Semantic Physical Science: the movie (includes scenes of a political nature)


I am editing the video material from our Semantic Physical Science symposium, and the first is my introduction (, ca 10 mins). This is partly because it’s short (so less technical hassle – though more editing) and partly because I can give myself permission, while I am still waiting for other speakers to give the OK. [All talks WILL be mounted, and all will be Open Knowledge Definition compliant (CC-BY 3.0, Creative Commons Attribution). This means that anyone can do anything with them, including cutting snippets and re-using them. Even (especially) for political purposes.] Here M.I.T.-bear strikes a blow for freedom (about 8 mins into the video)

NOTE: There are a few frame drops, interestingly on the titles. Maybe a more consistent background will help. (You haven’t missed anything)

My video is complex because it contains

  • Hello Participants and Hello World
  • The purpose of the symposium – to hand over 15 years of work to the world scientific community in an Open Manner
  • Tribute to my colleagues and funders
  • Context of semantic science
  • Political barriers to be overcome (ca 8:00 mins into video). Here M.I.T-bear strikes a blow for freedom against RWA/HR3699. Also PMR expresses his views on the proposed legislation.

Here are some of the links I mention – it’s easier to follow them here

and here is the programme. I am intending we post all of these, but it’s a lot of time experimenting with video conversion.


Elsevier: thy name is hypocrisy

The Elsevier Foundation just announced on the Liblicense list $650,000 in grants. Generous? Hang on a second – at the same time that the Elsevier Foundation is assessing medical library needs for an Eritrean future, helping Kenyan libraries serve health workers, and translating knowledge into practice for Uganda’s rural health clinics, Elsevier is doing its utmost to take down PubMedCentral, which would be a tremendous loss of medical research information in the U.S. and everywhere else.

I must admit it is nice to see a little bit of graft money going to deserving folks in the developing world, and not all of it going to the likes of U.S. Rep. Carolyn Maloney, but graft is graft, and Elsevier, thy name is hypocrisy.

When interpreting the enormous profits of STM publishers like Elsevier, it is important to take into account that the 36% profit margin comes AFTER graft pay-out, not before. This may help to explain how we can transition the whole of scholarly communication to a fully open access system – and save LOTS of money, too. Less than half of what we pay now, and up to 90% savings with a scholar-led system like most of the journals using Open Journal Systems.

A fully open access scholarly publishing system means that all of the Elsevier beneficiaries – and billions of others – will have access to all of the world’s knowledge – and the opportunity to contribute, too. Let’s not settle for a few crumbs, when all of us, everywhere, can have the whole pie, as is obviously doable when one copy of a scholarly work posted on the web is available to everyone, everywhere with an internet connection.

Major Cancer Societies to Support New Wiley Open Access Journal

 We are pleased to announce the launch of Cancer Medicine, a new Wiley Open Access journal. Cancer Medicine is a   peer reviewed, open access, interdisciplinary journal providing rapid publication of cutting edge research from global biomedical and clinical researchers across all the oncologic specialties in cancer biology, clinical cancer research and cancer prevention. The journal’s promise of full global reach is reinforced by its editorial leadership and support from prestigious journals and societies. Cancer Medicine has unprecedented support from three major cancer societies: American Cancer Society (ACS), Union for International Cancer Control (UICC) and Japanese Cancer Association (JCA). 

Cancer Medicine is steered by Editor-in-Chief Dr. Qingyi Wei, a highly published and cited author based at the world’s leading cancer research center in the United States.  Dr. Wei’s previous editorial work includes a role as a Senior Editor on the American Association for Cancer Research’s journal Cancer Epidemiology, Biomarkers & Prevention. His research is aimed at identifying individuals at high risk of developing cancer. Dr. Wei comments, “I am delighted to introduce Cancer Medicine, which will allow readers to have fast access to the most up to date global collaborations in cancer research and international approaches in practicing cancer medicine, as well as highlighting key achievements from the integration of basic, clinical and preventive research of cancer. In the years to come, I will work closely with the Wiley-Blackwell Cancer Medicine team to provide timely and impartial service to all contributors and readers, who will, without a doubt, make Cancer Medicine a success.”

The journal is open to submissions now and aims to publish its first content online in Spring 2012. Please visit the journal’s website for further information and future updates.

Semantic Physical Science


We ran a most rewarding workshop and symposium on Semantic Physical Science last Tue/Wed/Thu (2011-01-10/12). The program is below. This is an interim post to keep the momentum going and to let others know that there will be in important continuing activity. There were about 25 for the workshop and another 10 for the symposium.

The event covered a lot of ground, with a lot that was new for many people and many different possible ways of tackling semantics. The immediate outcome is there was very good agreement on:

  • The value of semantics
  • What to do in the first instance
  • Timescales
  • Resources

The areas we covered were:

  • Computational chemistry (participants included STFC (DL), PNNL, Cambridge (EarthSci, Chem, Chemeng, Cavendish), QMC, Bristol, Imperial (unfortunately Henry Rzepa had to miss the last day)
  • NMR. Concentrating on 1-D NMR spectra (Bruker, Varian, JCAMP), mainly (CSIRO and PNNL). Unfortunately Christoph Steinbeck (NMRShiftDB) couldn’t come but we have a very good outline of what needs doing
  • Crystal. Main interest in having a repository of published structures independent of any restrictions (e.g. Crystaleye)

The software is now clearly alpha or very close to it. We are particularly grateful to Andrew Walker for FoX and good prototype/proof-of-concept was made with NWChem and AMBER. To be successful we shall need the continuing support of the developers. JUMBOConverters is now distributable and straightforward to add new converters, validators and dictionary-lookup.

Chempound worked well and there is clearly demand for all 3 disciplines

We’ll try to get a fuller summary out in the next few days. Basically we have agreed that the immediate phase involves:

  • Firming up some conventions, especially NMR
  • Pulling the various CML websites and resources together
  • Deciding on how to do dictionaries. There are two schools of thought:
  1. One uber-dictionary for compchem. Anything that is program-specific isn’t important
  2. One dictionary per program and an uber-dictionary for compchem

I am deliberately neutral on dictionaries, but I think the software has to support (2) [That make it able to support (1) as well]. I think during development phase it will be necessary to have a number of dictionaries, but we must be careful they don’t get set in concrete. For NMR I suspect we shall have to have instrument-specific dictionaries

  • Firming up validator software
  • Firming up commandline converters

Many thanks to Charlotte Bolton for organizing all sorts of things. As with last time Charlotte will continue to support with documentation and publication.

I am also working hard on editing the videos. They aren’t too hard sequentially in that everyone talked well and in a linear fashion, but I’m still not on top of WMV => ffmpeg => MP4. Anything 1280*960 is likely to drop image frames; half size is fine, but it’s hard to read the screen. In any case they need editing. I’m going to post them privately to the participants in case there’s anything they want to delete/add. We need to do this as MP4 [ca 100 Mbytes / 30 mins] because WMV is just far too big.

Cameron and I have some political messages about SOPA/RWA etc so those will probably be the first out.

More later. [Next week I have Open Biblio sprint, so not much time for relaxation! But it’s fun].


HR3699 and SOPA restrictions hit Small businesses

AnnMaria is a small business owner and writes passionately about the harm that HR3699 does to her: I’ll quote extensively below. And I want you to get angry as well.

And start DOING something about it.

I’ve written before about the Scholarly Poor; small businesses are a major part of it. Every time I meet people in small business (and Cambridge is the UK centre of technology-based startups) I ask them whether they (a) want to read the scientific literature and (b) whether they can and (c) whether they suffer. And the answers are (a) yes and (b) generally no and (c) yes. Many businesses give up and only read freely accessible articles and do not re-use the data. There are illegal work-rounds:

  • Ask on Icanhazpdf (it is illegal to send people copies of closed articles)
  • Get a graduate student in your erstwhile to pipe through the articles (also illegal)

But ethical companies don’t do that. And also, as SOPA and RWA come nearer, we shall see prosecutions. If Wiley can threaten a graduate student for reproducing a single graph (an unethical and probably illegal act) are their hired guns in SOPA going to hold back? Because the scholarly publishers as well as the music industry are supporting SOPA. And SOPA won’t be policed by the nice people who we meet in publishers, it’ll be policed by professional enforcers. If you can sue a kindergarten child for pirating music you can also sue a small business.

Here’s AnnMaria:

Research Works Act: Latest Congressional Lie about Helping Small Business

I am pissed


As a small business owner, I am feeling very, very disappointed that there is certainly some law out there that would impose penalties if I drove on over to Riverside County and bitch-slapped [1] Darrell Issa. I’ve grown cynical enough in my old age and after having run a small business since 1985 that I am used to every politician under the sun spouting “Think of small business!” as a knee-jerk reaction to anything, whether their position is for it or against it. Usually, they are easy enough to ignore. Payroll taxes are not going to decide whether or not I hire people – business demand is. Health care – we’ve made that an option for our employees long before it was required by law.

This time, though, they are REALLY pissing me off. Let me tell you what the Research Works Act is and how it really does hurt my small business. As this succinct article by Janet Stemwedel on the Scientific American blog site explains well, not only does it require the American taxpayer (that’s me!) to pay twice for the same research, but also, the very people being protected and profiting are NOT those who produce the work to begin with.

Right now, if a person is funded by federal funds, say, the National Institutes of Health, they are required to submit the results of their research to PubMed’s repository within twelve months of publication. The idea is that if the public paid for this research then the public has the right to read it. Sounds fair, right?

In case you don’t know, rarely do authors get paid by journals.  I’ve published articles in the American Journal on Mental Retardation, Research in Developmental Disabilities, Educational and Psychological Measurement – to name a few. I’ve been a peer reviewer for Family Relations. For none of this did I get paid. That was fine. Almost all of the research I did was funded by federal funds and part of the grant proposals included dissemination – that is, publication of scientific articles. Fair enough. As a peer reviewer, I’m just repaying the service others have done in reviewing my work. Again, no problem.

Yet, in many cases, if I need a journal article for a grant or report I’m writing for a client, it is going to cost me $30 per article.  Contract research is a good bit of where the actual money comes into this company (you didn’t seriously think I made my living by drinking Chardonnay, spouting wanton programming advice and snarky comments, did you?)

The journal did not pay for the research to be conducted – the federal government did. The journal did not pay the author – the federal government did. The journal did not pay the reviewer – they volunteer.


I just pulled up a random small project I had done recently for a client and there were seven articles in there that I would be charged $210 to have used. As I said, this was a small project, and I calculated it would have brought the price up 7.5%

Not long ago, there was a huge outcry about the city of Santa Monica adding a ten cent cost for a paper bag and banning plastic bags. “It will hurt small business!” people cried. Actually, I have always made a major effort to shop at our local businesses, I still do and it has not hurt any business anywhere that I can tell. You know what else I can tell you? That increasing the cost of a $3,000 project to $3,210 is a hell of a lot more significant than paying ten cents for a paper bag!

So what exactly is this bill doing? It is moving money from small businesses, like me,  and like my buddy, Dr. Jacob Flores, who runs Mobile Medicine Outreach and into the hands of large publishing companies, who not coincidentally gave a huge amount of money  to Democratic congresswoman Carolyn Maloney of New York. I’d like to bitch-slap her, too, but being on the opposite side of the country, it would be a lot less convenient for me.

You can read more detail in this article from the Atlantic, where Rebecca Rosen asks, “Why Is Open-Internet Champion Darrell Issa Supporting an Attack on Open Science? ”

As Danah Boyd points out on her blog, there is this new thing for sharing knowledge now, called the Internet and a major point of the Research Works Act seems to be to prevent it being used to share knowledge that I paid for with the approximately 50%  of my income (yeah 38% federal, 10% state) that I pay in taxes. And you know what, being a graduate from that great institution, the University of California, that enables me to make the money to pay these taxes, I don’t object to that.

What I DO object to is paying again for the same resources I already paid for once just because some lobbyists for large corporations lined Issa’s and Maloney’s pockets.

While it may not be legal for me to bitch-slap Issa it is certainly legal for me to go to the next California event where that lying-ass mother has the balls to stand up and claim to be helping California small business. Anyone who knows the next public event where he’ll be speaking, please hit me up.

One thing, though, I don’t think I’ll be going to any of his fundraisers. I think he’s gotten quite enough money from the publishing industry.


AnnMaria shows the very simple equation:

Supporting the scholarly publishing industry profits = draining opportunity and profits from new technology companies.

The scholarly publishing industry is making profits out of monopolistic restrictions. In so doing it is destroying other industries. We’ve heard in the UK that IP restrictions prevent companies like Google setting up here. If SPOA/RWA are passed it won’t be possible to set up new Googles in California either.

So – if you want wealth generation in the future, support 21st century industries like Google, O’Reilly, and AnnMaria. And let the scholpub adapt or die.

[Peter Suber] Robert Heinlein responded to the [scholpub] position more than 70 years ago (Life-Line, 1939):  “There has grown up in the minds of certain groups in this country the notion that because a man or corporation has made a profit out of the public for a number of years, the government and the courts are charged with the duty of guaranteeing such profit in the future, even in the face of changing circumstances and contrary to public interest. This strange doctrine is not supported by statute or common law. Neither individuals nor corporations have any right to come into court and ask that the clock of history be stopped, or turned back.”  

[1] Bitch-slap f = (AnnMaria – please send pictures when you do)




Stop HR3699; The Open Access movement needs to get ACTIVE; the Scholarly Poor already do

I have been blogging for a week about HR3699 (Research Works Act). I have been trying to take personal action – apart from blogging I have mailed OUP and CUP asking them to stand up and be counted on their membership of AAP.

Yet if I hadn’t been actively involved in open data I wouldn’t even have known anything was happening – that there was anything I should be concerned about. And no-one has tried to reach me and get me involved – even to sign a petition.

In contrast other Open movements such as F/OSS, Avaaz, 38 Degrees mail me every week asking me to sign on all sorts of issues. In the internet age it’s easy to reach out to people and provide means to get them involved.

I’ve searched for “stop HR 3699 petition” and the first site that comes up is

This is a site (Care2, Jennifer P. – I’d never come across it) for “ordinary people” who care about access to information, especially health information. They are the “scholarly poor”. The people who – unlike rich Universities – actually feel the lack of access to healthcare information.

As soon as I heard about HR3699 I mailed the patent advocates I knew. And, of course, they have responded magnificently. Here’s Gilles Frydman, through the Society for Participatory Medicine. The Scholarly poor with real disease.

Here’s Gilles:

Before reading further, remember the definition of Participatory Medicine:

a movement in which networked patients shift from being mere passengers to responsible drivers of their health, and in which providers encourage and value them as full partners.

How can you be a responsible driver of your health if you don’t have direct access to all information? That’s why Dave has been fighting for his damn data and similarly why ACOR has been engaged in multiple efforts to maximize the dissemination of any and all scientific publication that relates to an ACOR group condition.

Seeing a corrupt travesty of the democratic process used today to promote the interests of a few gatekeepers at the expense of millions of people is very disturbing. The NIH and other agencies must be allowed to ensure timely, public access to the results of research funded with taxpayer dollars. Please oppose H.R. 3699. You’ll be in great company!

And there’s lots more [I quote from Gilles]

Tim O’Reilly [PMR One of the great entrepreneurs and thinkers of this century] Please don’t write laws that protect 19th century industries against 21st-century disruption!

[Gilles: ]Tim’s […] sentence may need some explanation, which thankfully has been provided by Microsoft Researcher and grand guru of social media’s influence on the youth, danah boyd, in her December blog post Save Scholarly Ideas, Not the Publishing Industry (a rant):

The scholarly publishing industry used to offer a service. It used to be about making sure that knowledge was shared as broadly as possible to those who would find it valuable using the available means of distribution: packaged paper objects shipped through mail to libraries and individuals. It made a profit off of serving an audience. These days, the scholarly publishing industry operates as a gatekeeper, driven more by profits than by the desire to share information as widely as possible. It stopped innovating and started resting on its laurels. And the worst part about it? Scholars have bent over and let that industry continuously violate them and the university libraries that support them. [..]

WTF? How did academia become so risk-adverse? The whole point of tenure was to protect radical thinking. But where is the radicalism in academia? [PMR emphasis]

Ironically, of course, it’s the government who is trying to push back against the scholarly publishing’s stranglehold on scholarly knowledge. [..]

Please, I beg you, regardless of whether or not we can save a dying industry, let’s collectively figure out how to save the value that prompted its creation: making scholarly knowledge widely accessible.


PMR: Yes “where is the radicalism in academia?” Where is the radicalism in the Open Access movement? The OA movement is playing pillowfights while the AAP hired guns play dirty with baseball bats. They spend their money on lobbyists. And the OA movement is not mobilising opinion.

[I acknowledge that there are people who are working hard to change opinion on Capitol Hill and I respect them. But it’s closed. It’s a small group of people who don’t tell the world what they are doing. Maybe this is necessary secrecy but it leaves the mass of people outside the OA movement uncoordinated. There’s Richard Poynder who has already mailed all the University Presses. But if there are other activities no one is publicising them sufficiently.]

As a result the activist response is either missing or fragmented. Some instances:

  • Where is the OA petition against HR3699? I couldn’t find one.
  • Where is the organisation of responses to Capitol Hill.? Am *I* (as a non-US citizen allowed to submit to OSTP? I asked on lists and got no reply. I tweeted (I have 1000 followers) – no reply.
  • Where is the count of people who have signed or written against HR3699?
  • Where is the communal Wiki for people to find resources for the protest?

Here’s a typical simple action – my avatar. I got the idea from Glyn Moody. YOU could do it. Don’t be afraid – it’s not illegal to protest publicly.

There are many more things that you could do, but I’ll use a separate post to give things that the Open Access movement could be doing now. All within the holy law of copyright. There’s hundreds of millions of dollars spent on OA (if you include Repositories) – there’s certainly enough resources to organize 21st century protest activities.

Late last year I gave a slogan for the OA movement: “Closed access means people die”. It’s simple. It’s a political slogan. But I was severely criticized because it hadn’t been proved in a scientific manner. (Actually there is quite enough evidence supporting it). The point is that the OA movement has to use slogans to reach out beyond its narrow boundaries. I’ve offered the apparent double negative: “Open Access saves lives”. This is the sort of message we should be using.

Because it’s obvious that the Scholarly Poor – Jennifer P, Gilles, Tim O’Reilly, Dana Boyd are doing their own activities without the coordination of the OA movement. Their anger and passion comes through and it reaches out to the Scholarly Poor in a way that academia does not.

So, OA community – if there is one – start engaging with people outside – and that’s increasingly including me.

UPDATE: Recent tweet: @petermurrayrust @PublicAccessYAY round up of OA coverage Place to vote against it #rwa

Fifth Belgrade International Open Access Conference 2012

Centre for Evaluation in Education and Science is pleased to announce that, in partnership with the National Library of Serbia, the Fifth Belgrade International Open Access Conference will be held on Friday&Saturday, May 18-19, 2012 in Belgrade, Serbia.
This year conference will focus on local and regional journals striving for international excellence and recognition. It will be assisted with a powerful partnering tool to ensure networking of the visitors, before, during, and after the conference duration.
We welcome contributions and participation from journal editors and publishers, science managers and administrators, research evaluators, librarians, information systems developers, and all others interested in issues listed in programme. Especially welcome are papers addressing evaluation and quality issues of journal publishing in developing, transition, and emerging market countries.

To decide, please consult Conference Overview.

Open Letter to OUP; request to repudiate H.R.3699 and Research Works Act

Dear Nigel Portwood,

I am an alumnus of Oxford University (Balliol, BA, MA, DPhil) and write to urge OUP to repudiate H.R.3699 and the Research Works Act promoted by the American Association of Publishers of which OUP is a member.

The AAP has proposed a bill which effectively legislates the restriction of access to scholarly publication with the sole intention of raising the income of publishers. I and many others feel this is unethical, immoral and unworthy of any organisation committed to the dissemination of knowledge. Some commentators have described it as an act of war by the publishing industry on the scholarly community. Balanced and factual accounts are given by Richard Poynder ( and related posts in his blog).

Already academic publishers are distancing themselves from this Act. MIT Press (link above) has stated:

“The AAP’s press release on the Research Works Act does not reflect the position of the MIT Press; nor, I imagine, the position of many other scholarly presses whose mission is centrally focused on broad dissemination.

I can see every reason why OUP should issue a similar, or even stronger, message repudiating the AAP’s position. I hope that you can assure me OUP was not involved in creating the AAP’s position and ask you to consider the downsides of belonging to an organisation such as AAP.

[This is not the first time that the publishing industry has created anti-scholarship initiatives – I wrote to OUP about the iniquity of the “PRISM” alliance in 2007. I doubt it will be the last.]


[PS. I do not have personal email addresses and assume that “press” will reroute this mail. In any case I have a heavily followed blog and will post this letter there – maybe someone at OUP will forward it if required].

Open letter to Cambridge University Press requesting repudiation of H.R.3699 and Research Works Act

[I have sent the following letter to If anyone knows better addresses for the addressees, please could you forward it. You might also wish to add messages of your own]

Dear Stephen Bourne,
Dear Andrew Brown,

I am a member of Cambridge University (Reader Emeritus, Chemistry and past Senior Research Fellow, Churchill) and write to urge CUP to repudiate H.R.3699 and the Research Works Act promoted by the American Association of Publishers of which CUP is a member.

The AAP has proposed a bill which effectively legislates the restriction of access to scholarly publication with the sole intention of raising the income of publishers. I and many others feel this is unethical, immoral and unworthy of any organisation committed to the dissemination of knowledge. Some commentators have described it as an act of war by the publishing industry on the scholarly community. Balanced and factual accounts are given by Richard Poynder ( and related posts in his blog).

Already academic publishers are distancing themselves from this Act. MIT Press (link above) has stated:

“The AAP’s press release on the Research Works Act does not reflect the position of the MIT Press; nor, I imagine, the position of many other scholarly presses whose mission is centrally focused on broad dissemination.

I can see every reason why CUP should issue a similar, or even stronger, message repudiating the AAP’s position. I hope that you can assure me CUP was not involved in creating the AAP’s position and ask you to consider the downsides of belonging to an organisation such as AAP.

[This is not the first time that the publishing industry has created anti-scholarship initiatives – I wrote to you about the iniquity of the “PRISM” alliance in 2007. I doubt it will be the last.]

Yours [Peter Murray-Rust]

[PS. I do not have personal email addresses and assume that “press” will reroute this mail. In any case I have a heavily followed blog and will post this letter there – maybe someone at CUP will forward it if required].

PLoS ONE News and Blog Round-Up: 2011 in Review

In this round-up, we would like to share with you some of the PLoS ONE articles covered by the media in 2011.  It was really difficult to narrow it down since we had over 450 manuscripts in the news, but here are a few of the papers the media found newsworthy.  The list begins in December and then works backward through the year.

In the manuscript, Dancing for Food in the Deep Sea: Bacterial Farming by a New Species of Yeti Crab, researchers discovered that the “Yeti Crab” (Kiwa puravida), which lives off the coast of Costa Rica, consumes the nutrient-rich bacteria it cultivates on its claws.  Wired, National Geographic and Scientific American covered the article.

On average, Twitter users tend to be the happiest on Saturdays. This trend, along with others, was reported in a study called, Temporal Patterns of Happiness and Information in a Global Social Network: Hedonometrics and Twitter.  It received media coverage from The Daily Dose, Gawker, and National Geographic. This is just for spacing

In the study, Suicidal Behavior and Depression in Smoking Cessation Treatments, researchers collected and analyzed data from the FDA’s Adverse Event Reporting System (AERS) database, spanning 1998 through September 2010. The results indicated that of 3,249 reported cases of suicidal/self-injurious behavior or depression, 90% reported use of varenicline, an anti-smoking drug sold under the brand name Chantix. The article was covered by CNN, ABC News, and TIME.

According to the paper, The Network of Global Corporate Control, 147 companies control 40% of the world’s economy. Swiss researchers have produced a map of the global economic structure, showing the intricate, interconnectedness among companies, similar to the relationships found in nature. This image highlights some of the major transnational corporations in the financial sector.  Media outlets that covered this paper included The Huffington Post, NewScientist, and Forbes.

The T-rex is heavier than previously thought according to the paper, A Computational Analysis of Limb and Body Dimensions in Tyrannosaurus rex with Implications for Locomotion, Ontogeny, and Growth. Researchers used computer models of four T-rex fossil specimens to assess its body mass. The results indicate that the adult dino was 30% heavier than formerly estimated. Xinhua, The Christian Science Monitor, and Slashdot are a few of the media outlets that covered this article.

Children as young as 15 months may have a basic understanding of fairness according to the research presented in the manuscript, Fairness Expectations and Altruistic Sharing in 15-Month-Old Human Infants.  Science 2.0, Scientific American, and WFAA-TV covered this article. This is just for spacin This is just for spacing.This is just for spacing.g.

In August, the Centers for Disease Control announced the results of its first multi-year analysis of HIV incidence in the United States from 2006 to 2009. The paper, which published in PLoS ONE, found that though the rate of HIV infection remained steady; it disproportionately affected several racial and ethnic populations in the United States. The paper received a lot of media attention and was covered by: NPR, The New York Times, CNN, Huffington Post, Washington Post, and the San Francisco Chronicle among others.

The paper, Functional Tooth Regeneration Using a Bioengineered Tooth Unit as a Mature Organ Replacement Regenerative Therapy received global media attention. Some of the media outlets that covered the paper include: Reuters, Times of India, and ABC News 24. This is just for spacing.This is just for spacing.This is just for spacing.This is just for spacing.

Researchers at MIT developed an antiviral therapy that could be used to treat variety of viruses. The drug, called Double-stranded RNA (dsRNA) Activated Caspase Oligomerizer (DRACO) enters mammalian cells and selectively kills cells containing viral dsRNA, without harming uninfected cells.  Details of the study can be found in the paper entitled, Broad-Spectrum Antiviral Therapeutics. News coverage on this article included articles by Voice of America, LA Times, and Forbes.

A science career affects the life satisfaction of science faculty according to the article, Scientists Want More Children. The Wall Street Journal and TIME’s Ecocentric blog covered this article.

In the paper, Epigenetic Predictor of Age, researchers from UCLA discovered that they could predict someone’s age using the DNA from their saliva.  There were many articles written on the paper. Some of these media outlets included Time, 80 beats, and CNET.

For Emperor penguins, huddling is essential to surviving the cold Antarctic winter. In the paper, Coordinated Movements Prevent Jamming in an Emperor Penguin Huddle, researchers show that penguins avoid jamming using coordinated movements. Media coverage of this article included pieces by The New York Times, News for Your Neurons and LiveScience.

Lisa Cosgrove et al. published an article entitled, Antidepressants and Breast and Ovarian Cancer Risk: A Review of the Literature and Researchers’ Financial Associations with Industry. The paper received media attention from CTV, Bloomberg Businessweek, and The Boston Globe.

The paper, Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees, received coverage from The Loom, The Economist, The Telegraph, and New Scientist.   To read the story behind this paper, check out Eisen’s blog, Phylogenomics.

Dr. David Hughes and colleagues published a paper about the Hidden Diversity Behind the Zombie-Ant Fungus Ophiocordyceps unilateralis: Four New Species Described from Carpenter Ants in Minas Gerais, Brazil.  Their paper received media coverage from: CNN, Wired, National Geographic, and 80 Beats. This is just for spacing. This is just for spacing.

In February, researchers described their recent findings of three ancient skull cups found with skeletal remains from Gough’s Cave in England. The paper, Earliest Directly-Dated Human Skull-Cups, received coverage from NPR, BBC, New York Times, Time, CNN and Not Exactly Rocket Science.

According to the paper, Dietary Fat Intake and the Risk of Depression: The SUN Project, those who had an increased consumption of trans-fat also had an increased risk of developing depression. The study by Almudena Sánchez-Villegas et al. received a lot of media attention in January.  Some of the coverage includes: TIME, Xinhua, Times of India and la Repubblica.