Features

If particles of dark matter are accumulating inside the Sun then we could use neutrinos to detect them.

A short article in this week’s Science, by Joseph Silk from Oxford University’s Department of Physics and Ilidio Lopes of the Instituto Superior Técnico, Portugal, suggests how this might be done.

They propose that the presence of dark matter in the Sun’s interior would cause a small but potentially significant drop in its central temperature. They calculate that in some scenarios an isothermal core – a region of constant temperature – should form, and this core could be picked up by neutrino detectors such as Canada’s Sudbury Neutrino Observatory [SNO].

“The existence of a dark matter isothermal core in the Sun would produce a unique signature written in the energies of solar neutrinos,” Joseph tells me.

“We calculate that the existence of dark matter in the Sun’s core could lead to a 4 per cent decrease in its central temperature and a 3 per cent increase in the central density of the Sun.”

Dark matter inside the Sun would decrease its central temperature by providing an additional way for redistributing the heat inside the solar core. The models developed by Joseph and Ilidio Lopes show that it should be possible to distinguish changes in the core produced by dark matter from those produced by other effects.

Professor Joseph Silk is based at Oxford University’s Department of Physics.

A study published in the journal PLoS One has found that taking daily high-dose tablets of certain B vitamins reduced the rate of brain shrinkage in people aged over 70 with mild memory problems.

All our brains shrink, especially with age. But the rate of shrinkage is seen to increase in those with mild cognitive impairment, and shrink faster again in Alzheimer’s, suggesting this is part of the disease process. So the observation that brain shrinkage rate can be reduced could be significant, but more work needs to be done to show that.

This finding is of interest because mild cognitive impairment is common – an estimated 1 in 6 people over the age of 70 have MCI – and it’s thought that up to half (so not everyone) go on to develop dementia within 5 years.

The result has been a large amount of media coverage, for example on BBC Online, The Times (subscription required), Daily Mail, and Daily Telegraph.

Despite some subeditors struggling to resist headlines suggesting beating Alzheimer’s or fighting dementia, some points should be stressed (which are actually being widely reported):

1)  It’s one reasonably small trial, although it does show a clear and very interesting difference in the rate of brain shrinkage over a two year period in those who took daily tablets of the combination of three B vitamins.

2)  A larger clinical trial, or certainly longer follow up of these people, is needed to see whether these particular B vitamins actually go on to slow any decline in cognitive ability and progression to dementia and Alzheimer’s before anyone can be confident they will have an effect.

3)  This was a study in people with mild memory problems who are not ill and are able to carry on their normal daily lives, not Alzheimer’s itself.

4)  The tablets included certain B vitamins – B6, B12 and folate – at a high dose; many times what you get in a well balanced diet. At these doses, they must be treated as drugs not just any dietary supplement, and should not be taken without medical advice as there could be side effects. Folate, or folic acid, at high doses and over long periods in some studies has been linked with cancer, for example, though the risk is low and shouldn’t worry anyone being advised to take it, such as pregnant women.

5)The researchers do not suggest people rush out and buy these B vitamins over the counter immediately on the basis of this one study, but call for that larger trial to be done.

The researchers held a press briefing in London communicating their excitement at these results but stressing all these points. Oxford University's David Smith, who led the study, talked about ‘a glimmer of hope’ with these ‘immensely promising results’ after recent failures of high-profile trials of Alzheimer’s drugs, and Helga Refsum said: ‘As a scientist, I would never be happy with the results of just one trial’.

And again, as David Smith says in our news story: ‘These are immensely promising results but we do need to do more trials to conclude whether these particular B vitamins can slow or prevent development of Alzheimer’s.'

Here’s what some other researchers elsewhere have said about the study that echo the interest in the work but offer some appropriate caution about how much we can take from this trial.

Paul Matthews, Professor of Clinical Neurology, Imperial College, London said: ‘This well-conducted study adds substantial new data to previous information suggesting that dietary B vitamins could have beneficial effects on neurodegeneration with aging.

‘Smith and his colleagues studied a mixed group of patients with mild cognitive impairment (MCI) and showed that 2 years of treatment with folic acid and vitamins B12 and B6 slowed rates of brain atrophy. Trends identified in their report suggest that the treatment could slow deterioration of cognition, but this was not demonstrated directly in this small study

‘It is important to appreciate that only some of the patients studied would be expected to develop Alzheimer’s disease; the results therefore should not be interpreted as providing evidence for a new treatment for this most common form of late life dementia.

‘The association between better treatment effects and blood levels of homocysteine - which can be elevated with a deficiency of B vitamins and an increased risk of stroke - raises the question of whether any benefits are related to effects on blood vessels supplying the brain.

‘Although the vitamins used are generally safe and inexpensive, the study should not drive an immediate change in clinical practice. Instead, it sets out important questions for further study and gives new confidence that effective treatments modifying the course of some dementias may be in sight.’ 

Dr Nicholas Timpson, MRC CAiTE Centre (Centre for Causal Analyses in Translational Epidemiology), University of Bristol said: ‘The trial based investigation of a series of homocysteine-lowering B vitamins (including folate and B12) and brain atrophy is of great interest.

'Authors note a reduction in the rate of atrophy in participants randomly allocated to treatment which is itself of great interest, however there are aspects of the work which need to be approached cautiously. These include comparison of observed effects to natural atrophy by age and the actual relationship between cognitive ability and the use of B vitamins. As to the latter of these, there is no direct analysis of cognition and whilst it is alluded to, the lack of this is a clear limitation.

'This work is good evidence of a causal relationship, but the reporting of mean effects in a study such as this does not guarantee impact at the level of the individual given adherence to the same vitamin regime.’ [David Smith points out to me that the study didn’t just report mean effects, but also divided out the results by baseline homocysteine level for example.] 

John Hardy, Professor of Neuroscience, UCL said: ‘The data is very interesting and I have seen it presented. Homocysteine is known to be involved in stroke-related diseases and so involvement in Alzheimer’s disease is plausible. But it is important to note that the study is rather small and needs replicating in a larger study.’ 

Chris Kennard, chair of the Medical Research Council’s Neurosciences and Mental Health Board said: ‘We welcome the findings of this MRC-funded study which bring us a step closer to unravelling the complex neurobiology of ageing and cognitive decline and holds the key to the development of future treatments for conditions like Alzheimer’s disease. However, we must be cautious when recommending supplements like vitamin B as there are separate health risks if taken in too high doses. Further research is required before we can recommend the supplement as a treatment for neurodegenerative diseases, such as Alzheimer’s.’

Figure 1 in the paper outlines the flow of participants through the two-year study. Drop out numbers at each stage are given with some of the reasons. There are some who drop out before the trial, some during, some were excluded, some were diagnosed with cancer, and two died. Of the initial 271 participants, 223 completed the two-year trial and cognitive tests.

But it does appear that there may be a high number of people in the two trial arms (vitamin tablets and placebo) not volunteering for MRIs. Only 168 people had the two MRI scans included in the study and which gave the paper’s main results. While the paper doesn’t describe the reasons for each case (I’m not sure how many papers do), there could be a number of reasons for this in what is an elderly group. It is after all a voluntary scan and some people may not, in the end, like the idea.

On asking David Smith, he adds further: ‘The important point is that in the trial we allowed for the fact that some subjects did not choose an MRI scan by including this in the initial minimization procedure. In other words, no bias was introduced.’

In the end, although these certainly appear promising results, we come full circle to where I started. So I’ll finish with Carl Heneghan’s last line in his blog at the Centre for Evidence-Based Medicine at the University of Oxford:

‘I'd call this an interesting result. But what is needed is a much larger trial, with a well defined clinically significant outcome. Ideally this would be progression to Alzheimer’s disease.’

Update 10 Sep: The Behind the Headlines section of the NHS Choices website has an analysis of the study here.

A new way of combining ultrasound images taken from different positions can result in sharper, better quality 3D images of the heart to help doctors make a diagnosis.

The new technique aims to improve on conventional 3D echocardiography which is not yet routinely used, partly because of problems with the quality of images produced and difficulties in imaging the whole heart.

A team of Oxford University biomedical engineers and cardiologists has developed a way of merging 3D data from ultrasound transducers placed in different positions on a patient’s body. The researchers recently reported in the journal JACC Cardiovascular Imaging that, in a pilot study of 32 people, this boosted the quality of good/intermediate quality images of the heart from 70% with existing methods to over 96%.

‘For the first time we’ve shown in a detailed clinical study how fusion of 3D data from different positions can improve the quality and completeness of the final image,’ Alison Noble of Oxford University’s Department of Engineering Science, a co-author of the report, tells me.

‘Our new technique saw significant improvements in the general image quality and the definition of features within the heart which should make it possible to spot even small abnormalities in, for example, the motion of the heart wall,’ adds Harald Becher of Oxford University’s Department of Cardiovascular Medicine.

The team's method is based on ‘voxels’ - 3D units of data similar to the 2D pixels on a TV screen. By matching similar-looking voxels of data from different positions it is possible to calculate the ‘best fit’ of a sequence of individual frames. This alignment is then applied first across ‘downgraded’ low-resolution images before these are ‘upgraded’ again to their original high-resolution – saving computation time.

‘This new approach is an exciting advance in echocardiography, as it enables us to see the sort of complete picture we weren’t able to before,’ Harald explains. ‘For instance, in this study a number of the participants were Oxford rowers with very large left ventricles which could not be imaged from a single position. By fusing our data we were able to produce accurate three-dimensional images of the entire heart within seconds.’

The team say these preliminary results are encouraging, although further studies are needed with larger groups of patients. The researchers hope their approach could lead to a greater use of 3D echocardiography in the future and are currently looking at how it could be combined with other heart imaging techniques, such as magnetic resonance imaging.

Video: Left and middle: 2D slices of conventional 3D echo images showing chambers of the heart. These four images were acquired from the same subject from four positions. Right: Resultant image by the fusion of four images shown on left and middle. Anatomical information and image quality is increased.

The Oxford University team included Professor Alison Noble, Dr Kashif Rajpoot, and Dr Vicente Grau of the Department of Engineering Science, and Professor Harald Becher, Dr Cezary Szmigielski, Saul Myerson, and Dr Cameron Holloway of the Department of Cardiovascular Medicine.

The research was supported by the EPSRC.

Last month young scientists and engineers from Oxford and Cambridge joined together in teams to learn how to pitch business ideas to a Dragon’s Den-style panel of judges.

The theme of the event - Oxbridge Connects - was renewable energy and the winner of the £1200 first prize was an Oxbridge team with an idea for setting up wind farms in rural Argentina.

I caught up with two members of the winning team, Claudio Silvestrin of Oxford University’s Department of Physics and Vihar Georgiev of Oxford’s Department of Chemistry, to ask them how they pitched a winner:

OxSciBlog: Why did you focus on wind power in Argentina?
Claudio Silvestrin: One of our team members, Julian Tuccillo, who became the project leader later on, is Argentine and he proposed a wind project for rural areas in his home country. He had a lot of background information on it and we all liked the idea of working on a project with an international context.

Looking back, it was a very good decision. In the process of developing our ideas we learned a lot about the challenges you face when setting up a business in an area like rural Argentina. For example, in a project set in the UK you most likely wouldn't need to think about people still living without electricity and how life-changing the installation of a small wind turbine might be for them.

Vihar Georgiev: Another reason was the fact that the project was supposed to be on a small scale and this particular topic made it realistic for us as students. The final reason behind choosing this topic was that it didn't touch upon the UK market, as we expected other teams to concentrate on this.

OSB: What did you learn about developing/presenting business ideas?
CS: We went through product and market research, financial modelling and risk analysis, all scheduled in a project plan. But we also learned how challenging it is to work together in a virtual team, since half of the team was in Cambridge and the other half in Oxford.

In terms of what to focus on and how to present your business plan in a very short time (presentations were 8 minutes + 4 minutes Q&A) we got a lot of help from our mentor, Professor David Upton of the Saïd Business School.

VG: Working on our business plan, I became familiar with business and technical terms and, thanks to this, was more confident in answering questions during the presentation. The bottom line is that I learned that before you do anything, you need to do your homework thoroughly. I also learned that to be successful you need to be able to explain your ideas clearly and with confidence.

OSB: What were the key points you stressed in your pitch?
CS: First of all we argued that our project provides social good to the local population. We also stressed that with it we are building capability (technical know-how, supply chain) in the communities. Other key points were the good wind resource in Argentina and the environmental benefit. But our project was also profitable and had a low risk for investors.

VG: Our calculations showed that the profit gained in a 20-year period would be 10 times the outlay. To compare, at the moment PV solar cells in the UK bring a profit of 3 times the outlay over 20 years. Our plan is very low-risk and I think, if implemented in real life, it could be even more profitable. It was also crucial for me to concentrate on an environmentally-friendly project.

OSB: How did having such an interdisciplinary (& inter-University!) team help you win?
CS: In some aspects the interdisciplinarity was vital for our success in terms of combining the technological component and the business side of the project. Also, having an interdisciplinary team made the work very interesting in terms of interacting with each other. But for some of us our individual backgrounds didn't play a large role. Most important was the dedication and effort everybody was willing to put in, in order to learn quickly how to produce good results in a field that you might be unfamiliar with.

VG: The biggest advantage was a chance to see many different points of view. Based on different cultures and education each of us had, everyone could see the project from a different angle. This way we had not only one way of thinking but five, which made the project more flexible and reduced the number of mistakes. Personally, if I work on a similar project in the future, I would like to work with such a diverse and interdisciplinary team.

OSB: How do you think this experience might prove useful in the future?
CS: I was amazed by what you can achieve in a team, which is put together almost randomly and works together through skype and email most of the time. Personally I believe that the experience is going to influence my future strongly since I developed an interest in building small businesses, which I knew very little about before. Bringing people from different backgrounds together in a workshop like this is a wonderful idea. 

VG: I'm sure this workshop will be very useful for me in the future because it only strengthens my interests in sustainable energy sources. Also, after researching the topic of wind power, I have a better idea of the key aspects in this new field of science and its importance for society. For me this workshop was a good way to motivate people engaged in science to think not only about the importance of a scientific breakthrough but also about the business and environmental aspects of their work.

Oxbridge Connects took place on 6 July 2010 at Kavli Royal Society International Centre, Chicheley Hall. It received support from Oxford’s MPLS Division and EPSRC.

At 389 years old, the Curator of the Oxford University Herbaria is one of the oldest positions in Oxford. Its current holder, Dr Stephen Harris, curates a vast collection of plant specimens, archived and housed in the Department of Plant Sciences.

These specimens have been brought back to Oxford from all over the world since 1608. Stephen stresses, however, that old herbaria like these are of vital importance to 21st Century environmental research. In the face of climate change, plummeting biodiversity and habitat loss, historical plant collections have a lot to contribute when it comes to confronting today’s environmental threats.

The history represented within the Oxford Herbaria makes the collections a rich resource. Whilst herbaria were founded originally for the purpose of correctly naming plants and recording their geographical distributions, they now have a key role in telling us how human activities over the last 400 years have affected our planet.

‘We are essentially a repository of biodiversity,’ Stephen explains. ‘We provide the evidence that a particular organism occurred in a particular time and space.’

Data like these are invaluable for investigating how plant species, and the animal communities that depend upon them, have changed in abundance and location as a consequence of human trade, agriculture and resource exploitation. The information contained in the Herbaria archives not only show changes in biodiversity - the species richness of an area - but also can be used to monitor conservation, providing evidence of how plant populations change in response to different conservation methods.

Identifying patterns, threats
Within the University of Oxford, the specimens of the Herbaria are key to a large number of research projects:

For example, the archive of plant material is essential to scientists in the Department of Plant Sciences who want to study a plant which has gone extinct or resides only in a current war zone. Dr Robert Scotland, Reader in Systematic Botany, has been using the collections over the last fifteen years to put together a new ‘monograph’ (an exhaustive and detailed description) of the plant genus Strobilanthes.

Detailed taxonomic work like this is essential for determining the global patterns of plant species and discovering which plants are under threat; and with 400 different species of Strobilanthes spread across 40 different countries, an undertaking of this size would have been impossible without access to Oxford’s collections.

Meanwhile researchers from the Oxford Environmental Change Institute use pollen to monitor changes in climate. They extract pollen from specimens which have been collected from around the world and correctly identified by the Herbaria’s experts and use it to identify the species of pollen present in ‘cores’ of the Earth’s crust.

By digging deep down at a certain site, and identifying all the plant species that were present at a certain time - the deeper you go, the further back in time you can see - it is possible to deduce the environmental conditions that once existed at that place, based only on the knowledge of the plants that used to live there. Studies like these can show us how climatic conditions in specific places have been changing over time, and the impact that this has had upon what types of plant grow there.

Herbaria were originally founded as research and educational collections, and the roles of the Oxford Herbaria in education today are of key importance to fighting extinction. The United Nations declared 2010 the International Year of Biodiversity, in an effort to emphasise the importance of preserving biological richness and the health of our natural environments.

However, faced with climate change and resource exploitation, the ‘Taxonomic Impediment’ stands in the way of conserving what we have. The problem is that the correct identification of the vast majority of our planet’s species requires expert training and education, a detailed knowledge of the ever-changing official species names, and confidence in using the Latin naming system.

Conservation on the frontline
Whilst these are possible in the well-funded universities of the developed world, the world’s most biologically rich areas - referred to as ‘biodiversity hotspots’ - tend to be located in economically poorer countries and under threat from destruction through industries like mining. It is almost impossible to conserve and protect a species if you are unable to correctly identify it, and the most conservative estimates suggest that we have discovered and named less than half of the total species on Earth so far.

With habitat destruction and species extinction occurring at accelerating rates, it has never been more important to remove the taxonomic impediment to biodiversity conservation, and projects like the Virtual Field Herbarium (VFH), based in the Oxford Herbaria, are using the Internet to transfer knowledge from Oxford archives to local scientists in biodiversity hotspots like Granada, Cameroon, Ghana and Mexico.

Dr Will Hawthorne, founder of the VFH project, explains ‘in the developing world, herbaria tend to be low priority for funding. Traditionally the names are twenty to thirty years out of date, and they cannot afford to get all the scientific journals.’

Before Will set up the VFH, Internet herbaria did already exist, but they consisted of photos of old, dried, preserved herbarium specimens: ‘It’s like trying to identify the mammals of Britain based on road-kill. Yes, you can probably do it, but it’s much better to have a lovely picture of a fluffy squirrel rather than a squashed one.’

Oxford’s VFH therefore has an emphasis on live plants, growing in the field. This enables local academics worldwide to use colour and three dimensional shape - features which are typically distorted through the traditional preservation of plant material - to compare plants to the VFH’s photos and correctly identify their species.

The mission of the VFH does not stop there. Its founders and curators want local scientists in the world’s most biodiverse habitats to write books. ‘We didn’t just want people sitting here in Oxford writing field guides for the rest of the world, we wanted to empower people,’ Will explains.

Confronting the Taxonomic Impediment head-on, users of the VFH online can access a step-by-step guide to producing scientific field guides, reference a glossary of useful plant characteristics, browse the online images and access key scientific literature - all the ingredients required to easily construct your own, user-friendly, field identification guide for a specific area.

Providing people in developing countries with the tools to identify their local flora not only benefits conservation efforts, but also local economies. ‘There are lots of other uses to which biodiversity is put these days,’ says Will, as he shows me a field guide for Granada specifically written to encourage visits from ecotourists.

Mapping hotspots
Oxford Herbarium researchers have just received funding to take the Virtual Field Herbarium to a new level. Whilst the identification of ‘biodiversity hotspots’ is useful for focusing conservation efforts on the world’s most biologically rich areas, these designated hotspots often comprise very large geographical areas, like the Andes or the Congo Basin. The residents of these areas need to live off their land, and to completely protect such vast areas from agriculture, mining and human exploitation is impractical and unrealistic.

Over the next 5 years, Phase Two of the Virtual Field Herbarium will go out to biodiversity hotspots and use Will’s ‘Rapid Botanical Survey’ technique to gather detailed information about plant species and their exact location at lightning speed. Working with BRAHMS - a tool developed in the Oxford Herbaria by Denis Filer for the worldwide tracking of herbaria specimens, species name changes, and biodiversity research - the project will precisely map biodiversity levels within these hotspots.

The end product will enable users to zoom into biodiversity hotspots in their web browser and view the differing levels of species richness across the region. From here, users will be able to access species data previously collected at these areas and links to related Oxford Herbaria specimens. This new tool will enable people living within biodiversity hotspots to identify the less biologically important areas and to develop these for economic use, leaving the areas of high significance more likely to be preserved and protected.

Whilst the Internet-based projects of the ‘e-taxonomy’ movement have the potential to add real momentum to conservation efforts worldwide, these projects depend upon a strong foundation of detailed, ‘old-school’ taxonomy. The very concepts of biodiversity and hotspots rely upon an understanding of basic information about species - location, abundance, endemism...

Home-grown taxonomy
‘Herbaria are often seen as being repositories of something that’s over,’ says Robert, ‘but they are incredibly dynamic collections of data. Not just collections of dead specimens, they are the best evidence we have for biodiversity.’

In the UK, however, we are experiencing our own Taxonomic Impediment: The decline in fully-trained, professional taxonomists in Britain has been steep, with Robert being one of only a few full-time university taxonomists left in the country. With the science of species identification and classification being of such great relevance to preserving the environment, the pressure is on for those remaining within the field. Robert is currently launching a pilot project, using the genus Convolvulus to experiment with high-speed taxonomy.

This group of plants has not been monographed since the 19th century Swiss botanist de Candolle attempted to describe all the plant species of the world. Robert and his colleagues aim to revise this untouched monograph in only 6 months, through reducing the number of objectives and using new imaging technologies. This project will seek to describe all species in the group, develop classification keys, and list herbarium specimens, and spend less time on the more complicated aspects of traditional monographs, like the evolutionary relationships between all the species.

This project will require no field work - cameras will be sent to different herbaria, and photos sent back of Convolvulus specimens. ‘We are exploring new ways to monograph the world’s flora,’ explains Robert. ‘There are very few initiatives addressing how to do the science that underpins taxonomy in a new and relevant way.’

When Phase Two of the Virtual Field Herbarium is complete, it will exemplify botany in the 21st Century. The sophisticated software of BRAHMS will link together large datasets from Oxford, The Royal Botanic Gardens at Kew, and others in a user-friendly interface mapped onto Google Earth and Google Maps, and this rich data resource will be made available to taxonomists and researchers worldwide over the Internet.

Whilst modern technology provides the key to ease-of-use and accessibility, projects like these still entirely depend upon the centuries-old practices of expert surveying and, at the heart of it all, historical and well-kept herbaria.

The Internet will be a key weapon in fighting the Taxonomic Impediment but Denis stresses that ‘the IT tail shouldn’t wag the taxonomy dog’. Investment is being increasingly channelled into Internet-based branches of taxonomic research, but in today’s world of changing climates and natural habitat destruction, the more ‘old-fashioned’ methods of taxonomy, and the herbarium specimens they depend upon, have never been more vital.

Penny Sarchet is based at Oxford University's Department of Plant Sciences.