Odyssey Press – an industry leader in digital medical and scientific reprints who have developed the new EzReprint ordering feature and have worked with us to implement it. EzReprint appears on nearly all PLoS articles. You can find out more about PLoS print on demand here.

Feel free to try EzReprint the next time you need professionally produced copies of PLoS articles, you’ll be glad that you did.

These challenges were posed to systems biology experts during the months of June to September 2008 and discussed at the third DREAM conference, held in late 2008 in Cambridge, MA.The Collection as a whole summarizes the lessons learned by the community and provides a much-needed context for interpreting claims of efficacy of algorithms described in the scientific literature.

DREAM was established to address the question of whether mathematical models can be used to help scientists go beyond experimental insight to better understand biological systems.  Every year, DREAM organize a challenge in which scientists from around the world are invited to use donated experimental data to produce quantitative models and make blind predictions of previously unseen benchmark experiments known to the DREAM organizers. These predictions are matched to the benchmarks, allowing for a rigorous evaluation of the usefulness of the models. This community effort aims to catalyze discussion about the design, application, and assessment of systems biology models. DREAM is sponsored by Columbia University Center for Multiscale Analysis Genomic and Cellular Networks (MAGNet) and the IBM Computational Biology Center.

Systems biology has embraced computational modeling in response to the quantitative nature and increasing scale of contemporary data sets; however, the volume of data being generated is accelerating as molecular profiling technology evolves. We hope that this Collection goes some way to explaining the role that Computational algorithms could play in the interpretation of systems biology data and an assessment of their limitations.