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When the first reports of swine flu cases in Mexico emerged in early April, it wasn’t just health authorities and governments that leapt into action. Researchers – including many at Oxford – also rushed to find out more about the new flu virus and its spread to help guide public health responses in the UK and worldwide.

The vast majority of people with swine flu continue to experience mild symptoms and there is little evidence so far that the virus is changing. But as we wait for an expected second wave in the autumn or winter, researchers are investigating questions that will guide the next phase of the response.

In August, the National Institute for Health Research (NIHR) announced funding for a number of projects around the UK to provide evidence to guide the government’s response in the coming months. These projects cover everything from how to tell which patients with suspected swine flu should be admitted to hospital to the impact of school closures in preventing spread of the virus.

Oxford is heavily involved in two of these studies: a comparison of two swine flu vaccines in children and an investigation of the effect of flu in pregnancy.

Which vaccine for children?
Professor Andrew Pollard of the Oxford Vaccine Group is chief investigator of a study running this month that is comparing head-to-head the use of two vaccines in children. The two vaccines are the ones the Department of Health has purchased to control the expected second wave this autumn, and from this week they are already beginning to be used among high-risk groups and frontline healthcare workers. Use of the vaccines could be expanded more widely later, but information about their most effective use in children is limited.

‘We will look at the immune response each vaccine generates in children, and also carefully study any side-effects that might occur such as soreness at the injection site and fever,’ says Professor Pollard. ‘Results should be available later in the autumn to inform government and guide immunisation strategy, but also to help decisions by healthcare workers and parents. The study will tell us the balance of protection against swine flu and side-effects.’

Around 1,000 children aged between six months and 12 years at five centres around the country (including Oxford’s Children’s Hospital) are being given two doses of a swine flu vaccine three weeks apart in the study being undertaken in collaboration with the Health Protection Agency. Blood tests are also taken using a local anaesthetic cream before and after the two immunisations to check each child’s response to the vaccines.

‘Children have poorer responses to influenza vaccines but are also one of the age groups likely to be most vulnerable to swine flu infection, so it is vital that we obtain information on their response to these vaccines. This study will help in decisions about which vaccine will be best for protecting children,’ Professor Pollard explains.

Advice for pregnant women
Pregnant women are known to be a group at higher risk from all types of flu including normal seasonal flu. To make sure the best information is available about managing swine flu during pregnancy, Dr Marian Knight at the National Perinatal Epidemiology Unit [NPEU] will be logging all admissions of women with swine flu at maternity units across the UK. This will go hand-in-hand with work led by Professor Simon Thomas at Newcastle University that will review how cases are handled by GPs and midwives in the community.

‘We’ll be looking at what treatments are used and the timing of those treatments to see what’s helpful. We’ll also see if any characteristics – the mother’s age, whether they’ve had babies before, when they got ill – are associated with any risk of complications for the mother or infant,’ explains Dr Knight. ‘It will help doctors and midwives give the best care during a pandemic.’

Data are already being recorded and the Oxford team are reporting the latest results monthly from the middle of this month. The researchers are collaborating with the Royal Colleges of Obstetricians, Midwives and General Practitioners, the Department of Health, and the Health Protection Agency, so that the best use of the data is assured.

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Swine flu origins
It’s easy to forget how little was known about swine flu in the very beginning with the first reported cases in Mexico and the US, not least its severity and where it came from. Right back at the start of the outbreak, when health agencies were racing to understand the new flu strain and how virulent it might be, Oliver Pybus of the Department of Zoology was part of international research groups that sought to characterise the new virus genetically.

The early papers they published in Science and Nature in June showed that the virus had come from pigs and had probably been circulating in people since the beginning of 2009 – three months before it was first identified. ‘This was reassuring at the time, as it suggested that the new H1N1 swine flu wasn’t very virulent in humans because it would have been picked up sooner,’ says Dr Pybus.

One other finding from that work might become more important in the future, Dr Pybus notes. Before it jumped into humans, the research suggest the new swine flu virus may have been hiding in pigs for around 10 years without being noticed by scientists.

‘Although we have good surveillance systems for monitoring flu strains in circulation in birds and humans, there may be a surveillance gap in pigs,’ says Dr Pybus. He is now part of an international consortium that aims to plug this gap.

Global response
Professor Jeremy Farrar also got involved at the start. He leads the University’s Clinical Research Unit [CRU] in Vietnam, which has been working on flu since 2004 when bird flu reached the country. The unit also coordinates the South-East Asia Infectious Disease Clinical Research Network (SEAICRN), supported by the US National Institutes of Health, the World Health Organisation, and the Wellcome Trust. Its largest focus is on flu.

With an interdisciplinary team of clinicians, pharmacologists, virologists, immunologists and ethicists, the unit aims to help lead thinking on how the world responds to pandemic threats, along with collaborators in the US and Europe. This also includes how the research world can put systems in place to be able to respond swiftly and learn lessons from new epidemics of infectious disease.

Professor Farrar has been involved in guiding the responses to swine flu in Mexico and Argentina, both countries that have seen a large number of cases. For example, he visited Mexico in May at the peak of the outbreak there, to share ideas and experiences from his involvement in H5N1 bird flu. Hospitals there were particularly keen to understand how they could share information better and work together as a group. Their initial response to swine flu had been slowed when no one hospital saw a noticeable increase in number of flu cases above the normal level. Teams in Mexico have now adapted research protocols from the CRU in Vietnam and translated them into Spanish.

He has also been involved in discussions in the UK to try and link the blood transfusion service and intensive care (ITU) units. The aim is to conduct a trial in the UK of plasma therapy for optimising the use of ITU beds in the event of a large number of severe cases this winter, making sure as many people as possible won’t require intensive care beds.

But there is still a lack of clinical research about some aspects of influenza, according to Professor Farrar. ‘For example, pregnant women and obese people seem to be more at risk, yet we don’t know why or whether such people need different doses of antiviral drugs and whether their bodies handle the drug differently. As part of the SEAICRN, we are conducting a large trial to determine appropriate does of oseltamivir (Tamiflu) in cases of severe influenza, whether that’s H5N1 bird flu, seasonal flu, or H1N1 swine flu.

‘We are also concerned about the potential for the virus to become resistant to the available drugs and there are individual reports now from many countries. Such a development could have major implications for treatment of more severe cases in a second wave.’

Use of antivirals
Drs Matthew Thompson and Carl Heneghan in the Department of Public Health have also been interested in the use of antivirals for flu. When swine flu emerged, they were working on a review of the available evidence on the effectiveness of antivirals in children for seasonal flu. Their paper, published in the BMJ in August, received a great deal of interest.

They showed that the benefits of taking Tamiflu or Relenza in terms of shortening the duration of flu symptoms and reducing spread of the virus were quite small. They suggested that the UK Government’s policy of making Tamiflu available to all who reported swine flu symptoms, regardless of their severity, was neither ‘a necessary nor appropriate strategy’.

Although the Government have stood by their ‘safety-first’ strategy, Matthew Thompson believes that the emphasis of the World Health Organisation and US Centre for Disease Control’s advice subsequently shifted to emphasise that antiviral use is not necessary in those with mild flu-like symptoms.

‘The Government’s vaccination programme for swine flu is now starting, added onto the normal seasonal flu programme’ says Dr Thompson, who is also a GP. ‘And there is likely to be a benefit for some patients, the same patients who get the flu jab every year. But Tamiflu will continue to be recommended on the flu helpline. With winter coming on, it will also become increasingly difficult to distinguish typical coughs and colds from the similar symptoms of swine flu, possibly leading to further inappropriate use of antivirals.’

Dr Thompson is now shifting his attention slightly. The research team to which he belongs is hoping to secure funding to carry out a trial of antibiotic use in children with flu. This would help show whether it is bacterial infections on top of flu that tend to cause the most severe complications, and whether antibiotics might have a beneficial effect.

It's clear from all of these examples that Oxford’s research on swine flu will continue to guide the public health measures taken and the care provided for us all.

How do we know who we are?

In tonight's Horizon Oxford mathematician Marcus du Sautoy explores this age-old question and comes up with some surprising answers thanks to the latest scientific discoveries about consciousness. 

Marcus told me: 'It's great that Horizon is prepared to tackle some of the biggest problems of science. Understanding how the brain gives us a sense of "I" has been one of the greatest challenges for scientists and philosophers for centuries.'

'It was a real privilege to make this programme with Horizon and to journey round the world to see the cutting edge research that is being done to unlock the mysteries of what happens in our heads. On the way I must have had my brain scanned, tricked, drugged, prodded and stimulated in every fashion imaginable. Hopefully the programme will tickle viewers' brains too.'

The programme takes in many of the different ways scientists have found to investigate our sense of ourselves, from the mirror test, devised by Gordon Gallup, that shows when babies can recognise themselves, to the latest research examining that building block of the brain: the neuron.

You can read more about tonight's show and what Marcus found out in this BBC Online article or on Marcus's blog.

What's clear about this fascinating topic is that consciousness touches on so many other areas science is only now beginning to tackle in earnest: such as why we sleep, how we make decisions, and how our minds deal with our sense of our own mortality.

Just writing about it makes me want to go back and read the works of Oliver Sacks and Antonio Damasio all over again...

'Horizon: The Secret You' airs tonight on BBC Two at 9pm. UPDATE: Watch it now on BBC iPlayer

Marcus du Sautoy is Professor of Mathematics and Simonyi Professor for the Public Understanding of Science at Oxford University.

Finding the meaning behind the words we use is something humans are so good at that it often seems simple.

But for computers, understanding the emotions embedded in text is a very difficult task.

I spoke to Stephen Pulman of Oxford University's Computing Laboratory about his research which is helping computers to see what we mean:

OxSciBlog: Why do computers find it hard to understand the meaning behind words?
Stephen Pulman: There are several reasons. Words can be ambiguous: for example, 'cap' can mean 'beat', as in 'I can cap that', or 'limit', as in 'the government will cap student numbers'. If I hear 'the Council is to cap parking charges' I know - or at least hope - that 'cap' means 'limit' in this context. Computers have to be told this kind of thing explicitly, because they don't know anything about the world. Linguistically, the sentence could also mean that the Council were trying to beat some other Council's charges.

Another reason is that frequently we make inferences from words. If I want to know when the new Vice-Chancellor started work in Oxford, and I find a press release saying 'Professor Andrew Hamilton will be ceremonially installed as Oxford's 271st Vice-Chancellor today' then - at least, when I know which date 'today' referred to: another potentially difficult problem -  I know when the new Vice-Chancellor (officially) started work.

OSB: How does your approach help them assess the emotional meaning of text?
SP: We have a very large list of words annotated for the emotional meaning they carry, and we also take account of the grammatical context in which these words occur, so that the effects of negation and other constructs that change meaning can be taken account of. A word like 'progress' is generally perceived as positive, but not when it is in a context like 'fail to progress', or 'little progress'.

OSB: What are the advantages of your approach over existing systems?
SP: By taking account of grammatical context, we can determine emotional attitudes towards the entities and relations mentioned in a text, rather than just characterising the text overall as positive or negative. For example, a movie review might be enthusiastic about the production, but critical of the plot, or praise one actor and criticise another.

OSB: How might systems using your approach be useful to firms and government agencies?
SP: Many large companies are concerned about their reputation, and the reception that their products receive in the marketplace. By analysing
news reports, blogs, or postings on social media like Facebook or Twitter, companies can get almost instant feedback about this. Government agencies can follow the attitudes of dissident or terrorist groups by using systems like ours to track mentions of people or places in intercepted emails and texts or on web sites, particularly when combining our technology with automated translation.

More about this work in an article in The Economist.

Stephen Pulman is Professor of Computational Linguistics at Oxford's Computing Laboratory.

A new study published last week in the New England Journal of Medicine has shown that a simple cooling treatment for babies that suffer a lack of oxygen at birth could avoid brain damage in over 100 babies a year.

The TOBY (Total Body Hypothermia for Neonatal Encephalopathy) trial was led jointly by Oxford University and Imperial College London and was funded by the Medical Research Council.

I talked to TOBY Study Co-ordinator, Brenda Strohm RGN of the National Perinatal Epidemiology Unit [NPEU] at Oxford University.

OxSciBlog: What is birth asphyxia and how can it harm babies?
Brenda Strohm: Birth asphyxia occurs when a baby experiences lack of oxygen during labour and delivery, which can result in damage to the brain and other organs. This can occur if the umbilical cord is tight around the baby or the placenta separates from the womb too early, for example. Asphyxia can occur in both preterm and full term births; the TOBY Study was concerned only with full term babies. It is estimated that about 2 in 1000 full term births are affected, which is about 1400 cases a year in the UK.

OSB: What are the problems in detecting or treating birth asphyxia?
BS: In some cases there is warning that the baby is at risk, with signs of distress in the baby during labour or if there is a haemorrhage for example. But there may be no warning at all; only when the baby is born needing resuscitation does the condition become apparent.

OSB: What did the TOBY trial set out to investigate?
BS: The aim of TOBY was to find out whether whole body cooling (or hypothermia) as a treatment for birth asphyxia improves the outcomes for these babies and is a safe treatment.

The treatment is simple to use: the baby is nursed on a mattress which is cooled by circulating fluid within it. Typically the mattress temperature is set at around 28°C to maintain the baby’s temperature at 33–34°C, instead of the normal 37°C. The cooling lasts for 72 hours and then the baby is slowly re-warmed.

Brain injury from lack of oxygen occurs in two phases: immediately, when the brain is starved of oxygen and then later when the blood supply is restored. There is a chemical cascade when the machinery of the cells breaks down when it is possible to intervene to prevent long-term damage. It is during this ‘therapeutic window’ that cooling treatment is used as the intervention.

OSB: What were the findings of the study?
BS: 325 babies were recruited immediately after birth and were randomly allocated cooling treatment with intensive care or standard intensive care. While there was no difference in the deaths that occurred in the two groups, there was a significant improvement in the rate of survival without neurological abnormality in the cooled group. The cooled group showed improved outcomes in a range of other developmental measures at 18 months of age.

The study is important because birth asphyxia is associated with high morbidity in survivors that is a major burden for the child and family and on health and educational resources as the child matures. Up to now there has not been an effective treatment to offer these babies. Any treatment or intervention that can reduce this burden not only improves quality of life but reduces the costs of providing ongoing care.

OSB: What should pregnant women take from this study?
BS: Fortunately the vast majority of pregnant women will never need to know about cooling for their baby. For those whose baby is affected by birth asphyxia, there is now the knowledge that there is a simple treatment that could make a real difference to their baby’s future, although not every baby is bound to benefit from it.

OSB: What would you like to see happen next based on these findings?
BS: Cooling is not currently considered to be a standard treatment, but clinicians are increasingly using it. In the TOBY Study there were 34 UK neonatal units equipped to offer cooling, now there are nearly 50 with others obtaining the equipment and undergoing preparatory training. Many babies are transferred to units that can provide cooling treatment.

The National Institute for Health and Clinical Excellence (NICE) will be reviewing cooling as a treatment for birth asphyxia in full term babies now that TOBY has published its results. If NICE do recommend cooling, then it will become a standard treatment in the UK.

What are you doing this Friday lunchtime?

If you are NASA's LCROSS spacecraft then you will be crashing into the surface of the Moon.

As Chris Lintott of Oxford's Department of Physics tells The Guardian's Science Weekly podcast this is no accident but exactly what it's been designed to do.

The purpose behind LCROSS's suicide mission is to find out more about water ice deposits hidden in the eternally dark depths of craters on the lunar surface. Finding such deposits is important as water would be a source of the hydrogen and oxygen needed to make rocket fuel as well as a boon for thirsty astronauts.

At 12:30 BST the spacecraft's rocket stage, Centaur, will smash into the lunar crater Cabeus. The LCROSS satellite will be following a few minutes behind so that it can fly through the plume of debris caused by the initial impact, analysing the materials ejected from the crater.

Chris tells us that, if you can get a clear view of the Moon, you should be able to see the glitter as the plume catches the sunlight. Hopefully those monitoring LCROSS's instruments will be able to see more, discovering much about the ancient history of the Moon and our solar system.

In the podcast Chris also gives an update on the Galaxy Zoo peas, discusses dark matter, and shares the excitement generated by the recent discovery of an extrasolar planet that orbits its star backwards.

Could this be evidence for a planet 'kidnapped' from a rival star? Or under the influence of some distant super-Jupiter?

At the moment we don't know, but as Chris comments these discoveries are making us realise just how weird other systems are: 'there's a whole zoo of different solar systems out there!' he tells The Guardian's Nell Boase.