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  • January 22, 2013
  • 02:07 PM

Healthcare professionals AS pain treatment!

by Kim Kristiansen in Picture of Pain

A recent study have found indications on how healthcare professionals can be part of pain treatment them self ... Read more »

Kim Kristiansen, M.D. (2013) Healthcare professionals AS pain treatment. Picture of Pain Blog. info:/

  • January 22, 2013
  • 04:09 AM

ToxBank: the next generation toxicology

by egonw in Chem-bla-ics

Before I moved to my current position in Maastricht, I had the great pleasure to work with Prof. Roland Grafström (check his pathway bioinformatics done with his then PhD Rebecca) and Prof. Bengt Fadeel at the Karolinska Institutet. During this year I part-time worked on ToxBank and part-time on nano-QSAR, and worked on semantics, predictive toxicology, and Open Data. This blog post is about the ToxBank work.

I promised firework, and the first rockets are heading upwards: a key ToxBank paper has now been published in Molecular Informatics. Pekka Kohonen wrote up a nice overview of the ToxBank project, the current platform (based on RDF, REST, ISATab, and OpenTox (my archives)), and the test compounds that the SEURAT-1 cluster identified. Various bioinformatics approaches were used to visualize the diversity of the selected compounds. The idea is that the all EU FP7 projects in the SEURAT-1 cluster (consisting of six consortia) will test at least these compounds, creating a rich data set of toxicology-related data for these compounds.

As a temporary, quick solution I proposed the Semantic MediaWiki to create a semantic knowledge base, which was extensively and very productively continued by David from Leadscope. This way, we could easily list all compounds, by doing a search, rather than manually adding them:

Each compound has extensive information on the mode of action, physicochemical properties and more (such as here for acetaminophen):

All this information is available as semantic data. For example, check this link. Network and Gene Ontology analyses on these compounds have been performed, and presented in the paper, further confirming the diversity of the compound set. This leads to possible integration of their work with WikPathways and PathVisio, and I will do my best to get the right people talking to each other.

The ToxBank project further develops Open Source software for an online data warehouse for hosting experimental data on these compounds. A mix of approaches is used here to base their warehouse on, including OpenTox (RDF and REST(-like)-based), ISATab, and various ontologies.

In designing their software, they use a pretty unique approach for EU projects, based on formal requirement analyses protocols, resulting in a user-oriented platform. Now, there is much to say about who the user is, and in fact, there are multiple user types, called personas, and ToxBank takes that idea into account.

Therefore, in many ways, ToxBank is, in my humble but somewhat biased opinion, a project that leads the (predictive) toxicology community into a new era. Congratulations to the full ToxBank consortium! It was great being part of it!

Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R., Healy, L., Helma, C., Jeliazkova, N., Jeliazkov, V., Maggioni, S., Miller, S., Myatt, G., Rautenberg, M., Stacey, G., Willighagen, E., Wiseman, J., & Hardy, B. (2013). The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing Molecular Informatics DOI: 10.1002/minf.201200114... Read more »

Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R., Healy, L., Helma, C., Jeliazkova, N.... (2013) The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Molecular Informatics. DOI: 10.1002/minf.201200114  

  • January 19, 2013
  • 03:41 AM

Journal Impact Factors and REF2014

by Dorothy Bishop in bishopblog

In 2014, British institutions of Higher Education are to be evaluated in the Research Excellence Framework (REF), an important exercise on which their future funding depends. Academics are currently undergoing scrutiny by their institutions to determine whether their research outputs are good enough to be entered in the REF. Outputs are to be assessed in terms of "‘originality, significance and rigour’, with reference to international research quality standards." Use of journal impact factors is explicitly vetoed in the guidelines, yet there is evidence that many institutions are reluctant to abandon them. We need a clear statement from those who administer the REF about whether any use of impact factors is acceptable, and if not, what sanctions will apply to institutions that use them.... Read more »

  • January 18, 2013
  • 09:47 AM

On "Join Papester Collective 1.0: How to reply to #icanhazpdf in 3 seconds"

by Eugenio Maria Battaglia in Science to Grok

I'm totally supporting this potential system theorized some days ago by Micah Allen and his friend Hauke on Allen's Neuroconscience blog . They discuss a quick and reliable strategy to share papers behind a paywall.
The proposed system is really easy and accessible by everyone, since it uses particular twitter's #hashtags for query and response.
I strongly believe that what started after Aaron Swartz's dead with #pdftribute, and continued with #sharecredentials (unfortunately and strangely still not so shared on twitter), and now followed by #icanhazpdf / #papester will quickly lead to a massive weaken of paywall systems. Therefore, this will push people to understand and to propose alternative ways that are more ethically correct and also apt to current science needs.... Read more »

Cook, J., & Attari, S. (2012) Paying for What Was Free: Lessons from the Paywall . Cyberpsychology, Behavior, and Social Networking, 15(12), 682-687. DOI: 10.1089/cyber.2012.0251  

  • January 18, 2013
  • 09:38 AM

Currently Necessary Evil: A (vegan’s) view on the use of animals in neuroscience research

by Grace Lindsay in Neurdiness

All research methodologies have their challenges. Molecular markers are finicky. Designing human studies is fraught with red tape. And getting neural cultures to grow can seem to require as much luck as skill. But for those of us involved in animal-based research, there is an extra dimension of difficulty: the ethical one. No matter how [...]... Read more »

Editors. (2011) Animal rights and wrongs. Nature, 470(7335), 435-435. DOI: 10.1038/470435a  

  • January 17, 2013
  • 01:54 PM

How to export, delete and replace your Mendeley account and library

by Duncan Hull in O'Really?

News that Reed Elsevier is in talks to buy will have many scientists reaching for their “delete account” button. Mendeley has built an impressive user-base of scientists and other academics since they started, but the possibility of an Elsevier takeover has worried some of its users. Elsevier has a strained relationship with some groups in the scientific community [1], so it will be interesting to see how this plays out.

If you’ve built a personal library of scientific papers in Mendeley, you won’t just want to delete all the data, you’ll need to export your library first, delete your account and then import it into a different tool.

Disclaimer: I’m not advocating that you delete your account, just that if you do decide to, here’s how to do it, and some alternatives to consider.... Read more »

  • January 17, 2013
  • 08:26 AM

A great example of Citzen Science

by Eugenio Maria Battaglia in Science to Grok

Crowd-funding isn't anymore  just a domain of independent movie makers. Independent science is starting to exploit this possibility.Here is a great example of Citzen Science![1] What about doing other big omic-like projects like this, by using crowd-funding? Any ideas?uBiome - Sequence Your Microbiome "Scientists recently discovered an important new organ in the human body. Incredibly, this organ isn’t made of human cells: It’s microbes!In fact, there are so many of these microbes in your body that they outnumber human cells 10 to 1.This is your microbiome.It's another world inside your body. Thousands of species, trillions and trillions of tiny organisms. We barely know who they are, let alone what they're doing -- or importantly, how they affect our health. It's been described as the greatest scientific mystery of our day.By joining uBiome, you can explore your own microbiome and participate in the exciting scientific discovery to unlock this mystery. In order for it to work, we need lots of samples and a little bit of money.By pulling together as a group, we can do cutting-edge biomedical research at a fraction of the normal cost. It's called citizen science." For more information and pledge this project:, B. (2012). Direct-to-consumer theranostics, 21st century collective innovation and entrepreneurship Expert Review of Molecular Diagnostics, 12 (8), 803-805 DOI: 10.1586/erm.12.122... Read more »

  • January 17, 2013
  • 06:00 AM

Accuracy of Medical Information on the Internet

by Jalees Rehman in Fragments of Truth

This study highlights the opportunities and pitfalls of using the internet to communicate medical information. The internet is providing an opportunity for patients and family members to obtain additional medical information that they did not receive from their physicians, as well as to address questions that may arise and do not warrant a visit to a physician. On the other hand, the study also demonstrates that the quality of medical information on the internet varies widely. Searches for certain key phrases can unwittingly lead a user to websites that promote certain products or treatments without taking the medical evidence and professional guidelines into account.... Read more »

Chung M, Oden RP, Joyner BL, Sims A, & Moon RY. (2012) Safe infant sleep recommendations on the Internet: let's Google it. The Journal of pediatrics, 161(6), 1080-4. PMID: 22863258  

  • January 17, 2013
  • 06:00 AM

Using Viagra To Burn Fat

by Jalees Rehman in The Next Regeneration

The researchers treated mice with Viagra (sildenafil), a drug that is normally used for erectile dysfunction. They found that only seven days of Viagra treatment increased the levels of the brown fat protein UCP-1 and that the white fat began showing the presence of "beige" (not quite white and not fully brown) fat. The choice of Viagra was not quite arbitrary, because they also showed that cultured fat cells contain cGMP-dependent protein kinase I (PKGI), which is part of the signaling pathway targeted by Viagra, and that increasing the levels of PKGI converted these cells into thermogenic brown fat cells.... Read more »

Mitschke, M., Hoffmann, L., Gnad, T., Scholz, D., Kruithoff, K., Mayer, P., Haas, B., Sassmann, A., Pfeifer, A., & Kilic, A. (2013) Increased cGMP promotes healthy expansion and browning of white adipose tissue. The FASEB Journal. DOI: 10.1096/fj.12-221580  

  • January 16, 2013
  • 03:00 AM

Considerations about #pdftribute and #sharecredentials

by Eugenio Maria Battaglia in Science to Grok

In the last post I gave for free my credentials for limited-access journals for which my university pay the subscription fee.

Micah Allen from his Neuroconscience blog address this licit question:

"We need an “research-reddit” rating layer - why not solve Open Access and peer review in one go? Is this feasible? There are about 50 million papers in existence[1]. If we estimate about 500 kilobytes on average per paper, that’s 25 million MB of data, or 25 terabytes."... Read more »

  • January 14, 2013
  • 08:32 PM

More Milk drinking in a Nation, More chances of winning Nobel Prizes

by Usman Paracha in SayPeople

Researchers have found that the nations that drink a lot of milk and consume milk products have more ability to win Nobel prizes.

This research has been published online in the journal Practical Neurology.

In the last quarter of the last year, a research was published in the New England Journal of Medicine showing that the nation’s chocolate consumption has strong relation to the Nobel Prize winning ability. The research proposed that the flavonoid content of the chocolate is responsible for the brain power. That research made authors to think, whether milk has any relation to the Nobel Prize winning ability or not!

Researchers worked on the 2007 data from the Food and Agriculture Organization on per capita milk consumption in 22 countries as well as the information provided by the author of the chocolate theory, and found a significant relation between the milk consumption and Nobel Prize.

Researchers found that Sweden has the most Nobel laureates per 10 million of its population (33) and it consumes most milk per head of the population having about 340 kg per year. (Some might argue that the country hosts Nobel committee but) Than Switzerland, with 300kg of milk per year consumption came on the second position with a good number of Nobel laureates (32).

On the other hand, China comes in the countries with the lowest number of Nobel laureates and the milk consumption in this country is also in the lowest number i.e. about 25kg per year.

Researchers are of the opinion that there could be a ceiling effect as shown by no impact on Finland’s Nobel Prize increase beyond an annual per capita consumption of 350 kg of milk.

Vitamin D in milk is thought to be the brain booster.

"So to improve your chances of winning Nobel prizes you should not only eat more chocolate but perhaps drink milk too: or strive for synergy with hot chocolate," Researchers concluded.


Linthwaite, S., & Fuller, G. (2013). Milk, chocolate and Nobel prizes Practical Neurology, 13 (1), 63-63 DOI: 10.1136/practneurol-2012-000471... Read more »

Linthwaite, S., & Fuller, G. (2013) Milk, chocolate and Nobel prizes. Practical Neurology, 13(1), 63-63. DOI: 10.1136/practneurol-2012-000471  

  • January 14, 2013
  • 05:26 AM

Can MOOC’s Really Transform Education?

by Jason Carr in Wired Cosmos

Traditional colleges often struggle with limited space availability in popular (or even core curriculum) courses. Higher education costs in the U.S. have sky-rocketed in recent years. A recent USA Today article reported that costs to attend a 4-year public university rose a staggering 15% between 2008 and 2010. To make matters worse, many graduates that [...]... Read more »

  • January 11, 2013
  • 11:59 AM

A joke about teaching and learning via Jason Bangbala

by Duncan Hull in O'Really?

What is the difference between primary, secondary and higher education?... Read more »

Vardi, M. (2012) Will MOOCs destroy academia?. Communications of the ACM, 55(11), 5-5. DOI: 10.1145/2366316.2366317  

Khan, S. (2013) What college could be like. Communications of the ACM, 56(1), 41. DOI: 10.1145/2398356.2398370  

  • January 11, 2013
  • 11:08 AM

On Selling and Over-Selling Science

by TheCellularScale in The Cellular Scale

Science!!! (source)Science communication is a persistent topic of ... well communication. Who is responsible for communicating science? How can science be best communicated to the public? What can we to do stop sensationalist and misleading articles from controlling what findings are generally accepted in the public sphere?All these questions rise up in science blogs and on twitter and then fade back into the background. Then something happens and a flurry of posts about communicating science float to the surface again. I have decided to join this party, and have written a Guest Editorial at the Biological Bulletin.It's called "On Selling and Over-Selling Science" and is about trying to find that perfect balance between communicating a scientific finding accurately and accessibly.I'd love to hear new opinions on this. So feel free to follow the link and leave a comment about it here.  © TheCellularScaleI was not able to use my 'blogging name' like Neuroskeptic was, so here is the article and my identity along with it:Evans RC (2012). Guest editorial on selling and over-selling science. The Biological bulletin, 223 (3), 257-8 PMID: 23264470... Read more »

  • January 11, 2013
  • 09:11 AM

Q: Why does skin lose its elasticity as we get old?

by Stuart Farrimond in Guru: Science Blog

Asked by Sam Whiley via Facebook Before we even jump to the answer, let’s define what elasticity actually is.  It’s not really the “stretchiness” of your skin as many people tend to think it is; that’s only half the definition.  If elasticity were to be defined as only how stretchy something can be, then your [...]... Read more »

  • January 8, 2013
  • 11:37 AM

The USA Dream for IMGs: Coming to an end? Analysing the 2012 Match

by Pranab Chatterjee in Scepticemia

My attention was drawn to an article in the JAMA today (1) by one of my friends who is actively pursuing the USMLE route. And after reading this, I guess I have to admit that one now has to make haste in order to prevent waste. Now I have long been wanting to write about [...]... Read more »

Traverso G, & McMahon GT. (2012) Residency training and international medical graduates: coming to America no more. JAMA : the journal of the American Medical Association, 308(21), 2193-4. PMID: 23212494  

  • January 8, 2013
  • 09:28 AM

High-impact Journals for Genetics and Genomics

by Daniel Koboldt in Massgenomics

One of the burdens of the information age is that there’s far more content produced than could ever be read by the population. This is categorically true of blogging, but also a fact of research publication. With hundreds of academic journals (ISI indexes over 11,000 science and social science journals) and thousands of articles published [...]... Read more »

  • January 7, 2013
  • 08:00 AM

A Story Behind A Paper - Part I

by J Zevin in The Magnet is Always On

We can't go around knocking out genes to see what effects they have in people, or raising children in caves to find out at what age they irreversibly lose the ability to learn language, but cognitive neuroscience uses non-invasive imaging techniques that show us patterns of brain activityrelated to particular behaviors or states. That seemed pretty awesome, and I wanted in...... Read more »

  • January 4, 2013
  • 11:43 AM

The Science of Choosing Space Pioneers

by Jason Carr in Wired Cosmos

I often ask others if they would live in space or on another planet if given the opportunity. More often than not, the answer is in the affirmative. But what if you were given the chance and actually wanted to go, but were declined because you weren’t selected by a computer algorithm as one of [...]... Read more »

Yusof, N., & van Loon, J. (2012) Engineering a Global City: The Case of Cyberjaya. Space and Culture, 15(4), 298-316. DOI: 10.1177/1206331212453676  

Saaty, T., & Sagir, M. (2012) Global awareness, future city design and decision making. Journal of Systems Science and Systems Engineering, 21(3), 337-355. DOI: 10.1007/s11518-012-5196-z  

  • January 4, 2013
  • 02:14 AM

Sweet Science

by Emarkham in GeneticCuckoo

A look at the new fun approach and interest taken in science and how this is being marketed and aimed at young people. ... Read more »

E Markham. (2013) Sweet Science. Blogspot. info:/

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