Features

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.

An astonishing and shocking story from the time of the Japanese occupation of Indonesia has been unearthed, thanks to the efforts of J Kevin Baird, who directs the Oxford University Clinical Research Unit based in Jakarta, and his Indonesian colleague, Professor Sangkot Marzuki, Director of the Eijkman Institute for Molecular Biology.

Reported in The Observer at the weekend, the events include hundreds of deaths of forced labourers, accounts of the torture of local doctors and researchers, and the beheading of a leading Indonesian scientist who is likely to have been innocent of any crime. A full account also appeared earlier this month in Science.

In July 1944, during the Japanese occupation of Indonesia, around 900 Indonesians in a forced labour camp outside Jakarta were injected with a vaccine. All of them died within a week.

The Japanese military police arrested local researchers, doctors and staff at a scientific institute in Jakarta, accusing them of sabotaging the vaccine. The Indonesian head of the Eijkman Institute and a leading light in clinical research at the time, Professor Achmad Mochtar, was executed for this crime by the Japanese military police in July 1945 as the War in the Pacific drew to an end.

Kevin Baird teamed up with Sangot Marzuki, who heads the present-day Eijkman Institute of Molecular Biology where the Oxford University Clinical Research Unit is based, to investigate what really happened.

They sought out documents from the time, written accounts, and interviewed former institute staff and family members of those who survived Japanese captivity and torture.

They are convinced their research exonerates the executed Mochtar, who appears to have confessed to the crimes to save his colleagues. They also suggest that the 900 deaths occurred not through contaminated vaccines, but may have occurred during the course of a Japanese medical experiment. Baird and Marzuki believe that the forced labourers were likely to have been given an experimental tetanus vaccine developed by the Japanese and intended for their troops, then given tetanus toxin to see if it worked.

Thanks to their work, some light has been shed on the causes behind hundreds of deaths in a forced labour camp some 65 years ago. And the standing of a remarkable scientist – and a remarkable man – Achmad Mochtar is on its way to restoration.

In mammals, many birds, and some invertebrates young offspring are totally dependent on their parents for food and protection.

But why is such helplessness a good strategy? And how has evolution resulted in 'lazy' youngsters trying to out-beg their siblings for a feed?

New research led by Andy Gardner of Oxford University's Department of Zoology, published in Proceedings of the Royal Society B, uses mathematical models to examine how some of these traits are related. I asked Andy about the costs and benefits of intensive parenting:

OxSciBlog: What are the advantages of having young that are more dependent on their parents for food/care?
Andy Gardner: In the animal world, the most basic form of parental care is when the parent guards their offspring from predators while the young forage for their own food. This can evolve as a simple extension of egg guarding, for example.

However, innovations in parental care that lead to parents actually feeding their own offspring can be favoured, because this allows parents to make their nests in safer - but food-scarce - environments.

An extreme example is when birds nest in trees. The safety of the canopy means that parents can leave the nest in search of food, without needing to guard their young. But, apart from the odd insect hovering around the nest, there isn't much scope for the offspring to feed for themselves - which makes them fully dependent upon their parents for survival.

OSB: How might ecological conditions drive species to have more dependent young?
AG: Whether the initial innovation of parental feeding is favoured depends upon a number of factors, for example the relative efficiency of parents feeding their offspring versus offspring feeding themselves. If food items are difficult for the young to process - they may not have very strong jaws - then it may be more efficient for parents to chew up the food for them.

OSB: What links have you found between this dependency and traits such as nest choice/sibling competition?
AG: The parents' choice of nest site can play a huge role in deciding how dependent the young will be on their parents for survival. Obviously, if the nest is situated far from sources of food, this leaves the young totally dependent upon their parents.

But, more subtly, parental feeding can lead to offspring being even more helpless, as natural selection will favour those offspring that give up even trying to feed themselves and instead compete with their siblings for the food that their parents bring to the nest.

OSB: Why do we think evolution of dependency is 'one way' - with species unlikely to reverse to evolve more independent young?
AG: Sibling competition for parentally-derived food puts parents in a cruel bind. The more food they offer to their offspring, to supplement that which the offspring have foraged for themselves, the less interested the offspring are in their own foraging, and the more effort they put into begging their parents for food.

Parents are then forced to increase the amount of food they give to their offspring, just to make up for their offspring's laziness. This reinforcement between parental feeding and sibling competition means that, once parental feeding is established as the norm, it is difficult to return the species to its ancestral state - even if environmental conditions change to make parental feeding less efficient.

This just emphasises that evolution progresses for the good of individuals, in this case lazy offspring, and will not generally find the most efficient solutions for the family unit.

Dr Andy Gardner is a Royal Society Research Fellow based at Oxford University's Department of Zoology. The research was carried out by Dr Gardner and Per Smiseth of Edinburgh University.