Underwater Compositions: Song Sharing Between Southern Ocean Humpback Whales

Whale Tail

Imagine a world where sight is limited by the extreme scattering of photons and smell is ineffective due to lethargic diffusion of molecules slowed by the density of water. In these conditions both sight and smell are limited. These conditions characterize, among other things, the ocean, where large sea mammals rely mostly on sound to communicate. The speed of sound is four times greater in water than in air at sea level. Male humpback whales have been observed communicating via ever-changing patterns of vocalization, which scientists have termed ‘song’. These whales compose their songs for the purposes of breeding, learning new songs as they come in contact with fellow crooners. Exactly how and when humpback whales learn these songs, however, remains a larger mystery.

To dive more deeply into the nebulous realms of humpback whale song sharing, researchers of a recent PLOS ONE study recorded instances of humpback whale song in the Southern Ocean.

Humpback whale song is identifiable because of its intricate pattern of structure. Songs are composed of multiple sounds types, for example, as these researchers suggest, ‘ascending cry,’ ‘moan,’ and ‘purr’. When units come together to form a pattern, these units form a phrase. Phrases repeated become a theme, and themes sung in a particular order compose a song. Researchers recorded these compositions by deploying radio-linked sonobuoys, which transmit underwater sound, and then digitized the recordings.

Here is an example of song recorded off the coast of New Caledonia in 2010: 

Recordings, like the one above, reveal a possible link between three distinct breeding populations (marked D, E, and F on the map below) off the shores of eastern Australia and the island to the east of New Caledonia with a shared feeding ground in Antarctica (Area V).

journal.pone.0079422.g001 map


In early 2010, the researchers identified four songs near Antarctica that matched themes from eastern Australia in 2009. By July, 2010, all four songs were then also identified in the group from New Caledonia. The themes recognized in New Caledonia in 2010 were entirely different than the themes of 2009, suggesting a movement of new songs eastward from eastern Australia to New Caledonia.

Consequently, the shared feeding grounds in Antarctica used by both the eastern Australia and New Caledonia groups in early 2010 may be the point at which these populations’ songs diverged.

By capturing sonobuoy recordings near feeding grounds off the Balleny Islands, researchers recorded the first instances of humpback whale song in Area V of Antarctica.

Sonobuoy recording


In addition, the inclusion of feeding grounds into the dynamic pattern of humpback whale song sharing helps shed new light on overall patterns of song learning and transmission from one breeding group to another.

Sound recording off the Balleny Islands near Antarctica, however, is challenging, and the sample of whale singers from this area remains relatively small. Regardless, the song documented here suggests Antarctica (Area V) as an emerging location for future study, and highlights the importance of feeding grounds in the transmission of humpback whale song. Through a better understanding of how and where these dynamic compositions radiate across the Southern Ocean, we can begin to understand humpback whale population connectivity and one of the best examples of non-human, large-scale learning demonstrated throughout the Southern Hemisphere.

To listen to more of the whale song recorded by these researchers, check out the Supporting Information of their article. For more on humpback whales, check out these PLOS ONE papers.

Citation: Garland EC, Gedamke J, Rekdahl ML, Noad MJ, Garrigue C, et al. (2013) Humpback Whale Song on the Southern Ocean Feeding Grounds: Implications for Cultural Transmission. PLoS ONE 8(11): e79422. doi:10.1371/journal.pone.0079422

Images and Acoustic Files:

Image 1: Humpback Whale Tail by Natalie Tapson

Acoustic File: doi:10.1371/journal.pone.0079422

Image 2: doi:10.1371/journal.pone.0079422

Image 3: doi:10.1371/journal.pone.0079422

I don’t want free online access: I want free online access with re-use rights!

I don’t want free online access: I want free online access with re-use rights!

But we don’t even have free online access yet…

I don’t want free online access: I want free online access with re-use rights!

But free online access is part of free online access with re-use rights…

I don’t want free online access: I want free online access with re-use rights!

But free online access is already within immediate reach and free online access with re-use rights is not…

I don’t want free online access: I want free online access with re-use rights!

But free online access will pave the way for free online access with re-use rights…

I don’t want free online access: I want free online access with re-use rights!

But re-use rights to only a fragment of the research in a field are near-useless…

I don’t want free online access: I want free online access with re-use rights!

But publishers allowing authors to provide free online access and re-use rights can immediately be undercut by free-riding rival publishers; publishers allowing authors to provide free online access alone cannot…

I don’t want free online access: I want free online access with re-use rights!

But publishers will sooner allow authors to provide free online access than allow them to provide free online access with re-use rights?

I don’t want free online access: I want free online access with re-use rights!

But institutions and funders can sooner mandate free online access than free online access with re-use rights?

I don’t want free online access: I want free online access with re-use rights!

But all non-subscribing users need free online access; not all or even most or many users need re-use rights…

I don’t want free online access: I want free online access with re-use rights!

But all authors already want all non-subscribing users to have immediate free online access; not all or even most or many authors know or care about re-use rights yet…

I don’t want free online access: I want free online access with re-use rights!

But free online access is better, even if free online access with re-use rights is best…

I don’t want the better: I want the best!

But the better is already within reach and the best is not…

I don’t want the better: I want the best!

An open access New Year’s wish

Being a professor comes with a few perks – for example, for me, having an office in a prominent spot on a floor of the Desmarais Building at the University of Ottawa that houses the Information Studies and Communication departments.

There is space to post things on the outside of my door. Many professors have posters about conferences that they are involved with, for example. Which gets me to my New Year’s wish – an open source poster to promote open access in these disciplines. It should be possible to build on some of the excellent work on promotional materials such as open access logos developed for open access week. How about a link to the DOAJ subject lists for these areas, the Social Sciences Research Network, E-LIS and PubMed (all relevant to faculty members in these areas).

A customizable poster would be optimal. For example, the institutional repository could be an example, for everyone to look up and substitute their own. People in different disciplines could switch to more relevant DOAJ lists and subject repositories.

If the poster were manipulable, then people could add information of local interest, such as journals we or our colleagues are involved in. A list of bullet points on why open access could be provided, with individuals selecting what is most likely to speak to people locally.

This is just a wish! Given the time of year, projects for next year’s OA Week may be more feasible.

Fish Beware – A New Species of Parasite is Discovered

Drawing of  Lethacotyle vera.

Drawing of Lethacotyle vera.

The world is full of creepy crawlers; some are harmless bugs while others are blood sucking parasites. Adding to the list of parasites this month is one identified in a recent PLOS ONE article, Lethacotyle vera n. sp, a new species of fish parasite, found in the South Pacific. Lethacotyle vera is part of the class Polyopisthocotylean monogenean, which are tiny (less than 1-cm long), parasitic flatworms that live on fish gills.

For any type of ectoparasite (parasites that live outside their host’s body) staying attached to their host is an important ability. One of the most notable features of Polyopisthocotylea is their multiple sucking clamps that allow them to keep their position on the fish. These clamps are found on the haptor, a body part developed specifically for attaching. Some parasites in this group can have hundreds of clamps as part of their haptor. In fact, Polyopisthocotylea literally translates to ‘many sucker-cups at the rear’. Thank goodness they only like fish!

However, there is one rare species discovered 60 years ago, Lethacotyle fijiensis, that appears to be clamp-less. The only available specimen for study is the one shown in the picture below.

The only available specimen of L. fijiensis

The only available specimen of L. fijiensis.


This close up below shows you what L. fijiensis actually looks like. The clamp-less haptor is the oblong protrusion on the very left end.


Close up of L. fijiensis

Because only four specimens of L. fijiensis have ever been found, and because having clamps is a major distinguishing feature of monogeneans, many researchers have assumed that L. fijiensis was incorrectly identified as clamp-less, and that these specimens probably lost their clamps through mishandling of the specimens by people.

In an attempt to verify the true nature of L. fijiensis, the authors went in search of additional specimens in the Pacific, where it was originally discovered. While they were unable to find any, they instead unearthed a hereto-undiscovered close relative, which they named Lethacotyle vera (vera is Latin for true, meaning that the genus Lethacotyle, is indeed real).

Haptor and Hooks

As it turns out L. vera is also a monogenean without clamps. The main physical difference between L. vera and L. fjiensis is the length in the male reproductive organ. The authors noted that L. vera has flaps on its haptor that are covered in many ridges, as well as hooks. A drawing of the haptor with its ridges and hooks can be seen in part F in the image to the right.


The authors sequenced the DNA from two of the eighteen specimens. The extracted DNA showed that the genetic information in L. vera is unique from all other known monogeneans. Then, in an effort to determine why L. fijiensis and L. vera don’t have the typical clamps of their family, they compared the ratio of clamp-to-body surface area in 120 different monogenean species. They found that members of the monogenean family to which L. vera and L. fijiensis belong, protomicrocotylids, had consistently the smallest clamp-to-body ratio. Additionally, many other species of polyopisthocotylean monogeneans had lateral flaps with ridges on their haptors.

From this observation, the authors concluded that in the family protomicrocotylids, their clamps are in fact slowly disappearing, and that in the specific case of L. fijiensis, the clamps have completely disappeared. The authors suggest that flaps can also hold onto the host, and that this process is assisted by the ridges and hooks along the flaps.

The discovery of a new species is always exciting, and as the case of L. vera shows us, can lead to insights about the larger family of related organisms. Read more about new species at PLOS ONE, such as this orchid or this Indonesian owl.

Citation: Justine J-L, Rahmouni C, Gey D, Schoelinck C, Hoberg EP (2013) The Monogenean Which Lost Its Clamps. PLoS ONE 8(11): e79155. doi:10.1371/journal.pone.0079155

Image 1 Credit: doi:10.1371/journal.pone.0079155.g001

Image 2 Credit: doi:10.1371/journal.pone.0079155.g002

Image 3 Credit: doi:10.1371/journal.pone.0079155.g007

Elsevier boycott: the cost of knowledge

Please join us in boycotting Elsevier at The Cost of Knowledge website.

Elsevier has bought two publishers of my works, including the publisher of my book (Chandos / Woodhead). I’m debating adding a clause to future publishing contracts that states no selling my work to Elsevier.

If anyone from Elsevier is reading this, please remove me from your Elsevier “Author Connect” list. I do not wish to connect.

Content Mine: Sunlight in California – can AMI help make Spending data Open?

Marc Joffe of http://www.publicsectorcredit.org/ has an ambition – to make Open vast amounts of spending data in California. The Sunlight Foundation has funded Marc (http://sunlightfoundation.com/blog/2013/07/05/opengov-voices-local-government-financial-transparency-scalling-it-up/ ) – the problem is that the data is present in PDFs. So Marc mailed #ami2 a typical document and asked if she could understand it:

She can get the pictures out easily, but that’s not what Marc wants – he wants the data. Like this:

AMI thinks she can find some time to tackle this and help Marc. She’s not interested in money (she has the emotional age of a FORTRAN compiler) but she needs to hack table for science and this one should be possible. (Of course #animalgarden is working with @TabulaPDF as well).

Marc’s blogged about it at http://blog.okfn.org/2013/12/19/pdf-liberation-hackathon-january-18-19/.

Open government data is valuable only to the extent that it can be used cost-effectively. When governments provide “open data” in the form of voluminous PDFs they offer the appearance of openness without its benefits. In this situation, the open government movement had two options: demand machine readable data or hack the PDFs – using technology to liberate the interesting data from them. The two approaches are complimentary; we can pursue both at the same time.


Whether your motive is to improve government, lower the cost of data journalism or free scientific data, you are welcome to join The PDF Liberation Hackathon on January 18-19, 2014 – sponsored by The Sunlight Foundation, Knight-Mozilla OpenNews and others. We’ll have hack sites at the NYU-Poly Incubator in New York, Chicago Community Trust, Sunlight’s Washington DC office and at RallyPad in San Francisco (one or two locations will have an opening social on the evening of the 17th). Developers can also join remotely because we will publish a number of clearly specified PDF extraction challenges before the hackathon. – See more at: http://blog.okfn.org/2013/12/19/pdf-liberation-hackathon-january-18-19/#sthash.n8e3HXH5.dpuf


PMR will be in Lithuania liberating crystallography but hopes to connect in.

And we hope you will too.


Institutions & Funders: Ignore Elsevier Take-Down Notices (and Mandate Immediate-Deposit)

See Exchange on Elsevier Website regarding Elsevier Take-Down Notices (and please note that this concerns only authors’ final drafts, not Elsevier’s PDF version-of-record):

December 17, 2013 at 9:05 pm
Stevan Harnad: Tom, I wonder if it would be possible to drop the double-talk and answer a simple question: Do or do not Elsevier authors retain the right to make their peer-reviewed final drafts on their own institutional websites immediately, with no embargo? Just a Yes or No, please? Stevan

December 18, 2013 at 2:36 pm
Tom Reller (Elsevier): Hello Dr. Harnad. I don?t agree with your characterization of our explanation here, but nevertheless as requested, there is a simple answer to your question ? yes. Thank you.

December 20, 2013
Stevan Harnad: Tom, thank you. Then I suggest that the institutions [and funders] of Elsevier authors ignore the Elsevier take-down notices (and also adopt an immediate-deposit mandate that is immune to all publisher take-down notices by requiring immediate deposit, whether or not access to the immediate-deposit is made immediately OA)? Stevan 

Do follow Peter Suber’s wise advice to authors to try to retain their right to self-archive with OA un-embargoed — but also deposit your final draft immediately upon acceptance whether or not you make your deposit OA immediately; and make sure your institution and funder both adopt an immediate institutional deposit mandate to ensure that all researchers deposit immediately. (And remember that this all concerns the author’s final draft, not the publisher’s PDF version-of-record.)

Paradoxically, publisher take-down notices for the publisher’s proprietary PDF version-of-record are a good thing for the adoption of sensible, effective OA policies and practices: Sleep-walking authors and their institutions need to be awakened to the pragmatics and implications of the difference between the author’s final, peer-reviewed, revised, accepted version and the publisher’s PDF version-of-record: Green OA is all about the former, not the latter.

Stevan Harnad

Read the inaugural issue of Pharmacology Research & Perspectives

53417-PRP-journalWe are pleased to announce that Pharmacology Research & Perspectives has now published its inaugural issue. Pharmacology Research & Perspectives is a new journal from the British Pharmacological Society (BPS) and the American Society for Pharmacology & Experimental Therapeutics (ASPET) and promotes research in all areas of pharmacology.   
The editor’s choice articles from the inaugural issue are:  
purple_lock_openGreen fluorescent protein fused to peptide agonists of two dissimilar G protein-coupled receptors: novel ligands of the bradykinin B2 (rhodopsin family) receptor and parathyroid hormone PTH1 (secretin family) receptor
Xavier Charest-Morin, Jean-Philippe Fortin, Marie-Thérèse Bawolak, Robert Lodge and François Marceau    

purple_lock_openEffects of D-amino acid oxidase inhibition on memory performance and long-term potentiation in vivo
Seth C. Hopkins, Una C. Campbell, Michele L. R. Heffernan, Kerry L. Spear, Ross D. Jeggo, David C. Spanswick, Mark A. Varney and Thomas H. Large    

purple_lock_open Cilostazol prevents retinal ischemic damage partly via inhibition of tumor necrosis factor-?-induced nuclear factor-kappa B/activator protein-1 signaling pathway
Fumiya Ishizuka, Masamitsu Shimazawa, Yusuke Egashira, Hiromi Ogishima, Shinsuke Nakamura, Kazuhiro Tsuruma and Hideaki Hara

Read inaugural issue

 Pharmacology Research & Perspectives invites authors to submit research articles and invites submission of several types of special articles. These are:
1. Target validation – publication of negative findings including preclinical papers that show a hypothesis is incorrect or papers on drugs that have failed in early clinical development
2. Drug discovery reviews – strategy, hypotheses and data resulting in a successful therapeutic drug
3. Frontiers in translational medicine – drug and target validation for an unmet therapeutic need
4. Pharmacological hypotheses – reviews that are oriented to inform a novel hypothesis

All articles are published under a Creative Commons License and comply with all open access mandates.


OKFN’s Open Science Working group is Global!

Jenny Molloy and Michelle Brooks have done a wonderful job in driving forward Open Science within the OKFN. Science is a huge topic and there are many areas where the Open philosophy and tools are now critical. Here’s Jenny’s end-of-year report – the easiest way to get involved is to subscribe to the mailing list and take it from there. Or contact any of us.

YOU DON’T HAVE TO BE A “PROFESSIONAL SCIENTIST” TO BE AN OPEN-SCIENTIST! We are very keen that citizens of any nation and activity are involved.

Hi All


I thought as we get to the end of 2013 it would be good to let you know where the working group is at currently and let you have your say on how we might proceed in our mission to open up science during the next year!

We have grown to over 630 members (!) on the mailing list and now have local groups or representation in:

UK (Oxford, London, Cambridge)




Which is fantastic, but we’d love to expand further! If you would like to be an open science ambassador for your region/country/city/university then get in touch.

To help us keep track of all these activities and make sure we’re being as effective as possible at providing a space for discussions and collaboration around open science, it would be great to hear from anyone who would like to be more involved in managing the working group (also, I have a thesis due in 9 months so any and all help is very much welcome from my perspective!).


We would like to put together a group of community organisers to contribute to a variety of roles. There can be a name for this group but we haven’t settled on one yet – suggestions welcome.The time commitment will be flexible and relatively low, but it will make a big difference to have someone keeping an eye on specific areas. The roles and tasks might include:


Organising working group meetings

Planning open science events at OKFest 2014

Documenting events and updates from the working group

Coordinating specific projects or documents

Blog Editing

Tech/Dev Liaison

Event Organisation

Designing publicity materials and logos etc.


Do get in touch if any of this sounds of interest even if you are only able to contribute a small amount of time. If you have any questions, please let Zara, Michelle and I know and we look forward to hearing from you! Look out for another email about specific projects, events and 2014 working group activities coming shortly.


open-science mailing list
Unsubscribe: https://lists.okfn.org/mailman/options/open-science

Read the December Issue of Cancer Medicine Online Now!

Cancer Medicine

Issue 2:6 of Cancer Medicine is live and available to read online.  A great range of articles in this collection, but here are some top articles which Editor-in-Chief Prof. Qingyi Wei has highlighted from the issue:


Phenotypic modifications in ovarian cancer stem cells following Paclitaxel treatment
Vinicius Craveiro, Yang Yang-Hartwich, Jennie C. Holmberg, Natalia J. Sumi, John Pizzonia, Brian Griffin, Sabrina K. Gill, Dan-Arin Silasi, Masoud Azodi, Thomas Rutherford, Ayesha B. Alvero and Gil Mor

Summary: We demonstrate that putative ovarian cancer cells with tumor initiating capacity that survive chemotherapy acquire molecular phenotypic modifications, which makes them distinct from the original tumor-initiating cells. The modifications that occur may not be the same in every patient. This suggests that treatment modalities should be modified to each individual patient. Further studies using our models will identify biomarkers for personalized treatment.


ADAM17-mediated CD44 cleavage promotes orasphere formation or stemness and tumorigenesis in HNSCC
Pachiyappan Kamarajan, Jae M Shin, Xu Qian, Bibiana Matte, Joey Yizhou Zhu and Yvonne L. Kapila

Summary: Our data demonstrate, for the first time that CD44 cleavage by ADAM17 is a critical determinant of orasphere formation or stemness and tumorigenesis in oral cancer. Our data support the concept that therapeutics that target CD44 cleavage mechanisms within the stem cell compartment can impair stemness and thus hold promise for treating aggressive oral cancer.


BRD4 associates with p53 in DNMT3A-mutated leukemia cells and is implicated in apoptosis by the bromodomain inhibitor JQ1
Helen Jayne Susan Stewart, Gillian Abigail Horne, Sarah Bastow and Timothy James Telfer Chevassut

Summary: The bromodomain inhibitor JQ1 blocks BRD4 binding to acetylated histones leading to apoptosis of acute myeloid leukemia cells. We find JQ1 exhibits synergistic activity with histone deacetylase inhibitors, Nutlin-3 and daunorubicin suggesting involvement of p53. We show that BRD4 interacts with p53, suggesting a role in DNA damage repair response that is disrupted by JQ1 in DNMT3A/NPM1-mutated OCI-AML3 leukemia cells.

Submit your paper here>     Sign up for Content Alerts here>

More Elsevier FUD and Bluff

The University of Calgary has been contacted by a company representing the publisher, Elsevier Reed, regarding certain Elsevier journal articles posted on our publicly accessible university web pages. We have been provided with examples of these articles and reviewed the situation. Elsevier has put the University of Calgary on notice that these publicly posted Elsevier journal articles are an infringement of Elsevier Reed?s copyright and must be taken down.

If Elsevier sends a take-down notice to a university, you have two simple options:

(1) Leave it up, and send the notice back to Elsevier with a copy of Elsevier?s policy on self-archiving.


(2) Re-set access as Closed Access and rely on the repository?s copy-request Button.

(If the take-down notice was because you deposited the publisher?s PDF, make the publisher?s PDF Closed Access and deposit the author?s final draft instead, and make that OA.)

And fix your mandate to make sure it specifies that the author?s final draft should be deposited immediately upon acceptance for publication, not the publisher?s PDF.

(Calgary would have done better to respond pragmatically to this latest round of Elsevier FUD and bluff — but, after all, this is exactly what FUD’s for, isn’t it?)

Awkward Silences: Technical Delays Can Diminish Feelings of Unity and Belonging


Smooth social interaction is fundamental to a sense of togetherness. We’ve all experienced disrupted conversations—some caused by human awkwardness and others by breakdowns in technology. The content of our interactions does influence our connection to each other, but the form and process of communication also play a role.  Technical delays that occur below our conscious detection can still make us feel like we don’t quite click with the person we are trying to communicate with. The authors of a recently published PLOS ONE article, funded by a Google Research Award, investigated how delays introduced into technologically mediated conversations affected participants’ sense of solidarity with each other, defined as unity, belongingness, and shared reality.

For this research, conducted at University of Groningen, The Netherlands, participants in three sets of experiments sat in cubicles with headsets connected to computers (conditions that many of us with desk jobs can relate to) and were asked to talk about holidays for five minutes with an assigned partner. Some conversations were uninterrupted. Others were manipulated by introducing a one-second auditory delay. Some pairs knew about the delay and others did not. Afterward, the conversationalists completed a questionnaire about their sense of unity, belonging, understanding, and agreement with their partners.


Researchers found that those participants whose conversations were interrupted expressed significantly diminished feelings of unity and belonging. Awareness of technical problems had no apparent effect on perceived solidarity.  Even acquaintances stated that they felt a disconnect, though to a lesser degree, than participants who did not know each other. Despite participants expressing that they felt less unity and belongingness with their partner even when they had the opportunity to attribute it to technical problems, technology did not get a free pass on the delayed signal. Those with an interrupted connection also expressed less satisfaction with the technology. Points may have been lost for both relationships and telecommunications.

In a world where our interactions are increasingly mediated by computers and mobile phones with less than perfect signals, the authors suggest that this research provides insight into how our daily interactions may be affected. The method of communication we choose may influence our personal and business relationships, especially among strangers. The authors also posit that technology meant to improve long distance communication by imitating face-to-face interaction may not measure up to expectations if it is not executed without interruptions or delays. Perhaps this is something to consider during your next awkward phone call or video conference— though your awareness of technology as a possible barrier ultimately may not make a difference in how you perceive the person on the other end of the line.

Citation: Koudenburg N, Postmes T, Gordijn EH (2013) Conversational Flow Promotes Solidarity. PLoS ONE 8(11): e78363. doi:10.1371/journal.pone.0078363

Images: First image by Villemard is in the public domain. Second image is Supplemetary Figure 1 from the article.

Content-mining: #animalgarden write a crawler


Chuff: Hello Gulliver! I’m the OKFN OKAPI.

Gulliver: Hello! I’m Gulliver, the BMC turtle.

C: I know – you’ve got a blog http://gulliverturtle.wordpress.com/ where you tell the world about #openaccess. What’s #ami2 doing?

G: She’s crawling BioMedCentral content.

C: Gosh! It looks painful.

G: It’s very painful for humans, but as you know #ami2 has no emotions. So it’s not a problem. She’s good at it.

C: Yes, she doesn’t get tired, angry, bored. She does exactly what she is told by PMR. So how does it work?

G: Here’s my content page: http://www.biomedcentral.com/content – that tells you where all the articles are

A: PMR told me to read each bibliodata and follow the link. I have to do that for all the papers.

C: Well there are only 25 so it won’t take too long.

G: We’re MUCH more popular than that. This is one PAGE. There’s nearly 6000 pages.

C: Wow! Is that because you’re Open Access?

G: Yes. PMR publishes many of his papers with me.

C: Let’s see. 25 * 6000 = 150,000. Wow! What a lot of Open Access papers. Can #ami2 do them all?

G: Yes. We’ll tell her how long she has to wait between reading each paper?

C: But #ami2′s very fast. She doesn’t need to wait.

G: If she tries to download papers too quickly – like 1000 per second –it might confuse our servers. Because that might look like a hostile robot.

C: But #ami2 IS a robot.

G: Yes, but she’s a friendly robot. We’ll tell her what the maximum speed is.

C: She told me it was 6 seconds for PLoSONE. (I wish PLoSONE would get a mascot – all #openaccess publishers should have animals).

G: Yes. PeerJ has Charlie the monkey. Anyway let’s do the sums. 6 secs is 10 papers per minute. We need 150,000 / 10 minutes. Which is 15,000 minutes.

C: which is about 10 days. That’s to get the backlog. How many would it be per day?

G: It think about 150. I’ll have to check with Amye. That’s BMC Amye!

C: Yes, I met her at the @OpenDrinks last week. That’s about the same number as PLoSONE. 150 articles is 15 minutes.

G: And you can do all BMC at the same time. Because you can alternate requests every 3 seconds.

C: That’s clever. Wow – there’s even a journal for data mining: http://www.biodatamining.org/. How big is an article?

G: depends what you want. http://www.biodatamining.org/content/pdf/1756-0381-6-21.pdf is about 6 MBytes. But there’s also HTML and XML.

C: Are they all the same?

G: not quite. The XML and HTML are quite similar. #ami2 can read them easily. They don’t have any pictures.

C: But I like pictures.

G: The pictures are there, but separate. You have to follow links.

C: #ami2 can do that. We have to organize it… But the PDF may contain vector graphics. PMR loves vector graphics because he can teach #ami2 to build real science from the pictures. He’s not so keen on PNGs and GIFs and TIFFs and JPEGs. But #ami2 isn’t perfect at reading PDFs. No one is perfect at reading PDFs except sighted humans. It’s hard to teach animals like #ami2. But she’s improving.

G: OK – sounds like you want the PDF AND the XML AND the HTML.

C: Sounds like it. So we have to let #ami2 know where they are. Trouble is every publisher does it differently. PMR’s just written AbstractCrawler.java .

G: So will that read BMC?

C: No. It won’t read anything. It only downloads things.

G: So will it download my articles?

C: Not yet. We have to write a special crawler for each publisher. PMR’s written PlosoneRecentCrawler. which extends
AbstractCrawler. He’s tried to make it easy to include a new publisher.

G: Please speak nicely to him and ask him to write a Gulliver Crawler.

C: I will try. He’s a bit tired. Humans need to rest.

G: How boring and inconvenient!

C: He sometimes writes code during the cricket. But he’s upset about the cricket…

G: I suppose #ami2 is pleased about the cricket?

C: No – remember she has the emotional apparatus of a FORTRAN compiler. PMR will point her at the BMC content page. She will start at the first article and then go on to the next. Let’s start at:


I *think* that means that we start at page 1. If we go to the next page we find:


G: That looks promising. But rember that these pages are updated. Their content could change as we add new papers>

C: Oh my stripes and paws! Let’s ask Amye.. She wrote to PMR: 

We have both a search API, an OAI-PMH API and an FTP location with a zip file of all our XML. The OAI-PMH API allows for retrieval of article metadata and fulltext XML for all articles or specific subsets. It also allows flexible date stamp restriction. So that should meet your needs. We also have a feed API (giving the latest articles, picks and most viewed) and a case report API for our Cases Database.

G: Well done. I think it will take another mail or skype to clarify…

C: Goodbye for now, and goodbye from #ami2






PLOS ONE Heads to the Big Easy for the 2013 Meeting of the American Society for Cell Biology

journal pbio 0020318 g001

PLOS ONE is excited for the opportunity to exhibit alongside PLOS Biology at the American Society for Cell Biology’s (ASCB) Annual Meeting in New Orleans from December 14 – 18. This year’s ASCB meeting will be held at the Ernest N. Morial Convention Center and is expected to draw approximately 7,000 cell biology enthusiasts. The conference will feature upwards of 100 scientific sessions and 2500 posters on a plethora of topics within cell biology research.  Additionally, as stated on the ASCB Annual Meeting website, Nobel Laureates Randy Schekman, a PLOS ONE author, and James Rotham will be special guest speakers.

We encourage all conference attendees to stop by booth # 211 on Publisher’s Row to speak with PLOS ONE staff and learn about the journal. We look forward to engaging with PLOS ONE authors—current and prospective alike—as well as reviewers, members of our Editorial Board (Academic Editors) and all others wanting to learn about PLOS ONE and PLOS as a whole. Additionally, Dr. Ines Alvarez-Garcia, a Senior Editor from our sister journal, PLOS Biology, will be at the exhibition booth for a “meet the editor” session from noon – 1 pm on Monday, December 16. Be sure to stop by and say hello. After the conference on the evening of the 16th PLOS ONE will be hosting a mixer for all Academic Editors who are in attendance at the event. Please contact Camron Assadi (cassadi@plos.org) to RSVP.

See you in New Orleans on December 14!

In celebration of all things cell biology, here are some of the most viewed and most cited cell biology-related papers published in PLOS ONE over the past year:

Most Viewed

Citation: Rundqvist H, Augsten M, Strömberg A, Rullman E, Mijwel S, et al. (2013) Effect of Acute Exercise on Prostate Cancer Cell Growth. PLoS ONE 8(7): e67579. doi:10.1371/journal.pone.0067579

Citation: Hanauske-Abel HM, Saxena D, Palumbo PE, Hanauske A-R, Luchessi AD, et al. (2013) Drug-Induced Reactivation of Apoptosis Abrogates HIV-1 Infection. PLoS ONE 8(9): e74414. doi:10.1371/journal.pone.0074414

Citation: Bhasin MK, Dusek JA, Chang B-H, Joseph MG, Denninger JW, et al. (2013) Relaxation Response Induces Temporal Transcriptome Changes in Energy Metabolism, Insulin Secretion and Inflammatory Pathways. PLoS ONE 8(5): e62817. doi:10.1371/journal.pone.0062817

Most Cited

Citation: Xu Y, Ding J, Wu L-Y, Chou K-C (2013) iSNO-PseAAC: Predict Cysteine S-Nitrosylation Sites in Proteins by Incorporating Position Specific Amino Acid Propensity into Pseudo Amino Acid Composition. PLoS ONE 8(2): e55844. doi:10.1371/journal.pone.0055844

Citation: Ohkura M, Sasaki T, Sadakari J, Gengyo-Ando K, Kagawa-Nagamura Y, et al. (2012) Genetically Encoded Green Fluorescent Ca2+ Indicators with Improved Detectability for Neuronal Ca2+ Signals. PLoS ONE 7(12): e51286. doi:10.1371/journal.pone.0051286

Citation: Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK (2013) Plastics Derived Endocrine Disruptors (BPA, DEHP and DBP) Induce Epigenetic Transgenerational Inheritance of Obesity, Reproductive Disease and Sperm Epimutations. PLoS ONE 8(1): e55387. doi:10.1371/journal.pone.0055387

Image Credit(2004) Protein Helps Orchestrate Cells’ Fluid Uptake. PLOS Biology 2(9): e318. doi:10.1371/journal.pbio.0020318.