Researchers from the Universidad Politécnica de Madrid’s Biomedical Informatics Group based at the Facultad de Informática have created a tool called PubDNA Finder. This tool is the first search engine specialized in linking biomedical articles to nucleic acid sequences.

PubDNA Finder is an on line repository created to link documents archived at PubMed Central with the nucleic acid sequences that they contain. PubMed Central is a free digital archive maintained by the United States National Institutes of Health. Developed and administered by the National Center for Biotechnology Information (NCBI), it contains the principal documentation related to biomedicine and the life sciences published in scientific journals all over the world.

PubDNA Finder extends the capabilities of the search engine provided by PubMed Central, enabling biomedical researchers to run advanced searches on nucleic acid sequences. One of its features is to search documents that cite one or more specific nucleic acid sequences and retrieve the genetic sequences appearing in different articles.

These additional consultation facilities are provided by a search index created by archiving all 176,672 documents available at PubMed Central and the nucleic acids that they contain.

The researchers used an original method to automatically extract the genetic sequences returned by each search: an innovative system combining combines natural language processing, text mining and knowledge engineering runs unsupervised searches to retrieve genetic sequences.

The database is automatically updated every month by means of a FTP connection to the PubMed Central site to retrieve the manuscripts and new indexes. Users can query the database over the Web.

The research team that has developed this tool is led by the Facultad de Informática faculty member Miguel García-Remesal. García-Remesal is also a member of the Biomedical Informatics Group led by Prof. Víctor Maojo.

http://www.fi.upm.es/?id=tablon&acciongt=consulta1&idet=663

Andrew Oswald

Emotional prosperity in Europe is falling, and this troubling fact needs to be faced by the European governments. That is the conclusion from a new research report from the University of Warwick which documents cross-country evidence on psychological health and mental well-being. The study, by Andrew Oswald, professor of behavioural science at Warwick Business School, draws together the latest statistical evidence from a range of social-science, science and medical journals. The study is to be published in the December issue of the British Journal of Industrial Relations.

It is wrong, Oswald argues, for policy-makers to continue to focus on traditional measures of growing material prosperity, because continued economic growth is pointless if people are becoming more distressed and feeling ever more pressurized.

“Fast cars and fast showers are everywhere in western society”, he says, “but the data show us plainly that all is not well psychologically”.

He describes research demonstrating that Scottish 15 year olds now suffer more anxiety and depression than in the 1990s, and that those young people in turn suffered more than 15 year olds a decade before them back in the 1980s. He shows, for randomly selected sample of adults, that in Britain, the Netherlands and Belgium, which are the countries in the world with the most reliable longitudinal information on mental health, there is evidence over recent decades of steadily worsening psychological distress in the population and a decline in what he terms ‘emotional prosperity’. He points to new evidence that in the UK approximately 15% of people are known to be suffering from at least one mental disorder.

The demands of ever-increasing intensification of work are, the study concludes, one likely explanation. Oswald argues that in political debate the criterion of emotional prosperity should replace the increasingly outdated idea of aiming for further material prosperity.

The paper “Emotional Prosperity and the Stiglitz Commission” can be downloaded at: http://bit.ly/bej2dE

Professor Stephen Jarvis, Royal Society Industry Fellow at the University of Warwick

New research from the University of Warwick, to be presented at the World’s largest supercomputing conference next week, pits China’s new No. 1 supercomputer against alternative US designs. The work provides crucial new analysis that will benefit the battle plans of both sides, in an escalating war between two competing technologies.

Professor Stephen Jarvis, Royal Society Industry Fellow at the University of Warwick’s Department of Computer Science, will tell some of the 15,000 delegates in New Orleans next week, how general-purpose GPU (GPGPU) designs used in China’s 2.5 Petaflops Tianhe-1A fare against alternative supercomputing designs employed in the US; these use relatively simpler processing cores brought together in parallel by highly-effective and scalable interconnects, as seen in the IBM BlueGene architectures.

Professor Jarvis says that:

“The ‘Should I buy GPGPUs or BlueGene’ debate ticks all the boxes for a good fight. No one is quite sure of the design that is going to get us to Exascale computing, the next milestone in 21^st-century computing, one quintillion floating-point operations per second (10^18). It’s not simply an architectural decision either – you could run a small town on the power required to run one of these supercomputers and even if you plump for a design and power the thing up, programming it is currently impossible.”

Professor Jarvis’ research uses mathematical models, benchmarking and simulation to determine the likely performance of these future computing designs at scale:

“At Supercomputing in New Orleans we directly compare GPGPU designs with that of the BlueGene. If you are investing billions of Dollars or Yuan in supercomputing programmes, then it is worth standing back and calculating what designs might realistically get you to Exascale, and once you have that design, mitigating for the known risks – power, resilience and programmability.”

Professor Jarvis’ paper uses mathematical modeling to highlight some of the biggest challenges in the supercomputing war. The first of these is a massive programming/engineering gap, where even the best computer programmers are struggling to use even a small fraction of the computing power that the latest supercomputing designs have and, which will continue to be a problem without significant innovation. Professor Jarvis says:

“if your application fits, then GPGPU solutions will outgun BlueGene designs on peak performance” – but he also illustrates potential pitfalls in this approach – “the Tianhe-1A has a theoretical peak performance of 4.7 Petaflops, yet our best programming code-based measures can only deliver 2.5 Petaflops of that peak, that’s a lot of unused computer that you are powering. Contrast this with the Dawn BlueGene/P at Lawrence Livermore National Laboratory in the US, it’s a small machine at 0.5 Petaflops peak [performance], but it delivers 0.415 Petaflops of that peak. In many ways this is not surprising, as our current programming models are designed around CPUs.”

But the story doesn’t end there. “The BlueGene design is not without its own problems. In our paper we show that BlueGenes can require many more processing elements than a GPU-based system to do the same work. Many of our scientific algorithms – the recipes for doing the calculations – just do not scale to this degree, so unless we invest in this area we are just going to end up with fantastic machines that we can not use.”

Another key problem identified by the University of Warwick research is the fact that in the rush to use excitingly powerful GPGPUs, researchers have not yet put sufficient energy into devising the best technologies to actually link them together in parallel at massive scales.

Professor Jarvis’ modeling found that small GPU-based systems solved problems between 3 and 7 times faster than traditional CPU-based designs. However he also found that as you increased the number of processing elements linked together, the performance of the GPU-based systems improved at a much slower rate than the BlueGene-style machines.

Professor Jarvis concludes that:

“Given the crossroads at which supercomputing stands, and the national pride at stake in achieving Exascale, this design battle will continue to be hotly contested. It will also need the best modelling techniques that the community can provide to discern good design from bad.”

Astronomers at the University of Warwick and the University of Sheffield have helped discover an unusual star system which looks like, and may even once have behaved like, a game of snooker.

The University of Warwick and Sheffield astronomers played a key role in an international team that used two decades of observations from many telescopes around the world. The UK astronomers helped discover this “snooker like” star system through observations and analysis of data from an astronomical camera known as ULTRACAM designed by the British researchers on the team.

Snooker Star System

They looked at a binary star system which is 1670 light years away from Earth. NN Serpentis is actually a binary star system consisting of two stars, a red dwarf and a white dwarf, which orbit each other in an incredibly close, tight orbit. By lucky chance Earth sits in the same plane as this binary star system, so we can see the larger red dwarf  eclipse the white dwarf every 3 hours and 7 minutes.

It was already thought that there may be at least one planet orbiting these two stars. However the University of Warwick and Sheffield astronomers were able to use these incredibly frequent eclipses to spot a pattern of small but significant irregularities in the orbit of stars and were able to help demonstrate that the pattern must be due to the presence and gravitational influence of two massive gas giant planets. The more massive gas giant is about 6 times the mass of Jupiter and orbits the binary star every 15.5 years, the other orbits every 7.75 years and is about 1.6 times the mass of Jupiter.

Given the overall shape of the system, and how this star system came to exist, it was hard for the British members of the research team not to think of the game of snooker.

One of the UK researchers on the project, Professor Tom Marsh from the University of Warwick’s Department of Physics, said:

“The two gas giants have different masses but they may actually be roughly the same size as each other, and in fact will also be roughly the same size as the red dwarf star they orbit. If they follow the patterns we see in our own star system of gas giants with a dominant yellow or blue colours, then it’s hard to escape the image of this system as being like a giant snooker frame with a red ball, two coloured balls, and  dwarf white cue ball.”

This star system will also have seen dramatic changes, in what is relatively recent times in astronomical terms: What is now the White Dwarf “cue ball” of the system may have suffered, and caused, violent changes to its own orbit and the orbit of all the planets and stars in the system.

Professor Vik Dhillon from the University of Sheffield, said:

“If these planets were born along with their parent stars they would have had to survive a dramatic event a million years ago: when the original primary star bloated itself into a red giant, causing the secondary star to plunge down into the present very tight orbit, thereby casting off most of the original mass of the primary. Planetary orbits would have seen vast disturbances. Alternatively, the planets may have formed very recently from the cast off material. Either way, in relatively recent times in astronomical terms this system will have seen a vast shock to the orbits of the stars and planets, all initiated by what is now the white dwarf at the heart of the system.”

The discovery was made possible by an international consortium of astronomers, from the UK (University of Warwick and the University of Sheffield), Germany (Georg-August-Universitat in Gottingen, Eberhard-Karls-Universitat in Tubingen), Chile (Universidad de Valparaiso), and the United States (University of Texas at Austin).

ULTRACAM is a high-speed, 3-channel CCD camera for astrophysical research ULTRACAM was funded by PPARC and is a collaboration between ), Professor Tom Marsh (University of Warwick) Professor Vik Dhillon (Sheffield) and the Astronomy Technology Centre (Edinburgh).

The full research paper is published in the journal “Astronomy and Astrophysics” and is entitled “Two planets orbiting the recently formed post-common envelope binary NN Serpentis” by  K. Beuermann, F. V. Hessman, S. Dreizler, T. R. Marsh, S. G. Parsons, D. E. Winget, G. F. Miller, M. R. Schreiber, W. Kley, V. S. Dhillon, S. P. Littlefair, C. M. Copperwheat and J. J. Hermes
Astronomy and Astrophysics  A&A 521 L60 (2010) DOI: 10.1051/0004-6361/201015472

The research paper can be found online:

http://www.aanda.org/index.php?option=com_article&access=standard&Itemid=129&url=/articles/aa/abs/2010/13/aa15472-10/aa15472-10.html

or

http://arxiv.org/abs/1010.3608

Observation of sample pivoting on `hook`

The single layer material Graphene was the subject of a Nobel prize this year but research led by a team of researchers at the University of Warwick has found molecular hooks on the surface of its close chemical cousin, Graphene Oxide, that will potentially provide massive benefits to researchers using transmission electron microscopes. They could even be used in building molecular scale mechanisms.

The research team, which includes Drs. Jeremy Sloan, Neil Wilson and PhD student Priyanka Pandey from the Department of Physics and Dr. Jon Rourke from the Department of Chemistry together with the groups of Drs. Kazu Suenaga and Zheng Liu from AIST in Japan and Drs. Ian Shannon and Laura Perkins in Birmingham were looking at the possibility of using Graphene as a base to mount single molecules for imaging by transmission electron microscopy.  As Graphene forms a sheet just one atom thick that is transparent to electrons it would enable high precision, high contrast imaging of the molecules being studied as well as the study of any interactions they have with the supporting graphene.

While this idea is great in theory, Graphene is actually very difficult to create and manipulate in practice. The researchers therefore turned to Graphene’s easier to handle cousin, Graphene Oxide.  This choice turned out to be a spectacularly better material as they found extremely useful properties, in the form of ready-made molecular hooks that could make Graphene Oxide the support material of choice for future transmission electron microscopy of any molecule with oxygen on its surface.

Sample binding to one of the “hooks” on he graphene oxideGraphene Oxide’s name obscures the fact that it is actually a combination of carbon, oxygen and hydrogen. For the most part it still resembles the one atom thin sheet of pure Graphene, but it also has “functional groups” consisting of hydrogen paired with oxygen.  These functional groups can bind strongly to molecules with external oxygens making them ideal tethers for researchers wishing to study them by transmission electron microscopy.

This feature alone will probably be enough to persuade many researchers to turn to Graphene Oxide as a support for the analysis of a range of molecules by transmission electron microscopy, but the researchers found yet another intriguing property of these handy hooks – the molecules attached to them move and pivot around them.

Dr Jeremy Sloan said:

“Under the right conditions the functional groups not only provide molecular tethers that hold molecules in an exact spot they also allow the molecule to be spun in that position. This opens up a range of new opportunities for the analysis of such molecules but could also be a useful mechanism  for anyone seeking to create molecular sized “machinery”.”