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New journal aims to tackle biggest problems in scholarly communication

9 hours 59 min ago

Experimental Results aims to tackle the crisis in the reproducibility of results, provide an outlet for standalone research that currently goes unpublished and to make peer review faster, less onerous and more transparent.

Submissions are now open for the journal, which will give researchers a place to publish valid, standalone experimental results, regardless of whether those results are novel, inconclusive, negative or supplementary to other published work.

It will also publish the outcome of attempts to reproduce previously published experiments, including those that dispute past findings.

The ambitious publication is the brainchild of Fiona Hutton, the Press’s Head of STM Open Access Publishing and addresses concerns she has had since her days in the lab as a cancer research scientist and throughout her career in research publishing.

She said: “Scholarly communication isn’t really reflective of the research process, because the focus is on publishing a concise narrative. The reality is that research results are often confusing, inconclusive, or don’t fit a narrative. Discovery is damaged when the focus becomes the research paper rather than the research output itself.

“I've had countless conversations with scientists about the value of publishing all valid experiments, not just those that fit the narrative of a particular paper or which are deemed to have a high impact. It would save so much time if researchers could see that a particular experiment had already been carried out and what the results were.

“Openly available raw results for these experiments could also be used and interrogated in different ways; ways that the original researcher did not identify, further facilitating discovery and justifying investment in that research."

In addition, Experimental Results will shake up peer review, introducing scorecards to make the process easier, more open and more attractive to potential reviewers, with each reviewer identified by name and with each review published alongside the article in question with its own DOI.

This will allow the journal’s reviewers to have their work recognised. They will also be given discounts on the cost of publishing their own articles in Experimental Results.

Fiona added: “Our goal is to be progressive, to ensure research outputs are correctly reviewed, and to ensure the reviewers we rely on so heavily are rewarded. This makes sense, much like the journal itself makes sense in its reflection of the actual research process.”

While some journals publish full-paper negative or inconclusive results, published stand-alone results are a rarity. Experimental Results will address the issue in a structured way, with open research practices underpinning the entire concept.

The journal will be fully open access, assessed through open peer review, and link to open data where possible.

Fiona said: “Part of the problem is that the peer review process doesn’t actually involve checking the results or repeating the experiment.

“Lots of results come out that people can’t repeat but what do they do? Even if they know of other labs that can’t repeat that experiment, if it’s published in a high impact journal then it’s very difficult to dispute those results. Experimental Results will be a venue for researchers to quickly publish reproducibility experiments.”

The Press’s STM Publishing Director, Caroline Black, said: "We are seeing an increasing acknowledgement that all research outputs – not just the positive, exciting results - should be part of the published record for the advancement of knowledge and reduction of wasted time on redoing work unnecessarily.

“In the past it would have been difficult to publish negative, confirmatory or inconclusive results, as journal editors made decisions on the basis of innovation, interest level and potential for citations. That's beginning to change now.

“People are also looking for alternative types of publication; it's not all about the traditional journal article, complete with introduction, discussion and conclusion setting out the importance of the results. It's great that we are at the forefront of providing them with a new platform."

Press release from Cambridge University Press

A new journal from Cambridge University Press will take a radical new approach to both publishing and peer reviewing research.

Scholarly communication isn’t really reflective of the research process, because the focus is on publishing a concise narrative. The reality is that research results are often confusing, inconclusive, or don’t fit a narrativeFiona Hutton


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Yes

Cambridge appoints first DeepMind Professor of Machine Learning

21 hours 22 min ago

Professor Lawrence joins the University’s Department of Computer Science and Technology from Amazon Cambridge, where he has been Director of Machine Learning for the past three years. He is also Professor of Machine Learning at the University of Sheffield, where he will retain a visiting position.

Professor Lawrence’s research interests are in probabilistic models with applications in computational biology, personalised health and developing economies. At Sheffield, he led the ML@SITraN group, and helped to develop an Open Data Science Initiative an approach to data science designed to address societal needs.

“There’s so much expertise at Cambridge, in all aspects of systems and data: that’s why I’m so excited about joining,” Lawrence said. “AI and machine learning have the potential to reshape almost every aspect of our lives, but we desperately need more machine learning specialists, or else the promise of AI will not be realised.”

Professor Lawrence completed his PhD at Cambridge’s Department of Computer Science and Technology in 2000. He has previously held positions at Microsoft Research Cambridge and the University of Manchester. In addition to his academic research, he hosts the Talking Machines podcast and is a contributor to the Guardian.

For the past five years, Professor Lawrence has been working with Data Science Africa, an organisation looking to connect machine learning researchers in Africa in order to solve problems on the ground. Professor Lawrence has an advisory role with the group, and says that many of the machine learning approaches used in Africa can have benefits in the developed world as well.

“With data and machine learning, you can have a more advanced data infrastructure in Africa than in some developed countries,” he said. “It’s rare in the UK or Europe that you’re asked to look at a machine learning problem from end to end, but you can do that in Africa, and it leads to better solutions. That’s the kind of approach I want to take to machine learning in my work at Cambridge.”

Demis Hassabis, co-founder and CEO, DeepMind, said: “I’m delighted to see Cambridge announce its first DeepMind Professor of Machine Learning. Professor Lawrence’s work in computational biology and his thoughtful advocacy for advancing technology in the developing world have been commendable. It’s an honour for DeepMind to be able to support the Department of Computer Science and Technology - from which I gained so much - in this way, and I look forward to seeing machine learning and AI flourish at Cambridge.”

“Neil will have a transformative effect on machine learning and artificial intelligence research at Cambridge,” said Professor Ann Copestake, Head of the Department of Computer Science and Technology. “He will build on our existing strengths in this area, and work with colleagues from across the University to develop new solutions in ethical and sustainable ways.”

“It is vital we have a deep pool of talented scientists in universities and industry so the UK can continue to be a world leader in artificial intelligence,” said Minister for Digital Mark Warman. “This Government is investing millions into skills and talent training, including a number of Turing AI Fellowships in partnership with The Alan Turing Institute, and I welcome the appointment of Professor Neil Lawrence as the inaugural DeepMind Professor of Machine Learning at Cambridge. This is one of a range of moves demonstrating the enormous strength of the UK’s research base.”

In addition to the gift to support the DeepMind Professorship, the company are also supporting four Master’s students from underrepresented groups wishing to study machine learning and computer science at Cambridge. The first students supported through this programme will be starting their studies this coming term.

Following an international search, Professor Neil Lawrence has been appointed as the inaugural DeepMind Professor of Machine Learning at Cambridge, supported by a benefaction from the world-leading British AI company.

There’s so much expertise at Cambridge, in all aspects of systems and data: that’s why I’m so excited about joiningNeil Lawrence


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Yes

Shakespeare’s mystery annotator identified as John Milton

Tue, 17/09/2019 - 14:33

It is well known that Shakespeare was a huge influence on Milton. From learning how to write nature poetry to creating charismatic villains, Milton’s debt to his forebear continues to fascinate experts. The younger poet once praised the 'wonder and astonishment' that this 'great heir of fame' conjured up in his readers. 

But now, Jason Scott-Warren from Cambridge’s English Faculty believes he has identified even more tangible evidence of this connection. The realisation began when Scott-Warren read an article by Professor Claire Bourne about an anonymous annotator of a Shakespeare First Folio housed in the Free Library of Philadelphia’s Rare Book Department.

Bourne dated the annotator to the mid-17th century and shared images of the handwritten notes. These include suggested corrections, cross-references to other works and the addition of material such as the prologue to Romeo and Juliet. Studying these, Scott-Warren was struck by how closely they resembled known examples of Milton’s handwriting and after identifying numerous compelling similarities, he decided to share his theory in a blog post for Cambridge’s Centre for Material Texts, of which he is Director. 

Milton is known to have made similarly intelligent and assiduous annotations in other books that survive from his library, but the evidence that Scott-Warren presents is strictly palaeographical. It includes the observation that in both the First Folio and in Milton’s handwriting, the right foot of an ‘h’ misses the ground before it heads up into an ‘e’.

Even more convincingly, Scott-Warren points out that “Milton has an enlarged italic hand, sometimes rather scratchy, sometimes quite elegant, that he uses for headings and suchlike.” The researcher compares, for example, the ‘R’ in the speech-heading for ‘Romeo’ in the Folio to a remarkably similar and distinctive ‘R’ from Milton’s ‘commonplace book’, a handwritten compilation of quotes and notes from the books that he was reading between the 1630s and 1660s.

Scott-Warren offered up his theory tentatively, admitting that further work would be needed to prove it beyond doubt. But several Milton experts from around the world have already expressed their enthusiastic support and offered further evidence.

Dr William Poole from New College Oxford says: “Not only does this hand look like Milton’s, but it behaves like Milton’s writing elsewhere does, doing exactly the things Milton does when he annotates books, and using exactly the same marks.”  

"I was gathering evidence with my heart in my mouth,” Scott-Warren says. “Now, every day someone is suggesting a new similarity. I feel 100% sure, but there are still people out there who remain to be convinced.”

As well as displaying many textual annotations, the folio contains line markings which record the annotator’s lively engagement with plays including Hamlet, Romeo and Juliet, Macbeth, The Tempest and King Lear. Scott-Warren says: “You don’t know why he’s singled out a passage for attention, but it forces you to think your way into Milton’s head and it chimes with a lot of what goes on in his poetry. You can really see him constructing himself through Shakespeare.”

In The Tempest, the annotator highlighted the song: 'Come unto these yellow sands, / And then take hands: / Courtsied when you have and kiss’d / The wild waves whist.' The unusual rhyme, of 'kiss’d' and 'whist', is echoed in Milton’s On the Morning of Christ’s Nativity: 'The winds with wonder whist, / Smoothly the waters kist.'

Scott-Warren says: “To see him marking it in the text and responding to it gives you a sense of his sensitivity and alertness to Shakespeare.” 

The First Folio, the first collected edition of Shakespeare’s plays, was published in 1623, seven years after his death, when Milton himself was fifteen. Around 750 were printed but only 233 are known to survive. Scott-Warren is now intending to collaborate with Professor Bourne on a series of articles about the findings.

John Milton was admitted to Christ's College Cambridge in 1624, gaining his BA in 1628 and his MA in 1632.

A Cambridge literary scholar suggests that the handwriting on a Shakespeare First Folio in Philadelphia matches that of the Paradise Lost poet, John Milton.

It shows you the first-hand encounter between two great writers, which you don’t often get to seeJason Scott-WarrenCourtesy of the Free Library of PhiladephiaThe prologue to Romeo and Juliet, transcribed on the last page of Titus Andronicus because it was omitted from the First Folio. Courtesy of the Free Library of Philadephia


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YesLicense type: Attribution-Noncommercial-ShareAlike

Nanoparticles used to transport anti-cancer agent to cells

Tue, 17/09/2019 - 10:35

Research led by Dr David Fairen-Jimenez, from the Cambridge Department of Chemical Engineering and Biotechnology, indicates metal-organic frameworks (MOFs) could present a viable platform for delivering a potent anti-cancer agent, known as siRNA, to cells.

Small interfering ribonucleic acid (siRNA), has the potential to inhibit overexpressed cancer-causing genes, and has become an increasing focus for scientists on the hunt for new cancer treatments.

Fairen-Jimenez’s group used computational simulations to find a MOF with the perfect pore size to carry an siRNA molecule, and that would breakdown once inside a cell, releasing the siRNA to its target. Their results were published today in Cell Press journal, Chem.

Some cancers can occur when specific genes inside cells cause over-production of particular proteins. One way to tackle this is to block the gene expression pathway, limiting the production of these proteins.

SiRNA molecules can do just that – binding to specific gene messenger molecules and destroying them before they can tell the cell to produce a particular protein. This process is known as ‘gene knockdown’. Scientists have begun to focus more on siRNAs as potential cancer therapies in the last decade, as they offer a versatile solution to disease treatment – all you need to know is the sequence of the gene you want to inhibit and you can make the corresponding siRNA that will break it down. Instead of designing, synthesising and testing new drugs – an incredibly costly and lengthy process – you can make a few simple changes to the siRNA molecule and treat an entirely different disease.

One of the problems with using siRNAs to treat disease is that the molecules are very unstable and are often broken down by the cell’s natural defence mechanisms before they can reach their targets. SiRNA molecules can be modified to make them more stable, but this compromises their ability to knock down the target genes. It’s also difficult to get the molecules into cells – they need to be transported by another vehicle acting as a delivery agent.

The Cambridge researchers have used a special nanoparticle to protect and deliver siRNA to cells, where they show its ability to inhibit a specific target gene.

Fairen-Jimenez leads research into advanced materials, with a particular focus on MOFs: self-assembling 3D compounds made of metallic and organic building blocks connected together.

There are thousands of different types of MOFs that researchers can make – there are currently more than 84,000 MOF structures in the Cambridge Structural Database with 1000 new structures published each month – and their properties can be tuned for specific purposes. By changing different components of the MOF structure, researchers can create MOFs with different pore sizes, stabilities and toxicities, enabling them to design structures that can carry molecules such as siRNAs into cells without harmful side effects.

“With traditional cancer therapy if you’re designing new drugs to treat the system, these can have different behaviours, geometries, sizes, and so you’d need a MOF that is optimal for each of these individual drugs,” says Fairen-Jimenez. “But for siRNA, once you develop one MOF that is useful, you can in principle use this for a range of different siRNA sequences, treating different diseases.”

“People that have done this before have used MOFs that don't have a porosity that's big enough to encapsulate the siRNA, so a lot of it is likely just stuck on the outside,” says Michelle Teplensky, former PhD student in Fairen-Jimenez’s group, who carried out the research. “We used a MOF that could encapsulate the siRNA and when it's encapsulated you offer more protection. The MOF we chose is made of a zirconium based metal node and we've done a lot of studies that show zirconium is quite inert and it doesn't cause any toxicity issues.”

Using a biodegradable MOF for siRNA delivery is important to avoid unwanted build-up of the structures once they’ve done their job. The MOF that Teplensky and team selected breaks down into harmless components that are easily recycled by the cell without harmful side effects. The large pore size also means the team can load a significant amount of siRNA into a single MOF molecule, keeping the dosage needed to knock down the genes very low.

“One of the benefits of using a MOF with such large pores is that we can get a much more localised, higher dose than other systems would require,” says Teplensky. “SiRNA is very powerful, you don't need a huge amount of it to get good functionality. The dose needed is less than 5% of the porosity of the MOF.”

A problem with using MOFs or other vehicles to carry small molecules into cells is that they are often stopped by the cells on the way to their target. This process is known as endosomal entrapment and is essentially a defence mechanism against unwanted components entering the cell. Fairen-Jimenez’s team added extra components to their MOF to stop them being trapped on their way into the cell, and with this, could ensure the siRNA reached its target.

The team used their system to knock down a gene that produces fluorescent proteins in the cell, so they were able to use microscopy imaging methods to measure how the fluorescence emitted by the proteins compared between cells not treated with the MOF and those that were. The group made use of in-house expertise, collaborating with super-resolution microscopy specialists Professors Clemens Kaminski and Gabi Kaminski-Schierle, who also lead research in the Department of Chemical Engineering and Biotechnology.

Using the MOF platform, the team were consistently able to prevent gene expression by 27%, a level that shows promise for using the technique to knock down cancer genes.

Fairen-Jimenez believes they will be able to increase the efficacy of the system and the next steps will be to apply the platform to genes involved in causing so-called hard-to-treat cancers.

“One of the questions we get asked a lot is ‘why do you want to use a metal-organic framework for healthcare?’, because there are metals involved that might sound harmful to the body,” says Fairen-Jimenez. “But we focus on difficult diseases such as hard-to-treat cancers for which there has been no improvement in treatment in the last 20 years. We need to have something that can offer a solution; just extra years of life will be very welcome.”

The versatility of the system will enable the team to use the same adapted MOF to deliver different siRNA sequences and target different genes. Because of its large pore size, the MOF also has the potential to deliver multiple drugs at once, opening up the option of combination therapy.

The research is part of a wider project, funded by the EPRSC and European Commission, into treatments for hard-to-treat cancers.

Read the full paper, published in Cell Press journal Chem.

Reference:
Teplensky et al., Chem 5, 1–16 November 14, 2019 ª 2019 Elsevier Inc. https://doi.org/10.1016/j.chempr.2019.08.015

Scientists from the University of Cambridge have developed a platform that uses nanoparticles known as metal-organic frameworks to deliver a promising anti-cancer agent to cells.

We focus on difficult diseases such as hard-to-treat cancers for which there has been no improvement in treatment in the last 20 yearsDavid Fairen-JimenezDavid Fairen-JimenezCells with MOFs carrying siRNA


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Yes

Harnessing tomato jumping genes could help speed-breed drought-resistant crops

Mon, 16/09/2019 - 19:00

Researchers from the University of Cambridge’s Sainsbury Laboratory (SLCU) and Department of Plant Sciences have discovered that drought stress triggers the activity of a family of jumping genes (Rider retrotransposons) previously known to contribute to fruit shape and colour in tomatoes. Their characterisation of Rider, published today in the journal PLOS Genetics, revealed that the Rider family is also present and potentially active in other plants, including economically important crops such as rapeseed, beetroot and quinoa. This highlights its potential as a source of new trait variations that could help plants better cope with more extreme conditions driven by our changing climate. 

This wide abundance encourages further investigations into how it can be activated in a controlled way, or reactivated or re-introduced into plants that currently have inactive Rider elements so that their trait diversification potential can be regained. Such an approach has the potential to significantly reduce breeding time compared to traditional methods. 

“Transposons carry potential for crop improvement. They are powerful drivers of trait diversity, and while we have been harnessing these traits to improve our crops for generations, we are now starting to understand the molecular mechanisms involved,” said Dr Matthias Benoit, the paper's first author, formerly at SLCU.

Transposons, more commonly called jumping genes, are mobile snippets of DNA code that can copy themselves into new positions within the genome - the genetic code of an organism. They can change, disrupt or amplify genes, or have no effect at all. Discovered in corn kernels by Nobel prize-winning scientist Barbara McClintock in the 1940s, only now are scientists realising that transposons are not junk at all but actually play an important role in the evolutionary process, and in altering gene expression and the physical characteristics of plants.

Using the jumping genes already present in plants to generate new characteristics would be a significant step forward from traditional breeding techniques, making it possible to generate new traits in crops that have traditionally been bred to produce uniform shapes, colours and sizes to make harvesting more efficient and maximise yield. 

 “In a large population size, such as a tomato field, in which transposons are activated in each individual we would expect to see diverse new traits. By controlling this ‘random mutation’ process within the plant we can accelerate this process to generate new phenotypes that we could not even imagine,” said Dr Hajk Drost at SLCU, a co-author of the paper.

Today’s gene targeting technologies are very powerful, but often require some functional understanding of the underlying gene to yield useful results and usually only target one or a few genes. Transposon activity is a native tool already present within the plant, which can be harnessed to generate new phenotypes or resistances and complement gene targeting efforts. Using transposons to generate new mutations offers a transgene-free method of breeding that acknowledges the current EU legislation on Genetically Modified Organisms.

“Identifying that Rider activity is triggered by drought suggests that it can create new gene regulatory networks that would help a plant respond to drought,” said Benoit. “This means we could harness Rider to breed crops that are better adapted to drought stress by providing drought responsiveness to genes already present in crops. This is particularly significant in times of global warming, where there is an urgent need to breed more resilient crops.”

This work was supported by the European Research Council and the Gatsby Charitable Foundation.

 

Reference
Matthias Benoit et al. Environmental and epigenetic regulation of Rider retrotransposons in tomato. PLOS Genetics (2019). DOI: 10.1371/journal.pgen.1008370


 

Once dismissed as ‘junk DNA’ that served no purpose, a family of ‘jumping genes’ found in tomatoes has the potential to accelerate crop breeding for traits such as improved drought resistance.

We could harness Rider to breed crops that are better adapted to drought stress. This is particularly significant in times of global warming, where there is an urgent need to breed more resilient crops. Matthias Benoit


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Yes

Women in STEM: Dr Cohl Furey

Thu, 12/09/2019 - 07:00

I first became interested in fundamental physics in secondary school, when a teacher described the basic idea behind a grand unified theory. 

Currently, physicists are able to describe the behaviour of the known particles using just four forces. These are called the strong force, the weak force, the electromagnetic force, and the gravitational force. A grand unified theory tries to combine the first three forces together into a single force. (A theory which attempts to also include gravity is known as a theory of everything.)

My current research focuses on how certain special number systems in mathematics might ultimately underlie the behaviour of elementary particles. This can be thought of as a form of unification, but not in the traditional sense.

Mathematical physics is a beautiful subject, which gets better and better the further you go. It is elegant, much unlike the sorts of things that you will learn in first- and second-year physics. If you are interested in physics and are mathematically inclined, then know that the abstract, beautiful material starts appearing more around your third year.

This area of research has not progressed in terms of gender diversity, as most other fields have. This means that if you would like to pursue this line of study, then you will need to develop a very strong sense of self. Sometimes even your own friends and teachers will unintentionally fix ridiculous stereotypes to you. Just do your work, and prove them wrong.

Dr Cohl Furey is a Walter Grant Scott Fellow in the Department of Applied Mathematics and Theoretical Physics, and a member of Trinity Hall. Here, she tells us about the elegance of mathematical physics, which 'gets better and better the further you go.'  


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Yes

‘Game-changing’ research could solve evolution mysteries

Wed, 11/09/2019 - 18:00

Researchers identified an almost complete set of proteins, a proteome, in the dental enamel of the rhino and the genetic information discovered is one million years older than the oldest DNA sequenced from a 700,000-year-old horse.

The findings by scientists from the University of Copenhagen and St John’s College, University of Cambridge, are published in Nature. They mark a breakthrough in the field of ancient biomolecular studies and could solve some of the biggest mysteries of animal and human biology by allowing scientists to accurately reconstruct evolution from further back in time than ever before.

Professor Enrico Cappellini, a specialist in Palaeoproteomics at the Globe Institute, University of Copenhagen, and first author on the paper, said: “For 20 years ancient DNA has been used to address questions about the evolution of extinct species, adaptation and human migration but it has limitations. Now for the first time we have retrieved ancient genetic information which allows us to reconstruct molecular evolution way beyond the usual time limit of DNA preservation.

DNA data that genetically tracks human evolution only covers the last 400,000 years. But the lineages that led to modern humans and to the chimp – the living species genetically closest to humans – branched apart around six to seven million years ago which means scientists currently have no genetic information for more than 90 per cent of the evolutionary path that led to modern humans.

Scientists also don’t know what the genetic links are between us and extinct species such as Homo erectus – the oldest known species of human to have had modern human-like body proportions – because everything that is currently known is almost exclusively based on anatomical information, not genetic information.

Researchers have now used ancient protein sequencing – based on ground-breaking technology called mass spectrometry – to retrieve genetic information from the tooth of a 1.77 million year old Stephanorhinus – an extinct rhinoceros which lived in Eurasia during the Pleistocene. Researchers took samples of dental enamel from the ancient fossil which was discovered in Dmanisi, Georgia, and used mass spectrometry to sequence the ancient protein and retrieved genetic information previously unobtainable using DNA testing. 
Tooth enamel is the hardest material present in mammals. In this study researchers discovered the set of proteins it contains lasts longer than DNA and is more genetically informative than collagen, the only other protein so far retrieved from fossils older than one million years.

Professor Jesper V. Olsen, head of the Mass Spectrometry for Quantitative Proteomics Group at the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, and co-corresponding author on the paper, said: “Mass spectrometry-based protein sequencing will enable us to retrieve reliable and rich genetic information from mammal fossils that are millions of years old, rather than just thousands of years old. It is the only technology able to provide the robustness and accuracy needed to sequence tiny amounts of protein this old.”

Professor Cappellini added: “Dental enamel is extremely abundant and it is incredibly durable, which is why a high proportion of fossil records are teeth.

“We have been able to find a way to retrieve genetic information that is more informative and older than any other source before, and it’s from a source that is abundant in the fossil records so the potential of the application of this approach is extensive.”

Lead author Professor Eske Willerslev, who holds positions at St John’s College, University of Cambridge, and is director of The Lundbeck Foundation Centre for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, at the University of Copenhagen, said: “This research is a game-changer that opens up a lot of options for further evolutionary study in terms of humans as well as mammals. It will revolutionise the methods of investigating evolution based on molecular markers and it will open a complete new field of ancient biomolecular studies.”

This rearranging of the evolutionary lineage of a single species may seem like a small adjustment but identifying changes in numerous extinct mammals and humans could lead to massive shifts in our understanding of the way the world has evolved.

The team of scientists is already implementing the findings in their current research. The discovery could enable scientists across the globe to collect the genetic data of ancient fossils and to build a bigger, more accurate picture of the evolution of hundreds of species including our own.

 

Reference: 
Enrico Cappellini et al. 'Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.' Nature (2019). DOI: ​10.1038/s41586-019-1555-y

 

Originally published by St John's College, Cambridge

 

An evolution revolution has begun after scientists extracted genetic information from a 1.7 million-year-old rhino tooth – the largest and oldest genetic data to ever be recorded.
 

This new analysis of ancient proteins from dental enamel will start an exciting new chapter in the study of molecular evolution.Enrico CappelliniMirian Kiladze, Georgian National MuseumStephanorhinus skull from Dmanisi


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Yes

Young leaders from UK and Latin America tackle future at Shaping Horizons

Wed, 11/09/2019 - 13:18

They will explore how emerging technologies like those underpinning genomics, AI, clean energy, and smart cities can be used and regulated to create a more equitable and sustainable global community as well as how to encourage sustainable leadership across disciplines and move beyond traditional diplomacy to address global challenges like climate change and social inequalities.

Shaping Horizons 2019 is a Summit and Action Programme rooted in science, policy, and innovation and will strengthen ties and build relationships between young Future Leaders and Senior Leaders from the UK and Latin America. The delegates have been selected from across academia, industry, and government.

Prof. David Cardwell, FREng, Pro-Vice-Chancellor for Strategy and Planning at the University of Cambridge, welcomed delegates at the start of the Summit on behalf of the University.

“On every front, the University has been and continues to be engaged with Latin America, including the pleasure of hosting this fantastic summit, Shaping Horizons, where the mission is to empower and promote youth, create networks and to drive change,” Cardwell said.

The week will culminate with the Future Leaders pitching for prize money to support their own innovative social impact projects they have developed through mentorship and learning during the Summit.

Winners will be supported in further developing and launching their projects through the Action Programme which will follow on from the Summit.

  

Nigel Baker, OBE MVO, Head of the Latin America Department at the Foreign and Commonwealth Office told delegates that all their ideas would help shape the future.

“Shaping Horizons is absolutely driven by the sense of entrepreneurship, innovation, and ideas of the young people involved. It is going to be fascinating to see the proposals that are coming out,” Baker said.

“There are 24 different teams and there are going to be some spectacular proposals and ideas. Some will win prizes, some will not, but I suspect that all of those ideas are going to be applicable in the future.”

Shaping Horizons is a non-profit initiative organised at the University of Cambridge with the support of the Office of Postdoctoral Affairs, and the Cambridge Hub of Global Shapers Community, which is an initiative of the World Economic Forum.

Shaping Horizons was founded by Dr. Matias Acosta, a UK-Canada Fellow at the Centre for Science and Policy, and Theo Lundberg, a NanoDTC PhD Student in the Department of Physics.

“Shaping Horizons was founded to promote sustainability using global, cross-disciplinary cooperation as our driving force,” Acosta said.

“We are a team of 40 undergraduates and academics from across more than 20 departments from the University of Cambridge bringing this initiative forward. Our goal is to build a shared and sustainable future between Latin America and the UK.

"We will be providing more than £30,000 in support for cooperative bilateral projects and also have designed a continuous mentorship programme to maximize the chance of success of each of the ideas.”

More than 100 future leaders from the UK and Latin America have gathered at the University of Cambridge to discuss the future of work and education in an increasingly global digital era at this year’s Shaping Horizons summit.

Shaping Horizons was founded to promote sustainability using global, cross-disciplinary cooperation as our driving forceShaping Horizons founder Dr. Matias Acosta


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Yes

University joins Mind initiative to boost mental health support

Tue, 10/09/2019 - 15:24

The pilot is being run under the collegiate University’s Student Mental Health and Wellbeing Strategy which emphasises the importance of interventions designed to promote good mental health.  

The Mentally Healthy Universities Programme – a £1.5 million partnership between Mind and Goldman Sachs – will offer specialist training for students on resilience, and workplace wellbeing workshops for final year students who are about to graduate and transition into the workplace. The pilot will be delivered collaboratively with a small number colleges.

According to the Higher Education Statistics Agency, the number of students nationally who disclosed a mental health condition almost doubled between 2012 and 2015 to nearly 45,000. However, research suggests that mental health difficulties within Higher Education are currently under-reported as just one in 125 students (0.8%) and around one in 500 staff (0.2%) currently disclose a mental health condition to their university. 

Chad Allen, Project Officer for the Student Mental Health and Wellbeing Strategy at the University of Cambridge, said: “We are committed to making sure our students’ academic successes are supported by personal wellbeing, so we’re delighted to be part of this new initiative which will help support the vital work already under way at the University, and ensure students flourish during their education both academically and personally.”

Paul Farmer, Chief Executive of Mind, said:  “We are really excited to be working with Goldman Sachs to better support thousands of university students and staff across England and Wales. We know that both students and staff face many pressures unique to the university environment. This timely opportunity allows us to deliver a programme that responds to the needs of university communities, building on good practice within the sector, to ensure everyone with a mental health problem receives support and respect.”

Richard Gnodde, CEO of Goldman Sachs International, said: “The transition through Higher Education and into the workforce is often a challenging and pressurised time in young people’s lives. We believe employers have an important role to play in changing attitudes towards mental health through providing support, resources and open conversation around an often stigmatised subject. We look forward to supporting Mind and Universities across the UK in establishing this critical programme.”


The 10 participating universities, are:

University of Cambridge

University of Bath

University of Greenwich

University of Bristol

Teesside University

The London School of Economics and Political Science

Leeds Beckett University

University of Sheffield

University of Central Lancashire

Oxford Brookes

Cambridge is one of 10 UK universities taking part in a new pilot programme to help support mental health provision for students and staff.

We’re delighted to be part of this new initiative which will help support the vital  work already under way at the University, and ensure students flourish during their education both academically and personally.Chad Allen, Project Officer, University of Cambridge


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Yes

Cambridge and Nanjing break ground on 'smart cities' Centre

Tue, 10/09/2019 - 05:03

Cambridge Vice-Chancellor Professor Stephen J Toope joined Zhang Jinghua, Party Secretary of Nanjing City Party Committee and Nanjing Deputy Mayor Jiang Yuejian to turn the first soil at the site where the Centre's dedicated building will rise in Nanjing's Jiangbei New Area.   

The Cambridge University-Nanjing Centre of Technology and Innovation will establish a home for joint research and innovation in collaboration with the Chinese government, industry and China's global research universities that is dedicated to the future of creating 'smart' cities.

"Here in Nanjing, an ancient city and former imperial capital, we are embarking on a unique enterprise," Vice-Chancellor Toope said at the groundbreaking ceremony. "The innovations emerging from this Centre will enable the development of 'smart' cities in which sensors can enable sustainable lifestyles, improve healthcare, limit pollution and make efficient use of energy."

Cambridge and its Chinese partners will share revenue derived from the commercialisation of Intellectual Property (IP) developed at the Centre. It is the University’s first overseas enterprise at this scale.

Funded by the Nanjing Municipality for its first five years, the project will have its own dedicated building as a pilot urban development based on high levels of technological innovation.

At the heart of the new Centre’s activities will be research into technologies that support a modern 21st century city with integrated IT, health care and building management. Innovations emerging from the Centre will enable the development of 'smart' cities in which sensors – applied at the individual level and all the way through to the level of large infrastructure – will enable sustainable lifestyles.

As well as supporting health and wellbeing in new cities, the new Centre will help deliver efficient energy use through its academic and entrepreneurial activities.

The agreement between Cambridge and Nanjing will fund positions in Nanjing, both academic and management, and will allow Cambridge-based academics to engage with specific, long-term projects in Nanjing. It will also support the establishment of a professorship, based in Cambridge, with responsibility as the Centre’s Academic Director.

The project has been driven by Cambridge’s Department of Engineering, although it is hoped that there will be opportunities to widen participation to other departments and Schools. IP generated by research funded through the Centre will be licensed for commercialisation by Cambridge University’s innovation branch, Cambridge Enterprise.

The Centre will seek to demonstrate the power of collaboration with China’s universities, industry, government and other partners to conduct the kind of academic research of excellence today that will make life better for the city dwellers of tomorrow.

One of the two initial projects already approved is to create a high resolution scanner that can provide a low-cost easily accessible method for examining difficult areas of the body, such as bent spines, without using large and expensive CT scans.

That project will be led by Cambridge Engineering Department Professor Richard Prager, in collaboration with China's Southeast University and established local ultrasonic manufacturer Vinno.

A second identified project led by Principal Investigator Professor Toni Vidal-Puig from Cambridge’s Clinical Biochemistry Department, will study the associated complications of increased obesity in China.

Both themes are closely linked to the focus area of local partner, NIHA (Nanjing International Healthcare Area).  

The Vice-Chancellor was joined at the groundbreaking ceremony by representatives from partners Nanjing University, Southeast University, Peking University. Tsinghua University, Fudan University and Zheijiang University as well as Professor Daping Chu of Cambridge's Electrical Engineering Department and Pro-Vice-Chancellor for International Relations Eilis Ferran.

The University of Cambridge and the Nanjing Municipal Government have broken ground on the Cambridge University-Nanjing Centre of Technology and Innovation.

Here in Nanjing, an ancient city and former imperial capital, we are embarking on a unique enterprise.Vice-Chancellor Stephen J Toope


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Yes

Removing beef and lamb from menu dramatically reduces food-related carbon emissions at Cambridge University

Tue, 10/09/2019 - 00:25

In October 2016, the University Catering Service (UCS), which is responsible for 14 outlets across the University of Cambridge and over 1,500 hospitality events each year, implemented the policy, which focused on the areas with the biggest impact without compromising on cost. These were:

  • Reducing the consumption of meat, in particular ruminant meat (beef and lamb)
  • Improving and increasing the availability of plant-based options
  • Removing unsustainable fish from the menu
  • Reducing food waste

Our Sustainable Food Journey, published by the University’s Environment and Energy team, reveals that since implementation, despite increases in how much food was purchased, overall carbon emissions across UCS were reduced by 10.5%. There was a 33% reduction in carbon emissions per kilogram of food purchased, and a 28% reduction in land use per kilogram of food purchased.

“Sustainability is extremely important to our students and staff and we wanted to ensure that we were not only responding to their needs, but pushing what was considered possible in a catering environment,” explains Nick White, Head of the UCS. “This has involved making sacrifices, but is has been absolutely the right thing to do. It’s about making the right choice easy.”

Securing support from catering service staff was key to making these changes. Catering staff were briefed on the environmental benefits of the Sustainable Food Policy and why the UCS wanted to implement it. As cooking with meat is a key part of most chef’s training, the UCS provided chefs with vegan cookery classes and a trip to Borough Market to get inspiration for plant-based menus. Meanwhile, café managers were given training on marketing for sustainability rather than profit.

To encourage changes in behaviour among the customers, UCS increased the number and variety of vegetarian and vegan options at the same time as removing ruminant meat. They also used subtle ‘nudge’ techniques, including placing the vegetarian and vegan options before the meat options and changing how food options were labelled.

“If you go to most restaurants, they’ll put a ‘V’ for vegetarian or label something as vegan,” says Catering Manager Paula White. “We didn’t do that, we just put what’s in it. You use your eyes, your nose. If you look at something and think ‘Wow, that looks good’, you’re not first of all thinking ‘Is there beef in that?’”

The Sustainable Food Policy has been widely supported by customers. The UCS now sells more sustainable, plant-based food, and as a bonus, they retain the same level of footfall, and have increased their gross profits by 2% from 2014/2015 to 2017/2018, despite increases in food costs.

Andrew Balmford, Professor of Conservation Science at the University of Cambridge, who advised UCS on how to make the necessary changes, says: “The University’s catering managers have, in a very short time, dramatically reduced the environmental footprint of their operation by removing ruminant meat from its menus, lowering food waste and eliminating unsustainably harvested fish– while simultaneously increasing sales and profit. It is hard to imagine any other interventions that could yield such dramatic benefits in so short a span of time.”

The UCS also decided to stop selling single-use plastic bottles, and have replaced these with glass bottles, cans or bio-degradable bottles. This has led to saving over 30,000 plastic bottles from landfill per year.

On the menu

A typical menu at the University Centre’s Main Dining Hall is:

  • Aubergine rogan josh
  • Butternut squash lasagne
  • Roast chicken
  • Breaded pork escalope

The full report is available to read at www.environment.admin.cam.ac.uk.

A Sustainable Food Policy at the University of Cambridge, which includes removing beef and lamb from the menu and promoting plant-based food options, has had a dramatic effect on food-related carbon emissions at the University, a report released today reveals.

It is hard to imagine any other interventions that could yield such dramatic benefits in so short a span of timeAndrew BalmfordSvenHilker (Pixabay)Vegetables


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YesLicense type: Public Domain

University of Cambridge admits record levels of underrepresented and disadvantaged students

Mon, 09/09/2019 - 00:01

One in four students at Cambridge will be from under-represented and disadvantaged backgrounds in the 2019/20 intake, while over two-thirds of UK undergraduates will be from state schools, according to provisional data.

The success of Cambridge’s UCAS Adjustment scheme pilot this year has contributed to the rise in underrepresented students being admitted.

The University of Cambridge is also developing a range of measures to widen access and help students make the most of their experience including enhanced and extended bursaries for those in financial need and the introduction of a Transition Year programme, the Course Director for which was appointed last week.

Director of Admissions for the Colleges at the University of Cambridge Dr Sam Lucy said: “We have been exploring different ways to identify talented students who will thrive on our courses and help to make our student population truly representative of the UK population; this has included challenging false perceptions that put off applicants.

“It is deeply encouraging to see that our actions to provide educational opportunity for all those who have the potential to study here are paying off.”

Under future plans for increasing access, the University has pledged to admit one third of its intake from the most underrepresented and disadvantaged groups and to eliminate gaps between various groups in continuation, attainment and progression by 2035.

Read the University of Cambridge Access and Participation Plan on the Cambridge Admissions Office web pages.

The University of Cambridge will welcome record numbers of students from low participation and deprived neighbourhoods and state schools this academic year after continued efforts to widen access to the institution.

It is deeply encouraging to see that our actions to provide educational opportunity for all those who have the potential to study here are paying offDirector of Admissions Dr Sam LucyStudents achieved top grades to get into Cambridge through Adjustment this year


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Yes

Nanowires replace Newton’s famous glass prism

Thu, 05/09/2019 - 19:00

The device, made from a single nanowire 1000 times thinner than a human hair, is the smallest spectrometer ever designed. It could be used in potential applications such as assessing the freshness of foods, the quality of drugs, or even identifying counterfeit objects, all from a smartphone camera. Details are reported in the journal Science.

In the 17th century, Isaac Newton, through his observations on the splitting of light by a prism, sowed the seeds for a new field of science studying the interactions between light and matter – spectroscopy. Today, optical spectrometers are essential tools in industry and almost all fields of scientific research. Through analysing the characteristics of light, spectrometers can tell us about the processes within galactic nebulae, millions of light years away, down to the characteristics of protein molecules.

However, even now, the majority of spectrometers are based around principles similar to what Newton demonstrated with his prism: the spatial separation of light into different spectral components. Such a basis fundamentally limits the size of spectrometers in respect: they are usually bulky and complex, and challenging to shrink to sizes much smaller than a coin. Four hundred years after Newton, University of Cambridge researchers have overcome this challenge to produce a system up to a thousand times smaller than those previously reported.

The Cambridge team, working with colleagues from the UK, China and Finland, used a nanowire whose material composition is varied along its length, enabling it to be responsive to different colours of light across the visible spectrum. Using techniques similar to those used for the manufacture of computer chips, they then created a series of light-responsive sections on this nanowire.

“We engineered a nanowire that allows us to get rid of the dispersive elements, like a prism, producing a far simpler, ultra-miniaturised system than conventional spectrometers can allow,” said first author Zongyin Yang from the Cambridge Graphene Centre. “The individual responses we get from the nanowire sections can then be directly fed into a computer algorithm to reconstruct the incident light spectrum.”

“When you take a photograph, the information stored in pixels is generally limited to just three components – red, green, and blue,” said co-first author Tom Albrow-Owen. “With our device, every pixel contains data points from across the visible spectrum, so we can acquire detailed information far beyond the colours which our eyes can perceive. This can tell us, for instance, about chemical processes occurring in the frame of the image.”

“Our approach could allow unprecedented miniaturisation of spectroscopic devices, to an extent that could see them incorporated directly into smartphones, bringing powerful analytical technologies from the lab to the palm of our hands,” said Dr Tawfique Hasan, who led the study.

One of the most promising potential uses of the nanowire could be in biology. Since the device is so tiny, it can directly image single cells without the need for a microscope. And unlike other bioimaging techniques, the information obtained by the nanowire spectrometer contains a detailed analysis of the chemical fingerprint of each pixel.

The researchers hope that the platform they have created could lead to an entirely new generation of ultra-compact spectrometers working from the ultraviolet to the infrared range. Such technologies could be used for a wide range of consumer, research and industrial applications, including in lab-on-a-chip systems, biological implants, and smart wearable devices.

The Cambridge team has filed a patent on the technology, and hopes to see real-life applications within the next five years.

Reference:
Zongyin Yang et al. ‘Single nanowire spectrometers.’ Science (2019). DOI: 10.1126/science.aax8814

Scientists have designed an ultra-miniaturised device that could image single cells without the need for a microscope or make chemical fingerprint analysis possible from within a smartphone camera. 

Our approach could bring powerful analytical technologies from the lab to the palm of our handsTawfique HasanElla Maru StudioArtist's impression of single-nanowire spectrometer


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Yes

Cambridge University Library unveils the rich histories, struggles and hidden labours of Women at Cambridge

Thu, 05/09/2019 - 11:27

Opening to the public on Monday 14 October, and curated by Dr Lucy Delap and Dr Ben Griffin, the exhibition will focus on the lived experiences of women at the University, the ongoing fight for equal educational rights, recognition, and inclusion in university activities, and the careers of some of the women who shaped the institution – from leading academics to extraordinary domestic staff and influential fellows’ wives.

The exhibition will showcase the history of women at the University, the persistent marginalisation they were subject to, and the ongoing campaigns for gender justice and change since the establishment of Girton College in Cambridge in 1869, the first residential university establishment for women in the UK. Visitors will have the opportunity to explore rarely seen collections from across the University and colleges. Through a mix of costume, letters and audio-visual material, the fascinating and little-known stories of individual women will be illustrated.

Dr Lucy Delap, exhibition co-curator and Fellow of Murray Edwards College, said: “From the founding of the first women’s college to the present day, the experience of women at Cambridge has differed greatly from their male counterparts.

"Though Girton College was established especially to give women the opportunity to study at the University, there were still many barriers that women faced – the first female students were required to ask permission to attend lectures, were not allowed to take exams without special permission, and usually had to be accompanied by chaperones in public until after the First World War. It was still not until 1948 that Cambridge began to offer degrees to women – the last of the big institutions in the UK to do so.

“Through The Rising Tide we hope to illustrate an all-encompassing picture of the incredible fight for gender equality within the University, while portraying the fascinating journeys of some of the militant, cussed and determined women of our institution too.”

Visitors to the exhibition will learn of the deep opposition and oppression women faced, including the efforts made to keep women out of student societies, the organised campaigns to stop women getting degrees, and the hostility faced by women trying to establish careers as academics. Surviving fragments of eggshells and fireworks illustrate the violent opposition to giving women degrees during the vote on the subject in 1897, as does the note written by undergraduates apologising for the damage that had been done to Newnham College during the riot of 1921.

The exhibition will also reveal the creativity and courage of the women who defiantly resisted such opposition to establish lives and careers within the University. Resistance included: the signing of the 400 page petition demanding women’s degrees in 1880, which will be displayed over the walls of the exhibition; setting up new student societies for women; and finding opportunities for women to lecture.

Sometimes, resistance meant finding ways of avoiding the rules that discriminated against women – between 1904 and 1907, Trinity College Dublin offered women from Newnham and Girton the opportunity to travel to Dublin to graduate officially and receive a full degree. The robes of one of the graduates, which have been stored for many decades, will be displayed in the Women at Cambridge exhibition.

Dr Ben Griffin, exhibition co-curator and Lecturer in Modern British History at Girton College, added: “By telling the story of women at Cambridge, this exhibition also tells the story of how a nineteenth-century institution, which served mainly to educate young men for careers in the church, transformed itself into a recognisably modern university devoted to teaching and research.”

The Rising Tide is a culmination of exhibitions, events and displays exploring the past, present and future of women at the University of Cambridge. Curated by Cambridge University Library in collaboration with students and staff, the events programme, pop-up exhibitions and displays will run at the Library and across the city. Women at Cambridge is the centre-piece of the programme and will launch on Monday 14 October, and run until March 2020. Entry is free.

One hundred and fifty years since the first women were allowed to study at the University of Cambridge, Cambridge University Library will be sharing the unique stories of women who have studied, taught, worked and lived at the University, in its new exhibition The Rising Tide: Women at Cambridge.  

From the founding of the first women’s college to the present day, the experience of women at Cambridge has differed greatly from their male counterparts.Lucy DelapGirton CollegeDomestic staff of Girton College, 1908


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YesLicense type: Attribution-Noncommercial-ShareAlike

Women in STEM: Dr Anna-Maria Pappa

Thu, 05/09/2019 - 07:00

I strongly believe that through diversity comes creativity, comes progress. I qualified as an engineer in the Department of Chemical Engineering at Aristotle University of Thessaloniki, Greece, and went on to earn a Master’s Degree in Nanoscience and Nanotechnology from the same university. My PhD is in Bioelectronics from École des Mines de Saint-Étienne in France, and a key moment for me was when I left home to study abroad. Leaving my comfort zone for something unknown was very difficult in the beginning, but proved to be an invaluable experience. I met people from all over the world with different cultures and mind-sets, stretched my mind and expanded my horizons.

I find it very difficult to be around like-minded people; I always look for those with different views. I’m working on a drug discovery platform using bioelectronics, and my work sets out to improve and accelerate drug discovery by providing novel technological solutions for drug screening and disease management. My research focuses on the application of a new class of electronic materials and devices that could replace the in-vitro drug screening assays currently used in medical diagnoses with electronic arrays similar to the electronic chips found in mobile phones.  These could quickly assess the health of our cells, outside of our bodies. 

As an engineer, creating solutions to important yet unresolved issues for healthcare is what truly motivates me. I hope my research will lead to a product that will impact healthcare. The convergence of new technologies with life sciences will revolutionise both diagnosis and therapy. I imagine a healthcare system where the standard one-size-fits-all approach shifts to a more personalised and tailored model.

My most interesting project is one that is working to tackle the global challenge of antimicrobial resistance from a technological standpoint. We are developing biomimetic bacterial membranes on top of our devices and screening newly synthesised antibiotics. Investigating drug-bacterial membrane interactions allows us to directly test the efficacy of known drugs on bacterial resistant strains, as well as allowing us to better understand the action of novel drugs on the membrane properties, and ultimately aid the design and synthesis of target-specific antibiotics. 

I joined Cambridge as a postdoctoral researcher in 2017. My daily routine involves some lab work in the Department of Chemical Engineering and Biotechnology, a lot of reading and writing, and some project management. I spend time in the Maxwell Centre too, where I participate in an entrepreneurship program called Impulse, exploring all the aspects of technology transfer.

Being part of a University where some of the world's most brilliant scientists studied and worked is invaluable. Cambridge combines a historic and traditional atmosphere with cutting edge technological and scientific research in an open, multicultural society. The state-of-the-art facilities, and the openness in innovation and collaborations, along with great science, provide a unique combination that can only lead to excellence.  I also travel frequently for conferences, as well as visiting other laboratories across Europe, the United States and Saudi Arabia. When you work in a multidisciplinary field it is essential to establish and keep good collaborations; since this is the only way to achieve the desirable outcome.

To be successful in a postdoctoral role requires management, teaching, networking, proposal writing and travelling. The amount of time you get to spend in the lab drops significantly compared to the PhD research period. This is in part due to the fact that you are more experienced, thus more efficient, and since you are more independent in research you need to be on top of things.

I think it’s absolutely vital, in every opportunity, for all of us to honour and promote girls and women in science. In October 2017 I was delighted to be awarded a L'Oréal-UNESCO For Women in Science Fellowship, an award that honours the contributions of women in science. For me, the award not only represents a scientific distinction but also gives me the unique opportunity, as an ambassador of science, to inspire and motivate young girls to follow the career they desire. Unfortunately, women still struggle when it comes to joining male-dominated fields, and even to establish themselves later at senior roles. We still face stereotypes and social restrictions, even if it is not as obvious today as it was in the past. This is in part due to the fact that still, the key senior roles are predominantly male-occupied, and so there is a lack of female role models as well as female mentality. This makes it harder for women to believe in themselves and achieve their goals.

A question I always ask during my outreach activities at schools is ‘do look like a scientist?’  The answer I get most times is ‘no’! I think this misperception of how professionals in STEMM look, or about what they actually do on a daily basis is what discourages girls early on to follow STEMM careers. This needs to change. On top of that, my advice to women would be to be open, never underestimate themselves and never be put off by stereotypes especially in male-dominated industries. There are excellent examples of highly successful women – leaders in their fields - who managed to excel despite the difficulties. Importantly, many of them successfully combined career and family. 

 

 

Dr Anna-Maria Pappa is a postdoctoral researcher in the Department of Chemical Engineering and Biotechnology and holds the Oppenheimer Research Fellowship and Maudslay-Butler Research Fellowship from Pembroke College. Her research is focused on the global challenge of antimicrobial resistance. 

Anna-Maria Pappa


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Yes

Eight Cambridge researchers awarded major European starter grants

Tue, 03/09/2019 - 14:35

The European Research Council (ERC) Starting Grants have been awarded to 408 researchers from across Europe. The awards will help individual researchers to build their own teams and conduct world-leading research across all disciplines, creating an estimated 2,500 jobs for postdoctoral fellows, PhD students and other staff at the host institutions.

The successful Cambridge researchers are:

  • Roland Bauerschmidt - Renormalisation, dynamics, and hyperbolic symmetry
  • Quentin Berthet - Computational Trade-offs and Algorithms in Statistics
  • Felix Deschler - Twisted Perovskites: Control of Spin and Chirality in Highly-luminescent Metal-halide Perovskites
  • Lorenzo Di Michele - A DNA NANOtechology toolkit for artificial CELL design
  • Louise Hirst - Gliding epitaxy for inorganic space-power sheets
  • Sertac Sehlikoglu - Imaginative Landscapes of Islamist Politics Across the Balkan-to-Bengal Complex
  • Blake Sherwin - CMB Lensing at Sub-Percent Precision: A New Probe of Cosmology and Fundamental Physics
  • Margherita Turco - Human Placental Development and the Uterine Microenvironment

Commenting on the awards, Dr Peter Hedges, Head of the University Research Office at the University of Cambridge, said: “The success of UK researchers, and in particular Cambridge researchers, demonstrates the world-leading position that our country holds in research and innovation. This is a position we have will have to fight hard to maintain in the face of competition from other nations across Europe, the US and China.

“Six of our successful researchers are non-UK nationals, showing once again that Cambridge has the ability to attract the very best talent from around the world to carry out research at its world class facilities.”

The ERC-funded research will be carried out in 24 countries, with institutions from Germany (73), the UK (64) and the Netherlands (53) to host the highest number of projects. The grants, worth in total €621 million, are part of the EU Research and Innovation programme, Horizon 2020.

Carlos Moedas, European Commissioner for Research, Science and Innovation, said: “Researchers need freedom and support to follow their scientific curiosity if we are to find answers to the most difficult challenges of our age and our future. This is the strength of the grants that the EU provides through the European Research Council: an opportunity for outstanding scientists to pursue their most daring ideas.”

President of the ERC, Professor Jean-Pierre Bourguignon, added: “In this year’s ERC Starting Grant competition, early-career researchers of 51 nationalities are among the winners - a record. It reminds us that science knows no borders and that talent is to be found everywhere. It is essential that, for its future successful development, the European Union keeps attracting and supporting outstanding researchers from around the world. At the ERC we are proud to contribute to this goal by supporting some of the most daring creative scientific talent.” 

Eight Cambridge researchers are among the latest recipients of European Union awards given to early-career researchers from over 50 countries.

Six of our successful researchers are non-UK nationals, showing once again that Cambridge has the ability to attract the very best talent from around the world to carry out research at its world class facilitiesPeter HedgesGéry PARENT Naturally-occurring perovskiteResearcher profile: Dr Margherita Turco

 Among this year’s successful awardees is Dr Margherita Turco from Cambridge’s Centre for Trophoblast Research (CTR).

Margherita began her career studying the development of embryos in domestic animals during her studies for Veterinary Biotechnology at the University of Bologna, in Italy. During her PhD in Molecular Medicine at the European Institute of Oncology in Milano, she became interested in how early cell lineage decisions are made and began using various stem cells models to address this question.

This led Margherita to come to Cambridge in 2012 to carry out her postdoctoral work on human trophoblast stem cells at the CTR. Her goal is to understand how the human placenta grows and develops during pregnancy.

“The placenta is a remarkable organ that is formed early in pregnancy. It plays the crucial role of nourishing and protecting the baby throughout its development before birth,” she says. However, there is a lot that can go wrong during this period.

“Complications occurring during pregnancy, such as pre-eclampsia, fetal growth restriction, stillbirth, miscarriage and premature birth, are principally due to defective placental function. These conditions, which collectively affect around one in five pregnancies, can pose a risk to both the baby and mother’s health. Understanding early placental development is the key to understanding successful pregnancy.”


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Vintage film reveals Antarctic glacier melting

Tue, 03/09/2019 - 10:20

Newly digitized vintage film has doubled how far back scientists can peer into the history of underground ice in Antarctica, and revealed that an ice shelf on Thwaites Glacier in West Antarctica is being thawed by a warming ocean more quickly than previously thought. This finding contributes to predictions for sea-level rise that would impact coastal communities around the world.

The researchers made their findings by comparing ice-penetrating radar records of Thwaites Glacier with modern data. Their results are reported in the Proceedings of the National Academy of Sciences.

“By having this record, we can now see these areas where the ice shelf is getting thinnest and could break through,” said lead author Dustin Schroeder from Stanford University, who led efforts to digitize the historical data from airborne surveys conducted in the 1970s. “This is a pretty hard-to-get-to area and we’re really lucky that they happened to fly across this ice shelf.”

Researchers digitized about 250,000 flight miles of Antarctic radar data originally captured on 35mm optical film between 1971 and 1979 as part of a collaboration between Stanford and the Scott Polar Research Institute (SPRI) at the University of Cambridge. The data has been released to an online public archive through Stanford Libraries, enabling other scientists to compare it with modern radar data in order to understand long-term changes in ice thickness, features within glaciers and baseline conditions over 40 years.

Professor Julian Dowdeswell, Director of the Scott Polar Research Institute, a co-author of the paper, commented: “These early records of ice thickness provide an important baseline against which we can measure the rate of change of the Antarctic Ice Sheet over the past 40 or so years. The high-resolution digitization of these records crucially makes them available for a series of important investigations on aspects of Antarctic environmental change.”

The information provided by historic records will help efforts like the Intergovernmental Panel on Climate Change (IPCC) in its goal of projecting climate and sea-level rise for the next 100 years. By being able to look back 40 to 50 years at subsurface conditions rather than just the 10 to 20 years provided by modern data, scientists can better understand what has happened in the past and make more accurate projections about the future, Schroeder said.

“You can really see the geometry over this long period of time, how these ocean currents have melted the ice shelf – not just in general, but exactly where and how,” said Schroeder. “When we model ice sheet behaviour and sea-level projections into the future, we need to understand the processes at the base of the ice sheet that made the changes we’re seeing.”

The film was originally recorded in an exploratory survey using ice-penetrating radar, a technique still used today to capture information from the surface through the bottom of the ice sheet. The radar shows mountains, volcanoes and lakes beneath the surface of Antarctica, as well as layers inside the ice sheet that reveal the history of climate and flow.

The researchers identified several features beneath the ice sheet that had previously only been observed in modern data, including ash layers from past volcanic eruptions captured inside the ice and channels where water from beneath the ice sheet is eroding the bottom of ice shelves. They also found that one of these channels had a stable geometry for over 40 years, information that contrasts their findings about the Thwaites Glacier ice shelf, which has thinned from 10 to 33 percent between 1978 and 2009.

“The fact that we were able to have one ice shelf where we can say, ‘Look, it’s pretty much stable. And here, there’s significant change’ – that gives us more confidence in the results about Thwaites,” Schroeder said.

The scientists hope their findings demonstrate the value of comparing this historical information to modern data to analyse different aspects of Antarctica at a finer scale. In addition to the radar data, the Stanford Digital Repository includes photographs of the notebooks from the flight operators, an international consortium of American, British and Danish geoscientists.

“It was surprising how good the old data is,” Schroeder said. “They were very careful and thoughtful engineers and it’s much richer, more modern looking, than you would think.”

Reference:
Dustin M. Schroeder et al. ‘Multidecadal observations of the Antarctic ice sheet from restored analog radar records.’ Proceedings of the National Academy of Sciences (2019). DOI: 10.1073/pnas.1821646116

Adapted from a Stanford press release.

Newly available archival film has revealed the eastern ice shelf of Thwaites Glacier in Antarctica is melting faster than previous estimates, suggesting the shelf may collapse sooner than expected.

The high-resolution digitization of these records crucially makes them available for a series of important investigations on aspects of Antarctic environmental changeJulian DowdeswellNASAThwaites Glacier


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Yes

Unhappy mothers talk more to their baby boys, study finds

Tue, 03/09/2019 - 00:55

It is well known that having a child can put a strain on the parents’ relationship, but whether this then has an impact on the child’s own development in its first few years is not known. The quality of a couple’s relationship is known to be related to developmental outcomes such as their behaviour and educational attainment in school-aged children, but has been little studied in relation to parent-infant talk, despite parent-infant talk being important for the child’s development.

To examine the relationship between the quality of a couple’s relationship and parent-infant talk, researchers from the Centre for Family Research at the University of Cambridge studied 93 first-time, heterosexual parents and their interactions with their infants. The team asked parents about the quality of their couple relationship and how satisfied they were and then gave the infants at age seven months a wearable ‘talk pedometer’ that recorded naturalistic parent-infant talk for a full day in which both parents were at home.

The researchers used software to provide an automated analysis of the frequency of adult spoken words to their infant and of parent-infant ‘conversations’.

The findings of the research, which was supported by Wellcome and the Economic and Social Research Council, are published in the Journal of Family Psychology.

After taking depression into account (because of its links with both couple relationship quality and parent-infant talk), the researchers found that the more dissatisfied a couple reported their relationship to be, the more the mother spoke to her infant. Mothers who reported the quality of their relationship to be ‘low’ used around 35% more words than a mother whose relationship was ‘average’ and started around 20% more conversations. However, these effects were only found with infant sons, not daughters.

The researchers did not analyse the content of the mother-infant talk, so it is not possible to say whether the mother was complaining to her infant or talking positively.

“It’s possible that the mum is trying to compensate for the poor relationship she has with her partner by putting more time and effort into her relationship with her other close male social partner, her son,” says Dr Elian Fink from the Centre for Family Research and the Faculty of Education.

“What is particularly interesting is that mums only seem to compensate when they have infant sons, not daughters. It could be that mothers view their daughters as mini versions of themselves rather than of their partners.”

Regardless of infant gender, fathers showed significantly less overall talk and initiated fewer conversations than did mothers, even though the fathers are increasingly becoming involved in parenting and the recordings were taken specifically on a day when both parents were at home. However, the amount that they spoke to their infants was unrelated to the quality of the couple’s relationship.

“Even when dads spend more time around their infants, this doesn’t necessarily mean they are interacting with them more,” adds Dr Fink. “One possible reason may be that there’s still an imbalance in who responds to the basic care needs of their infant. So, for example, if it’s the mother who still shoulders the burden of changing the nappy, this at least offers an opportune time to engage in direct communication with her infant.”

Dr Fink hopes the findings will encourage parents to make a conscious effort to talk more to their infants, whether they are boys or girls.

“Parent-child interaction is important for a child’s development, with conversation playing a particular role for the child’s language development,” she says. “Finding time to talk to children is very important. Using opportunities within the daily routine, such as mealtimes and bedtime, to have conversations with your child may help foster later child talk.”                                        

Reference
Fink, E et al. Couple relationship quality and the infant home language environment: Gender-specific findings. Journal of Family Psychology; 22 Aug 2019; DOI: 10.1037/fam0000590

Mothers who are dissatisfied with their male partners spend more time talking to their infants – but only if the child is a boy, according to a new study from researchers at the University of Cambridge.

It’s possible that the mum is trying to compensate for the poor relationship she has with her partner by putting more time and effort into her relationship with her other close male social partner, her sonElian FinkPaul Hanaoka (Unsplash)Mother and child


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YesLicense type: Public Domain

AI learns the language of chemistry to predict how to make medicines

Tue, 03/09/2019 - 00:00

University of Cambridge researchers have shown that an algorithm can predict the outcomes of complex chemical reactions with over 90% accuracy, outperforming trained chemists. The algorithm also shows chemists how to make target compounds, providing the chemical ‘map’ to the desired destination. The results are reported in two studies in the journals ACS Central Science and Chemical Communications.                                            

A central challenge in drug discovery and materials science is finding ways to make complicated organic molecules by chemically joining together simpler building blocks. The problem is that those building blocks often react in unexpected ways.

“Making molecules is often described as an art realised with trial-and-error experimentation because our understanding of chemical reactivity is far from complete,” said Dr Alpha Lee from Cambridge’s Cavendish Laboratory, who led the studies. “Machine learning algorithms can have a better understanding of chemistry because they distil patterns of reactivity from millions of published chemical reactions, something that a chemist cannot do.”                                                                                                                                             

The algorithm developed by Lee and his group uses tools in pattern recognition to recognise how chemical groups in molecules react, by training the model on millions of reactions published in patents.

The researchers looked at chemical reaction prediction as a machine translation problem. The reacting molecules are considered as one ‘language,’ while the product is considered as a different language. The model then uses the patterns in the text to learn how to ‘translate’ between the two languages.

Using this approach, the model achieves 90% accuracy in predicting the correct product of unseen chemical reactions, whereas the accuracy of trained human chemists is around 80%. The researchers say that the model is accurate enough to detect errors in the data and correctly predict a plethora of difficult reactions.

The model also knows what it doesn’t know. It produces an uncertainty score, which eliminates incorrect predictions with 89% accuracy. As experiments are time-consuming, accurate prediction is crucial to avoid pursuing expensive experimental pathways that eventually end in failure.

In the second study, Lee and his group, collaborating with the biopharmaceutical company Pfizer, demonstrated the practical potential of the method in drug discovery.

The researchers showed that when trained on published chemistry research, the model can make accurate predictions of reactions based on lab notebooks, showing that the model has learned the rules of chemistry and can apply it to drug discovery settings.

The team also showed that the model can predict sequences of reactions that would lead to a desired product. They applied this methodology to diverse drug-like molecules, showing that the steps that it predicts are chemically reasonable. This technology can significantly reduce the time of preclinical drug discovery because it provides medicinal chemists with a blueprint of where to begin.

“Our platform is like a GPS for chemistry,” said Lee, who is also a Research Fellow at St Catharine’s College. “It informs chemists whether a reaction is a go or a no-go, and how to navigate reaction routes to make a new molecule.”

The Cambridge researchers are currently using this reaction prediction technology to develop a complete platform that bridges the design-make-test cycle in drug discovery and materials discovery: predicting promising bioactive molecules, ways to make those complex organic molecules, and selecting the experiments that are the most informative. The researchers are now working on extracting chemical insights from the model, attempting to understand what it has learned that humans have not.

“We can potentially make a lot of progress in chemistry if we learn what kinds of patterns the model is looking at to make a prediction,” said Peter Bolgar, a PhD student in synthetic organic chemistry involved in both studies. “The model and human chemists together would become extremely powerful in designing experiments, more than each would be without the other.”

The research was supported by the Winton Programme for the Physics of Sustainability and the Herchel Smith Fund.

References:
Philippe Schwaller et al. ‘Molecular Transformer: A Model for Uncertainty-Calibrated Chemical Reaction Prediction.’ ACS Central Science (2019). DOI: 10.1021/acscentsci.9b00576

Alpha Lee et al. ‘Molecular Transformer unifies reaction prediction and retrosynthesis across pharma chemical space.’ Chemical Communications (2019). DOI: 10.1039/C9CC05122H

 

Researchers have designed a machine learning algorithm that predicts the outcome of chemical reactions with much higher accuracy than trained chemists and suggests ways to make complex molecules, removing a significant hurdle in drug discovery.

Our platform is like a GPS for chemistryAlpha LeeДенис Марчук from Pixabay Background abstract line


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Yes

Lost Irish words rediscovered, including the word for ‘oozes pus'

Fri, 30/08/2019 - 08:00

If you were choosing where to live in medieval Ireland you might insist on somewhere ogach which meant ‘eggy’ or ‘abounding in eggs’, but in reference to a particularly fertile region. By contrast, you would never want to hear your cook complaining brachaid, ‘it oozes pus’. And if you were too boisterous at the dining table, you might be accused of briscugad (making something easily broken).

All three words have been brought back to life thanks to a painstaking five-year research project involving a collaboration between Queen’s University Belfast and the University of Cambridge. The team has scoured medieval manuscripts and published texts for words which have either been overlooked by earlier dictionary-makers or which have been erroneously defined.

Máire Ní Mhaonaigh, Professor of Celtic and Medieval Studies at Cambridge says: “The Dictionary offers a window onto a fascinating and important past world. The project extends our understanding of the vocabulary of the time but also offers unique insights into the people who used these words. They reveal extraordinary details about everyday lives, activities, beliefs and relationships, as well as contact with speakers of other languages.”

The revised dictionary spans the development of the Irish language over a thousand years from the sixth century to the sixteenth, from the time just after the arrival of St Patrick all the way down to the era of Elizabeth I. The team has amended definitions, presented evidence to show that some words were in use much earlier than previously thought, and even deleted a few fake words. One of these is tapairis which had been taken to be some kind of medicinal substance but in effect is not a word at all, since it arose from an incorrect division of two other words literally meaning ‘grains of paradise’, the term for Guinea grains.

Lost words

The rediscovered lost words include a term for ‘becomes ignorant' – ainfisigid, based on the word for knowledge: fis. Other words have been shown to have been attested hundreds of years earlier than was previously thought, such as foclóracht meaning vocabulary. Yet, other examples emphasise that the medieval world continues to resonate. One of these is rímaire, which is used as the modern Irish word for computer (in its later form ríomhaire). 

Professor Ní Mhaonaigh explains: “In the medieval period, rímaire referred not to a machine but to a person engaged in the medieval science of computistics who performed various kinds of calculations concerning time and date, most importantly the date of Easter. So it’s a word with a long pedigree whose meaning was adapted and applied to a modern invention.”

The historical dictionary on which the electronic one is based was originally published by the Royal Irish Academy in 23 volumes between 1913 and 1976. “Advances in scholarship since the publication of the first volume had rendered parts of the dictionary obsolete or out of date,” says Greg Toner, leader of the project and Professor of Irish at Queen’s University Belfast. “Our work has enabled us to resolve many puzzles and errors and to uncover hundreds of previously unknown words.”

The online Dictionary serves up a feast of information on subjects as diverse as food, festivals, medicine, superstition, law and wildlife. One of the newly added phrases is galar na rig, literally the king's disease, a term for scrofula which is known in English as king's evil.

Leprechauns, outlaws and turkeys

One of the most globally recognisable words in the Dictionary is perhaps leipreachán. This character is now regarded as quintessentially Irish but scholars now think that leipreachán, and its earlier form lupracán, is not even a native Irish word but one derived from the Luperci, a group associated with the Roman festival of Lupercalia. This included a purification ritual involving swimming and like the Luperci, leprechauns are associated with water in what may be their first appearance in early Irish literature. According to an Old Irish tale known as ‘The Adventure of Fergus son of Léti’, leprechauns carried the sleeping Fergus out to sea. On route, he managed to capture three of them and, in return for sparing their lives, they granted him the ability to breathe underwater.

The project sheds new light on Ireland’s interactions with foreign languages, cultures and goods in the medieval period. The Dictionary points out that útluighe, meaning an outlaw, ultimately goes back to the Old Norse word útlagi, though the term was perhaps borrowed into Irish through English or Anglo-Norman. Its use appears to have been limited – the researchers have only found it once, in a thirteenth-century poem by Giolla Brighde Mac Con Midhe.

Another loanword in Modern Irish is turcaí (turkey) but before this was borrowed from English, this bird was known as cearc fhrancach (turkey hen) or coilech francach (turkey cock). Strictly speaking, the adjective Francach means 'French' or 'of French origin'. This usage to denote a bird native to the Americas may seem odd but in other languages, it is associated with various countries including France, for reasons which remain unclear.

Spreading the word

Professor Toner says: “A key aim of our work has been to open the Dictionary up, not only to students of the language but to researchers working in other areas such as history and archaeology, as well as to those with a general interest in medieval life.”

In a related project, the researchers have been developing educational resources for schools in the United Kingdom and the Republic of Ireland.

The Dictionary launched on 30 August 2019 at the Royal Irish Academy, Dublin. A History of Ireland in 100 Words, drawing on 100 of the Dictionary's words and tracing how they illuminate historical changes will be published in October 2019 by the Royal Irish Academy

For more on the newly discovered words, see a piece by Dr Sharon Arbuthnot, a researcher on the project, in the Brainstorm series on National Irish Television (RTÉ).

Researchers from Cambridge and Queen’s University Belfast have identified and defined 500 Irish words, many of which had been lost, and unlocked the secrets of many other misunderstood terms. Their findings can now be freely accessed in the revised version of the online dictionary of Medieval Irish (www.dil.ie).

The Dictionary offers a window onto a fascinating and important past worldMáire Ní MhaonaighNational Library of Ireland, Manuscript G11 403a10. Image, Irish Scripts on ScreenNational Library of Ireland, Manuscript G11 403a10Funding

Work on the Dictionary has been supported by the UK’s Arts and Humanities Research Council. The related project developing schools’ resources is funded by a grant from the University of Cambridge, School of Arts and Humanities Impact Fund.


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YesLicense type: Attribution