Cervical Health Awareness Month

Health risks can be frightening, but ignorance to these risks can be even more terrifying. In the past, we have discussed a range of women’s health issues, including obesity, cardiovascular disease and ovarian cancer.  To continue our commitment to health awareness, we would like to honor January as Cervical Health Awareness month.

PLOS ONE has published research tackling many aspects of cervical health, including cervical cancer and human papillomavirus.

Human papillomavirus, better known as HPV, is the most common sexually transmitted virus in the United States. According to the U.S. Center for Disease Control, at least 50% of sexually active people will contract the virus at some point in their lives.  There are more than 40 types of HPV, some of which may lead to cervical cancer. Cervical cancer is highly preventable with regular screening and vaccination to help prevent human papillomavirus.

To further expand our knowledge and understanding of cervical health, researchers from across the globe continue to explore HPV, the vaccine and its social effects.

For example, in a study published in PLOS ONE, authors in Tanzania explored the reasoning behind young girls receiving or not receiving the HPV vaccination. After interviewing both adults and students, researchers found that vaccine education and parental meetings were crucial for vaccine acceptance. Knowing women who had suffered from cervical cancer was also a factor in the decision-making.

The effectiveness of the vaccine is also a common concern. In another article, Canadian researchers developed a system to track the effectiveness of the HPV vaccination in preventing the virus.  The authors created a protocol for linking multiple data registries to allow for ongoing monitoring of the vaccines effectiveness, while also ensuring patient privacy was taken into account. This research aims to understand the long term effects of the vaccine and future vaccination tracking initiatives.

This study expands our knowledge on the vaccination results, but what about transmission of the virus? In a third PLOS ONE report, researchers explored the prevalence of HPV in the DNA of males with infected female sexual partners.  The authors found that HPV was prevalent in 86% of the male participants surveyed. These men had the same high risk viral type as the infected women, supporting the importance of awareness in men to protect themselves and their partners. This area of investigation is important in expanding our knowledge of transmission of the virus and the risk of cervical cancer development.

All these studies are aimed at improving our understanding of HPV risks and vaccination, and there are many more. As Cervical Health Awareness month draws to an end, explore more PLOS ONE research on the subject here.


Watson-Jones D, Tomlin K, Remes P, Baisley K, Ponsiano R, et al. (2012) Reasons for Receiving or Not Receiving HPV Vaccination in Primary Schoolgirls in Tanzania: A Case Control Study. PLoS ONE 7(10): e45231. doi:10.1371/journal.pone.0045231

El Emam K, Samet S, Hu J, Peyton L, Earle C, et al. (2012) A Protocol for the Secure Linking of Registries for HPV Surveillance. PLoS ONE 7(7): e39915. doi:10.1371/journal.pone.0039915

Rocha MGdL, Faria FL, Gonçalves L, Souza MdCM, Fernandes PÁ, et al. (2012) Prevalence of DNA-HPV in Male Sexual Partners of HPV-Infected Women and Concordance of Viral Types in Infected Couples. PLoS ONE 7(7): e40988. doi:10.1371/journal.pone.0040988

Image: Glass sculpture of human papillomavirus.  Photograph by Luke Jerram, “Papilloma 2011″

Latest Article Alert from BMC Public Health

The latest articles from BMC Public Health, published between 17-Jan-2013 and 24-Jan-2013

For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.
A fully formatted PDF and full text (HTML) version will be made available soon.

Study protocol
Efficacy of ‘Tailored Physical Activity’ or ‘Chronic Pain Self-Management Program’ on

It’s late January; do you know where your resolutions are?

New Year’s festivities have come and gone, and now, a few weeks into 2013, a few earnestly made resolutions may have fallen by the wayside. If you’re struggling with yours, two PLOS ONE studies could offer some hints for success.

The first report describes an investigation into three facets of goal attainment: keeping a goal active in your working memory; being aware of your current state, monitoring progress, and adjusting performance; and not behaving contrary to the goal.

The researchers used brain imaging during a simple task to explore interactions between these processes. They found that high demand for “goal maintenance” — keeping a goal active in your working memory — was correlated with lowered brain activity related to avoiding counterproductive behaviors, called “response inhibition.” In other words, if participants had to spend a lot of energy trying to remember their goals, they didn’t seem to have the brain energy to stop negative behaviors. The authors suggest that people might be able to counter this effect by increasing visual reminders of their goal, thereby decreasing the need for goal maintenance and freeing up resources for response inhibition.

Alternatively, you could try adding a financial bonus to the mix; results from a second study show that the promise of a monetary reward can immediately improve performance, even on an intermediate task not directly associated with the reward.

Participants in the study were presented with a simple aural task — identify whether two tones were high-pitched or low — and offered a financial reward for making a quick decision on the second note. The researchers found that this promised reward improved the participants’ performance for the entire task.

It isn’t clear, however, if the observed effect requires similarity between the intermediate task and the rewarded task. In this study, the two were identical, but the authors suggest that this may not need to be the case. They note that very different tasks may require similar preparation, and their results suggest that preparing for the future rewarded task is a key part of the observed effect.

So, if you’ve fallen off your resolution wagon and are looking for a way to get back on track, it’s not be too late — and you may even be able to make a little money out of the deal.


Berkman ET, Falk EB, Lieberman MD (2012) Interactive Effects of Three Core Goal Pursuit Processes on Brain Control Systems: Goal Maintenance, Performance Monitoring, and Response Inhibition. PLoS ONE 7(6): e40334. doi:10.1371/journal.pone.0040334

Zedelius CM, Veling H, Bijleveld E, Aarts H (2012) Promising High Monetary Rewards for Future Task Performance Increases Intermediate Task Performance. PLoS ONE 7(8): e42547. doi:10.1371/journal.pone.0042547

Image: alykat on Flickr

Update: Travels, Semantic Computing for Science, Reproducibility, and Open Stuff


I have been silent on this blog for too long (over 1 month) because I have been obsessively concentrating on two major software projects. This post is to keep you up to date and reassure those of like mind that I continue to be very active in trying to liberate knowledge.

Travels. I am off back to CSIRO Melbourne for a month where I’m helping Nico Adams with his Materials Summer School and Workshop. I think the semantic tools that we have all been developing are going to be valuable in creating better informatics and computational approaches to materials. I’m particularly interested in crystalline materials and computational processes.

I’m taking a week off to fly to Auckland, NZ for the tail of the Open Research meeting (Fabiana Kubke) and then Kiwi Foo. Very excited. I’m sorry I can’t spend more time with Fabiana but the Summer School overlaps.

In late Feb/March I have been invited to speak at the Columbia Research Data Symposium (http://conferences.cdrs.columbia.edu/rds/index.php/rds/rds ). This will be a very exciting meeting and I’m very grateful to Columbia. Originally I declined because I would have been sponsored by Elsevier and I have publicly stated that I am boycotting all Elsevier activities. Columbia’s sponsorship means I do not have to take an Elsevier-friendly line. I will blog this meeting before I go and outline some of the issues that the world has to decide on. In simple terms our academic digital freedom is at stake. Data presents a huge opportunity and doubtless large additional income. Academia and governments should act wisely and not outsource their decisions and ethics.

Then I’m off to Kitware , a scientific/consultancy company that makes money out of open Source, including VTK and Avogadro. I am really excited as I hope to bounce the Declaratron design off them. As always my software is not only Open but non-competitive. Anyone can join in the meritocracy.

AMI2 (http://bitbucket.org/petermr/pdf2svg ) is a project to turn PDFs into fully semantic computable, searchable, executable documents with human intervention. There are >2 million STM PDFs published each year in EuropePMC alone (more on that later). More and more are Open Access of some kind. We have developed a relatively comprehensive and high accuracy converter and tested it on some thousands of PDFs from several hundred publishers. (Don’t rush for your lawyers, publishers, I’m not going to publish your holy PDFs). The results of this are:

  • The technical standard of publishers’ PDFs is AWFUL. I don’t think I have found one that conforms to the PDF standard
  • We have learnt how to turn them into Unicode
  • The result is technically better than what the publishers produce.
  • The next stage, turning SVG into semantic form is doing well. I am particularly keen on extracting maths equations in semantic MathML form. Equations aren’t copyright are they? Perhaps they are – Pythagoras only died 2500 years ago, so maybe he is still in copyright somewhere. JSBach still is.

I’d love to hear from anyone interested in developing content mining

The Declaratron. This is a new declarative approach to reproducible semantic computing and directly addresses things like:

  • Can scientific computation be reproduced? The current answer is generally – only partially. To do so completely requires the complete semantic unification of all components – data, specification, computational engine and visualisation/publication.
  • Have we eliminated all syntactic error and as much semantic error as possible? For example are our units consistent? Are data linked to computable ontologies?
  • Can the algorithm be transported to a different environment without writing code?
  • Can we follow the progress of the computation?
  • Can we modify the algorithm, even in mid computation?
  • Can the machine document the complete course of the calculation at whatever granularity we desire?
  • Can the results be re-used in another context without human intervention?

… and a great deal more. I think the answer to all of these is yes and I’ll be showing how the Declaratron works.

Open Access/Knowledge. I shall try and blog something on Aaron Swartz. I didn’t know him, but I know people who did, and the wealth of tributes has been impressive in itself and also given me more insight into his passion for liberation. The smell of injustice is pervasive.

Content Mining. Hargreaves is going to turn its recommendations into law. No arguments. So in October 2013 I can legally mine anything I have access to and publish as CC-NC. Publishers will whinge scream lobby etc. But that will be UK law (it doesn’t require re-legislation and done through statutory instruments). There’s a lot of to-and-fro-ing. Neelie Kroes and colleagues are running something in Brussels in 2 weeks’ time – Ross is representing OKF. The publishers are running semi-closed lobbying shops. We all have to remain very vigilant as publishers have people who are paid to stop progress and we have to rely on volunteers, spare time, etc. That is why I am grateful to Wellcome and the RCUK for their very clear impetus and drive. They have shown passion where the Universities have been spineless or ultra-timid. I’ll write more on this before Columbia.

Chuff will be going to AU and NZ… and I’ll be meeting with OKF people there. Tweet or mail if you’re around Auckland/Warkworth 2013-02-07/12


Evolutionary biology steps up to the fight against cancer

EVA 6 1Cancer organizations in developed nations predict that 2 in 5 people will be diagnosed with cancer during their lifetime.  Worldwide, the number of deaths due to cancer surpasses that of HIV, tuberculosis and malaria combined (American Cancer Society, 2011).  In response to these ominous statistics, the fight against cancer has spread into branches of science that are not traditionally associated with cancer research.   The field of evolutionary biology is a key example.

How can evolutionary biology help combat cancer?  The journal Evolutionary Applications has devoted the entire January 2013 issue to showcasing the many ways that evolutionary approaches can improve the understanding, treatment and prevention of a number of different types of cancer.  The multi-authored opening paper states: “an accurate evolutionary approach should unite and explain, rather than replace” the many avenues of cancer research (Thomas et al 2013).

This is the first compilation of its kind, and was spearheaded by international scientists affiliated with the Darwinian Evolution of Cancer Consortium in France and with the Center for Evolution and Cancer at the University of California, San Francisco. The issue is guest edited by Frederic Thomas, Michael Hochberg, Athena Aktipis, Carlo Maley and Ursula Hibner.

The general theme linking articles featured in the January issue of Evolutionary Applications is that improvements to our understanding of cancer can be gained by considering cancer as a complex ecosystem. Using the analogy of a forest, the fate of a forest depends both on the individual characteristics of trees, as well as the interactions of each tree with its biotic and abiotic environment.  Similarly, tumors can be comprised of cells that are genetically and physically distinct, and the fate of tumors depends both on cell-to-cell interactions within the tumor, as well as on the interactions of the whole tumor with the highly complicated environment of the human body.  

Evolutionary questions addressed in the issue include: Why do we get cancer?  How do evolutionary principles like natural selection, mutation, and genetic drift, work in a cancer ecosystem? How can we use evolutionary theory to minimize the rate of cancers worldwide?  Many novel results are reported in the published articles, including how blood vessels affect the internal environment of a tumor (Alfarouk et al. 2013), and how certain characteristics of tumors can help explain patterns of metastasis (Daoust et al. 2013).

Papers from the Evolution and Cancer Special Issue are all freely available on the Evolutionary Applications website: www.evolutionaryapplications.org

Michelle Tseng, Managing and Founding Editor


 Alfarouk, K. O., Ibrahim, M. E., Gatenby, R. A. and Brown, J. S. (2012), Riparian ecosystems in human cancers. Evolutionary Applications. doi: 10.1111/eva.12015

American Cancer Society. Global Cancer Facts & Figures 2nd Edition. Atlanta: American Cancer Society 2011.

 Daoust, S. P., Fahrig, L., Martin, A. E. and Thomas, F. (2012), From forest and agro-ecosystems to the microecosystems of the human body: what can landscape ecology tell us about tumor growth, metastasis, and treatment options?. Evolutionary Applications. doi: 10.1111/eva.12031

 Thomas, F., Fisher, D., Fort, P., Marie, J.-P., Daoust, S., Roche, B., Grunau, C., Cosseau, C., Mitta, G., Baghdiguian, S., Rousset, F., Lassus, P., Assenat, E., Grégoire, D., Missé, D., Lorz, A., Billy, F., Vainchenker, W., Delhommeau, F., Koscielny, S., Itzykson, R., Tang, R., Fava, F., Ballesta, A., Lepoutre, T., Krasinska, L., Dulic, V., Raynaud, P., Blache, P., Quittau-Prevostel, C., Vignal, E., Trauchessec, H., Perthame, B., Clairambault, J., Volpert, V., Solary, E., Hibner, U. and Hochberg, M. E. (2012), Applying ecological and evolutionary theory to cancer: a long and winding road. Evolutionary Applications. doi: 10.1111/eva.12021

Latest Article Alert from Breast Cancer Research

The latest articles from Breast Cancer Research, published between 07-Jan-2013 and 21-Jan-2013

For research articles that have only just been published you will see a ‘provisional PDF’ corresponding to the accepted manuscript. Fully formatted PDF and full-text (HTML) versions will be made available soon.

How relevant is hormone receptor status in the context of outcome to HER2-

Set the default to open: my response to Canada’s Access to Information Act Consultation

The Office of the Information Commissioner of Canada is conducting a public consultation into modernization of the Access to Information Act. Comments are due January 31. Following is my response.

Office of the Information Commissioner of Canada
Consultation on Access to Information Act
January 21, 2013
Dear Suzanne Legault,
Re: Consultation on Access to Information Act
This is a response from an individual scholar and librarian who is active in the area of information policy and open access. Thank you very much for the opportunity to participate in this consultation. In brief, my recommendation is to set the default to open. Narrow the scope of limitations to open access to information to substantive matters of national security or personal privacy, with an empowered and sufficiently funded Office of the Information Commissioner of Canada to act as an effective monitor to ensure these limitations are respected. Expand the range of information that falls under the Act to include Cabinet confidences. Expand the entities covered under the Act to include companies that are contracted to undertake work on behalf of the federal government, and companies that receive contracts and or subsidies from the federal government.  Detailed responses to the General Questions follow.
Right of access
Question: In an environment of increasing globalization, should any person be able to obtain government held records, notwithstanding their physical presence or citizenship?
Response: yes, in an environment of increasing globalization, anyone should be able to obtain government held records, notwithstanding their physical presence or citizenship. In the spirit of open government, the default for government information should be open access to anyone, anywhere. Canadian benefit from access to information provided by other governments.
Coverage of the act
Question: Should all federal entities be subject to the Act as a matter of principle, or should some be exempt from the Act’s requirements? What criteria or principles should determine which entity is covered by the Act?
Response: the act should cover all federal entities, all entities undertaking work on behalf of the government, and all entities receiving funding of any kind from the government.  That is, when work is contracted by the federal government out to companies, the companies should also be covered by the act, exactly as if the work were being done by the government department. When a company is awarded a contract by the government, or is given a subsidy, any information relating to the contract or subsidy should be subject to Access to Information Requests and a general expectation of open access to this information.
Limitation on the right of access
Question: In what circumstances should a universal right of access be limited? Should federal institutions have the discretion to limit disclosure? If so, should they be required to demonstrate that a defined injury, harm or prejudice will probably result from disclosure? Should the public interest be considered in the decision to withhold records?
Response: Any limitations should apply to particular information, and then only for substantial reasons – information that is classified for security purposes or that cannot be released without compromising personal privacy. The default should always be open. It is essential that a watchdog such as the Office of the Information Commissioner be empowered and sufficiently funded to monitor and ensure that any limitations on access to information fall within this scope.
Cabinet confidences
Question: Should the Access to Information Act exclude records that directly inform Cabinet decisions? If the exclusion is permitted, on what should it be based? Should the Information Commissioner be able to review Cabinet confidences?
Response: Canada is part of the Open Government Partnership. It is timely to make a serious commitment to openness. Cabinet should conduct its work in the open. The criteria for keeping information confidential by Cabinet should be exactly the same for all other federal information – national security or personal privacy. This is important for the work of the government to be, and to appear to be, transparent.
Awareness and education
Question: What role can or should the Office of the Information Commissioner play in helping Canadians to become more aware of their rights under the Access to Information Act?
Response: The Office of the Information Commissioner should provide education and awareness through a variety of activities (website, information sessions both virtual and in-person), and should leverage opportunities to work with other organizations with education and awareness mandates such as schools and libraries [disclosure: I am a librarian].
Once again thanks for the opportunity to participate. I will post this response to my blog.
Heather Morrison, PhD
hgmorris at sfu dot ca
The Imaginary Journal of Poetic Economics