Month: July 2012

Bird flu, swine flu, now seal flu H3N8

US scientists have identified a new strain of influenza in New England harbor seals – H3N8. They say the strain, presumably made the species leap from birds, might now be a reservoir for an emergent human flu virus.

H3N8 is an influenza type A virus (Orthomyxoviridae) endemic in birds, equines and dogs and although highly contagious was not as such considered a risk to people. A flu outbreak in people in 1889 or 1900 was blamed on this strain but evidence suggests that it was due to H2N2. If H3N8 has mutated and evolved from an avian form into one that infects harbor seals (Phoca vitulina), there is a chance that it could now infect people. Indeed, the virus already has the relevant structure to attack a protein in the human respiratory tract.

Experts have for some time recognised that emergent flu viruses need not only come from East Asia, swine flu, H1N1, being a case in point, the pandemic of 2009 emerging from South America. So, the emergence of a putative pandemic strain in the waters off New England, USA, is worrying, but perhaps not surprising.

It is worth noting that a paper in the same group of journals from 1984 reports on the emergence of an avian influenza virus (H4N5) in harbor seals in the early 1980s. There are presumably other instances so this would suggest that transfer to harbor seals from birds is not an uncommon leap.

BBC News – New flu virus found in seals concerns scientists.

Moscona et al, 2012, mBio; DOI: 10.1128/mBio.00166-12

Influenza A viruses are classified into subtypes based on the antibody response to the viral proteins hemagglutinin (HA), neuraminidase (NA). This distinction gives us the different names, e.g. H5N1, H1N1, H3N8 etc. There are 16 H and 9 N subtypes known, but only H 1, 2 and 3, and N 1 and 2 are usually found in people.

Blog mining in reduced dimensions

Despite exaggerated predictions about the death of the blog, it seems numbers continue to grow. Everyone and their dog seems to want to share their innermost thoughts, echo the news and comment on everything from the Higgs Boson to the Gaga Biebon. Efficiently pulling useful information from the millions of blogs with all their various formats and multimedia content, however, is no simple task and the old-school data mining techniques do not appear to be as effective with these disparate networks as they are with standardised databases.

Writing in the International Journal of Data Mining, Modelling and Management, Flora Tsai of the School of Electrical and Electronic Engineering at Nanyang Technological University in Singapore hopes to remedy that situation. She is developing a data visualisation approach that involves reducing the number of “dimensions”, the different aspects of the collected blogs so that title, content, tags (labels and/or categories), authors (blogger or guest), URL (permalink), and time-date stamp, outbound and inbound links, optional geotag (location) are flattened into a more usefully searchable database. She explains the approach:

Dimensionality reduction is the search for a small set of features to describe a large set of observed dimensions. By performing dimensionality reduction, hidden structure can be uncovered that aids in the understanding as well as visualisation of the data.

The reduction in dimensions does not discard information it simply projects it on to a system that can be examined more easily and so allows the data miner to find useful patterns and information. What dimensionality reduction can do is quickly remove noise words and spurious “tags”, so that large data sets, although probably not the whole blogosphere, could be analysed quickly.

Research Blogging IconTsai, F.S. (2012). Dimensionality reduction framework for blog mining and visualisation, International Journal of Data Mining, Modelling and Management, 4 (3) DOI: 10.1504/IJDMMM.2012.048108

Multitasking and listening to mood music

When you’re feeling blue, put on a sad song. Getting in the party spirit? Turn up the dance music. We are all well aware that music can fit our mood and even reinforce certain emotions. Now, researchers at Philips Research in The Netherlands have demonstrated that background music can affect our mood even while we are directly focused on another task. Their work, described in the International Journal of Human Factors and Ergonomics might have implications for those investigating the benefits of music therapy, music in the workplace, commercial environments or even in healthcare.

Music is almost ubiquitous for many people, they listen wherever and whenever and with modern portable electronic gadgets it is almost impossible to be without one’s music collection even when on the move; at least until the batteries are expended. Music is often the primary activity at any given time, listening for pleasure and relaxation. It is well known that music can strongly influence a person’s mood under such circumstances. However, what was not entirely clear from previous scientific research was whether music can influence mood so significantly if it is being played in the background, secondary to a person involved in another activity.

Marjolein van der Zwaag and Joyce Westerink specialists in human perception and interaction with technology have now observed participants in sequential experiments in which people were first asked to listen to happy or sad music while doing nothing or solving a Sudoku puzzle. They also did the Sudoku with no music as a control. Later, they were asked to listen to the other type of music under the same conditions. The team measured changes in the participants’ skin electrical conductance and tension in facial muscles during the experiments as indicators of changing mood. They also interviewed the participants to obtain a more subjective but personal view of each individual’s mood.

The team found that participants’ mood responded to the different kinds of mood music – happy or sad – in approximately the same way regardless of whether listening to the music was the person’s focus or simply background sound to their solving the puzzle. The team suggests that mood music might thus be useful in calming or energising a user even when they are involved in an independent task, at work, in school or in other situations, such as driving, for instance.

Research Blogging IconZwaag, M.D.V.D. & Westerink, J.H.D.M. (2012). Inducing moods with background music, International Journal of Human Factors and Ergonomics, 1 (2) DOI: 10.1504/IJHFE.2012.048035

It’s an ant’s life

I relocated a planter in our back garden and inadvertently exposed an ants’ nest. I needed the tub elsewhere in the garden so these creatures had to undertake frenzied remedial action in the face of a man-made disaster. In the name of science, I videoed their efforts, Needless to say, the population was not affected significantly and we still see trails of Formicidae relocating crumbs and other debris around our garden patio and into our conservatory…

I wonder what the pair of wood lice at about 43 seconds in thought of the disastrous events taking place around them, they were probably first to tweet it…or maybe not.

Oh the music? That was me messing around with a drum loop and a few guitar chops, it sounded like I’d at once ripped off both Pink Floyd and Jimi Hendrix badly, hence the title – Breathe the Wing.

Shakespeare’s Sonnets on the iPad

TouchPress has done it again giving us an aesthetically pleasing collision of art and technology – akin to the Leonardo Anatomy app I mentioned a while back. This time The Sonnets by William Shakespeare gets the modern treatment with videos and readings featuring Patrick Stewart (always a draw for the Trekkie classicist), Stephen Fry (for the Apple fanboys) and David Tennant (for the Whovians) and Kim Cattrall (who was in the TV series of Logan’s Run, of course) and others. All 154 pieces are performed to camera by the all-star cast.

The app includes scholarly notes from the Arden Shakespeare that the developers say bridge the gap between Elizabethan and modern English given that the original folio pages are presented.

Be wary of miracles too good to be true

Not for the first time I’ve suspected that lyricist and drummer with the Canadian rock band Rush, Neil Peart has been reading my blog. First time was having written about the concept of earthshine, the band’s next album featured a song on that very concept, the reflected light from the Earth illuminating the dark face of a new moon ‘cradled’ in the old. Of course, I didn’t really believe he was reading my stuff, it was a kind of bizarre, displaced hero worship surely?

Well then what to make of a song on the recently released album from the progressive power trio Clockwork Angels that discusses what I’ve come to refer to as deceived Wisdom in my forthcoming book. The song is called The Wreckers and uses the allegory of those who would draw sailors on to rocky shores by lighting fake beacons offering safe harbour. The idea is captured in Peart’s quite lyrical lines:

All I know is that sometimes you have to be wary
Of a miracle too good to be true
All I know is that sometimes the truth is contrary
Everything in life you thought you knew
All I know is that sometimes you have to be wary
‘Cause sometimes the target is you

The Darwin Lost Weekend

A man tries to convince his friend that Charles Darwin conceived his book ‘Origin of Species’ on the concept of evolution in the town of Cromer, Norfolk, England and not in the Galapagos Islands. This video was premiered at the first Science Online conference back in 2009 but has only just this last week reached the virtual hallowed halls of Youtube. Thanks to Graham Steel for the alert. I knew I’d seen it somewhere before…

Meanwhile, for fans of the North Norfolk Coast, here’s a little poem wot I wrote about the village of Stiffkey.

Ever been taken up the North Norfolk Coast?

There’s a place on the coast name of Stiffkey
Which surprisingly yet rhymes with hookie
Now in near disgrace a priest of said place,
spent his time up The Smoke after nookie

This priest, must be said, was the rector
And claimed souls he would save as a lector
A girl of SoHo, took him ever so low,
Defrocked she would be, he’d inspect her

The village was shocked but kept quiet
’bout those happenings, they’d cause a riot
in the street and the lane where the people are plain
But the papers they scooped that old the story quite righ-ut

A court case was held, “Immoral!” they yelled and the rector was morally shaken
thrown out of the church but escaping the birch
he frowned as reached Stiffkey quakin’

But those stuffky old folks on the North Norfolk coast,
will never admit to his truancy
They claim that it’s right, he did fight the good fight,
and it’s Stiff-Key not Stookie if you’ve fluency

Incidentally, the Rev Dr Ezekiel Gee (played by Henry Gee aka CromerCrox) is not the Rector of my poem.

Who do you follow back on Twitter?

There is almost no limit to the number of people you could follow on Twitter, but when someone follows you, how do you decide whether to follow back or not? I’ve updated my handy cut-out-and-keep Twitter Decision Flowchart for the scientific age. You may wish to add your own block words, so print it in pencil and use an eraser ;-)

Please retweet and share wildly, we should all be applying these principles to boost the overall Twitter signal-to-noise ratio. With apologies to Star Wars fans, a little joke at their expense I was having.