Mendeley Data adopts Google Science Datasets standards

Mendeley Data is pleased to announce that we’ve adopted the new Google Science Datasets markup standard for datasets.

For the non-computer science buffs amongst us, this means we describe our datasets in a structured way recognised by Google – which helps Google to index our datasets, and makes them more readily available in their search results.

This also means Google could eventually show datasets in a special way within search results, perhaps by presenting a “rich snippet” for a dataset like the example for a research article below. This makes them more visible and easier to scan by readers.

An example of a “rich snippet” search result, in this case for a research article

 

This applies to all datasets posted so far, as well as any new datasets.

This is all part of our efforts to make the data you share as discoverable as possible by researchers, so that it can be valuable to the community and you can get credit for generating and sharing it.

Any questions, thoughts or suggestions, we would love to hear from you.

 

What a disaster! (but this Pint of Science blog post isn’t one!)

 

Earthquakes don’t kill people; People kill people. That is the (maybe?) controversial statement Ilan Kelman is putting forth in his Pint of Science talk next week. Kelman, a reader at University

Ilan Kelman

College London (UK) and University of Agder (Norway), explains how typical environmental events such as earthquakes and storms are made to become disasters through human actions and decisions.

Mendeley is proud to be partnering with Pint of Science for the third year running.

As an introduction to the great talks on offer we’re going to be previewing some of the most interesting here on the Mendeley Blog, featuring speakers from across all Pint of Science themes. You can follow along on our blog under the tag PintofScience17 or on Twitter under the hashtag #pint17.

You can book tickets to hear Ilan live in London on 15 May or follow him on Twitter @IlanKelman.

 

Saving lives in earthquakes

How many deaths have been caused by earthquakes throughout history? Tens of millions? Millions? Hundreds of thousands? The answer, perhaps, is close to zero.

This response sounds odd. We remember Haiti’s devastation in 2010. Christchurch, New Zealand has not recovered from 2011. Italy, too frequently, has been in the news as rescuers go in after tremors and, sadly, sometimes come out without success. It seems disrespectful to those who died and to those who survived to claim that the earthquakes did not cause the deaths.

Let’s examine more closely what happened during these quakes. Haiti was known to be seismically active. Buildings, from dwellings for the poor to hotels, collapsed due to shoddy construction. Nearly two-thirds of the 185 Christchurch deaths occurred in one badly designed building. Despite Italy’s long history of fatal earthquakes, many structures are not retrofitted.

As many earthquake engineers’ business cards read: Earthquakes don’t kill people; collapsing buildings do.

We know how to design and build all types of structures—bridges, homes, apartments, schools, hospitals, and office blocks—to withstand earthquakes. Sometimes we do and sometimes we don’t.

Corruption, design, and history

On 11 March 2011, a massive, shallow earthquake off Japan’s east coast sent high-rises swaying hundreds of kilometres away in Tokyo and rocked nuclear power plants. The earthquake’s damage was low thanks to exceptional engineering. The tsunami was another story, for both people killed and Fukushima.

We can choose how nature’s forces affect us. Too often, others make the choice for those affected by increasing their vulnerability.

Haiti achieved independence in 1804. Foreign interference marked the two centuries which followed. France demanded post-independence reparations, wrecking Haiti’s economy. The US occupied the country from 1915-1934. A father-son team of externally supported brutal dictatorships dominated after WWII. The Haitian people barely had an opportunity to control their own affairs, including building codes and seismic resistance.

The 2010 earthquake shattered a country wracked by two hundred years of poverty, exploitation, oppression, and underdevelopment. It took this long to create the overpopulated slums and the swathes of poorly engineered or non-engineered structures which crumbled in less than a minute of shaking. Haiti being the poorest country in the Western hemisphere was the cause of death of over 250,000 people, not the tremors.

Around the world, causes of earthquake deaths are shown to be corruption, lack of planning and building regulations, poor monitoring and enforcement of existing rules, inadequate construction, siphoning of funds, exploitation by an élite, and poverty creation. Seismicity is low down on the list of factors correlated with earthquake fatalities.

Seismicity is also the easiest factor to address. Our understanding of earthquakes and engineering is far enough advanced to know how to design and maintain infrastructure to withstand earthquakes. Our understanding of how to ensure that we implement adequate design and maintenance remains woefully lacking.

So people will continue to die in earthquakes. These deaths are caused by human, not natural, factors. The challenge is not about dealing with the earth shaking, but with ourselves.

Further reading:

 

Photo caption:

  • NZ: A base isolator for seismic design at the Museum of New Zealand Te Papa Tongarewa in Wellington (photo: Ilan Kelman).

Conservation at the Bristol Zoo: A Pint of Science preview

African penguins (Spheniscus demersus)

Going to the zoo was always a treat as a kid — and still is for many of us adults! But beyond seeing cute critters is some serious research and conservation work. Dr. Alison Cotton, a lecturer in conservation science at The Bristol Zoo, talks about how this West Country’s zoo has major global impact.

Dr. Alison Cotton

Mendeley is proud to be partnering with Pint of Science for the third year running.

As an introduction to the great talks on offer we’re going to be previewing some of the most interesting here on the Mendeley Blog, featuring speakers from across all Pint of Science themes. You can follow along on our blog under the tag PintofScience17 or on Twitter under the hashtag #pint17.

You can book tickets to hear Alison live in Bristol on 16 May or follow her other talks on Speakezee.

 

Bristol Zoo: A Conservation Tale

As many of you walk past the lemurs or the penguins at Bristol Zoo, what you might not be aware of, is that a team of scientists are working behind the scenes to help conserve these amazing species, and many more besides. This is a very important element of the zoo’s mission, but many people are unaware of the conservation work that occurs beyond the animals on view at the zoo.

We have a great team that work on native species conservation, including those that work at the Avon Gorge and Downs, which is home to over 30 rare plants including many species endemic to the gorge, as well as bats, nesting peregrine falcons and Kashmir goats. Since the education programme for the Avon Gorge and Downs project started in 2001, almost 100,000 people have engaged with local Bristol wildlife on their doorstep. There is also a huge effort being undertaken to help protect the native white-clawed crayfish throughout the South West, as well as a team dedicated to tackling the spectre of invasive weeds, such as Himalayan balsam, in the Bristol area. Internationally, we work across the globe, in countries such as South Africa, Madagascar, Cameroon, Tanzania, Costa Rica, French Polynesia, The Comoros Islands and The Philippines.

The Penguin’s Progress

My work is in South Africa, where the charismatic African penguin has undergone a dramatic population decline of over 70% in the last 17 years, as overfishing and climate change have decimated the fish stocks on which they rely. Our work to date has focussed on supporting our partner organisation in Cape Town, SANCCOB, who rescue, rehabilitate and release penguin chicks, as part of our Chick Bolstering Project, that have been abandoned by parents that are in too poor condition to care for them (as a result of depleted fish stocks), as well as penguins caught in oil spills.

Giving these chicks a head start in life has been hugely successful, and the survival rates of released chicks have been shown to mirror those of parent-reared chicks. In addition, we are heavily involved in research work, including investigating the effect of temporary fishing bans around colonies near Cape Town, monitoring penguin populations on Robben Island and investigating options for the translocation of individuals into new colonies in regions where there are more substantial fish stocks. There is so much work to be done to fully understand this catastrophic decline in penguin numbers, and there is much more than we will be doing in the future, so watch this space!

Like lemurs for chocolate

Golden-crowned sifaka (Propithecus tattersalli)

In Madagascar, the biodiversity situation is dire, with between 80-90% of forests having already been lost to slash and burn agriculture, and with 94% of all lemur species, the charismatic and emblematic primates that are endemic to Madagascar, already threatened with extinction. The human population is very poor, with 92% of Malagasy people surviving on less than US$2 a day. Chocolate and vanilla are both important exports for Madagascar, and much effort is being done to encourage sustainable, under-canopy production methods that minimise negative effects on habitats and biodiversity.

Our team are in the field evaluating the biodiversity impact of different production methods in both cacao (chocolate) and vanilla crops. This will provide a scientific basis to move forward with those practices that promote biodiversity. In addition to this, we are heavily involved in long-term lemur and sacred ibis conservation projects, and reforestation efforts in Madagascar.

It is vitally important that zoos are more than just a source of public entertainment. We are committed to addressing the conservation issues that threatened species face, both in terms of captive breeding of threatened species, but also through our efforts to conserve species in situ, in their natural habitats. With your support, we are doing our best to maintain as much biodiversity as possible on this amazing planet.

Borrowing parts from Nature: A Pint of Science preview post

It is fairly hard to improve upon Nature’s designs. But Pint of Science speaker Adam Wollman is trying. His research combines biology and technology to learn how nature designs it’s molecules and figure how we can learn from and harness it’s perfect design.

Mendeley is proud to be partnering with Pint of Science for the third year running. 

As an introduction to the great talks on offer we’re going to be previewing some of the most interesting here on the Mendeley Blog, featuring speakers from across all Pint of Science themes. You can follow along on our blog under the tag PintofScience17 or on Twitter under the hashtag #pint17.

You can book tickets to hear Adam live in York on 17 May or follow him on Twitter @a_wollman.

(YouTube video caption:  “The nanoscale railway in action. Microtubules in red. Cargo in green.”)

Nanotechnology: Borrowing parts from nature

Nature is very good at building complex things. Plants and animals grow from tiny single cells containing all the information needed to build the organism encoded in DNA.

In contrast, humans need vast factories and machines to build anything near as complex. But to build like nature requires knowledge of biological processes which aren’t fully understood. My research work is split between investigating basic biological processes and using what has been learned to try to build things.

Interrogating biology

I investigate biology using advanced optical microscopes, capable of observing individual molecules at work inside living cells. These microscopes exploit fluorescence where certain molecules called fluorophores emit longer wavelength light when excited by a shorter wavelength. By filtering out the excitation light and only observing light emitted by fluorophores, a very high signal to noise ratio is achieved. Using very sensitive high speed cameras and high intensity lasers, single molecules of fluorophore can be observed.

Most biological processes in cells are driven by proteins, so to observe them, they must be replaced with fluorescent copies. This is done directly at the genetic level, replacing the gene for a protein of interest with a functional fluorescent copy. I’ve used this technique to observe lots different biological processes including DNA replication, cell division and photosynthesis.

Learning to build like nature

The cells in our body are made sturdy through a structure called the cytoskeleton, which is as it sounds: a molecular skeleton inside each cell. It expands out from the nucleus to the edges of the cell in a dense network.

But the cytoskeleton has another role, it also serves as a kind of railway, allowing other protein transporters called motor proteins to transport cargo around the cell. Inspired by this, I tried to employ the same design ideas to build my own nanoscale railway. I extracted motor proteins from cells, as well as the cytoskeleton tracks, called microtubules. To control everything, I borrowed another component from the cell, DNA, using the information carrying capabilities of DNA to instruct the motor proteins. Some of them became assemblers, putting the tracks together into a star shaped network called an aster. Others became shuttles, carrying cargo or other DNA signals into the centre of the aster.

The nano-railway could be used to gather components to speed up chemical reactions or help detect very dilute analytes in a biosensor.

 

 

 

The world’s most diabolical virus: Pint of Science preview

We’re hoping this post goes viral, but only because we’re rabid for the subject. Okay, puns aside, Dr. Kirstyn Brunker’s research into rabies and viruses as part of Pint of Science is a fascinating look at some of the work scientists are doing to solve global hazards.

Mendeley is proud to be partnering with Pint of Science for the third year running. 

As an introduction to the great talks on offer we’re going to be previewing some of the most interesting here on the Mendeley Blog, featuring speakers from across all Pint of Science themes. You can follow along on our blog under the tag PintofScience17 or on Twitter under the hashtag #pint17.

You can book tickets to hear Kirstyn live in Glasgow on 16 May or follow her on Twitter @kirstynbrunker.

THE WORLD’S MOST DIABOLICAL VIRUS

Diabolical literally means “characteristic of the devil”, a term that quite aptly describes one of the most fearsome diseases known to man: Rabies.

Rabies is an infectious viral disease largely transmitted to humans by the bites of infected animals. Domestic dogs are the main culprits, responsible for >95% of human cases. With a fatality rate of nearly 100% rabies has the grim accolade of being the deadliest disease on the planet. Once symptoms appear death is inevitable. These symptoms include: vomiting, confusion, hydrophobia (fear of water), excessive salivation, severe agitation, aggression, hallucinations and paralysis. Descriptions of rabies have included such terms as raging monsters, savage madness and inhuman possession, giving an idea of the terrible trauma it inflicts on victims and their families.

The nightmare and reality

Rabies has established itself in popular culture and mythology as a symbol of evil, inspiring a multitude of books, film and television. An obvious inspiration for vampires, zombies and werewolves it’s responsible for much of the horror film genre! Start to look for it and you’ll find rabies everywhere- Hector’s “strong fury” on the battlefield attributed to a “violent lyssa” (an old name for rabies) in Homer’s epic Odyssey; the symbolism of the rabid dog in Harper Lee’s To Kill a Mockingbird; the rage in 28 days later; Old Yeller

Such is the cultural mythology surrounding rabies it is almost unbelievable as a real-world disease. Yet rabies is still widespread, killing over 59,000 people every year- that’s one person every ten minutes. Perhaps even more unbelievable is that it is entirely preventable via vaccination. Post-exposure vaccination for humans is guaranteed to prevent disease if given promptly after a bite but can be costly and hard to obtain. Alternatively, mass vaccination of the dog population has proven to be an effective, cost-effective means to eliminate rabies in humans. This approach has rid the developed world of rabies but its burden still lies heavily on low- and middle-income countries across Asia and Africa.

A minion for evil

A major stumbling block to rabies control is a lack of adequate surveillance systems that enable resources to be directed effectively. This can be challenging to achieve in resource-limited settings. As a postdoctoral scientist at the University of Glasgow, I work with a dynamic group of rabies researchers across the UK and Tanzania. My research focuses on how we can use genetic information from the virus as part of our surveillance of rabies in Tanzania. Lately this has involved finding ways to do this in the field, using only basic laboratory equipment and limited resources.

Conventional genetic sequencing technologies require expensive equipment, specialist training and state of the art facilities- generally out of the question in the impoverished settings where rabies is most prevalent. Usually samples from Tanzania have to be shipped to the UK for lab work and analysis. This is not only expensive, slow and detrimental to sample quality- it limits capacity building in Tanzania and causes a major lag in feedback to communities.

Step in the minion. No, not the cute little yellow things from that film. The MinION is a pocket-sized genetic sequencer; robust and portable it may help overcome some of these problems. It works by taking electrical current measurements as single strands of DNA pass through nanopores in a membrane, outputting DNA sequence in real-time. I’m hoping to use one as part of a “lab in a suitcase” setup, establishing a ready-to-go genetic surveillance toolkit to use in Tanzania. This will enable rapid feedback to help manage outbreaks.

With a global target to eliminate dog-mediated human rabies by 2030, tools like these are crucial in the fight against rabies.

 

 

Dealing with Dementors: How to Handle Negative Workplaces

 

It seems wholly appropriate to publish a piece on workplace negativity on Wednesday — the middle of the week can sometimes feel impossible to get over, especially when negative colleagues are dragging you down. Can you believe there is a scientific reason for why your aggravating colleague acts the way he or she does? Dr. Alexandra Gerbasi explains in this Pint of Science preview post!

Mendeley is proud to be partnering with Pint of Science for the third year running. 

As an introduction to the great talks on offer we’re going to be previewing some of the most interesting here on the Mendeley Blog, featuring speakers from across all Pint of Science themes. You can follow along on our blog under the tag PintofScience17 or on Twitter under the hashtag #pint17.

You can book tickets to hear Alexandra live in Guilford on 17 May or follow her on Twitter @gerbilocity.

Dealing with Dementors: Handling Negative Workplaces

When people find out that I study negative workplace interactions, I am usually flooded with stories like “This guy I work with Steve is such a jerk. Every time I have to deal with him, I feel like he is sucking out my soul.” It is rare that someone tells me that they work in the best place ever and everything is sunshine and rainbows. This isn’t surprising, given the recent finding that over 50 percent of people experience rude or uncivil behaviour at work on a daily basis. This could lead us to think that we are surrounded by jerks or generally rude people. In that same study, researchers found that less than 5 percent of people are intentionally rude to their colleagues. So, two possible things are going on that small group of people are just going around being horrible to everyone, or the majority of the negative interactions are not intentional, and something else is at the core of those behaviours.

How do people become dementors?

If most people aren’t intentionally jerks, why are they acting that way? Most of the time, it is stress. Again and again, in my research, I see stress as the common cause of the negative behaviours. One common theme I see is people who have been promoted into leadership roles, but do not have the skills to handle the demands. Another common themes are role conflicts, people are constantly being torn in multiple directions and overworked.

What effects do dementors have on the workplace?

Research has also repeatedly shown that negative experiences and interactions are more powerful and involve much more cognitive processing than positive experience, it is no wonder that people are always reflecting on these experiences and individuals. Dealing with dementors reduces individual well-being and increases stress. High performers are likely to leave companies when they have to deal with dementors. Those who can leave are likely to become demotivated and can become dementors themselves. Negative behaviours can spread,

What can you do to manage dementors?

If the dementor is a co-worker, often the easiest thing to do is work around them. People who are consistent dementors become excluded. Building up your social support network is also important, having positive support is essential. If you are the supervisor or manager of a dementor, first, using 360 degree feedback can be useful for the individual, so they can see how their actions are affecting others, simply being aware can make a huge difference. Provide training, if you are dealing with someone who needs skill development, give it to them, and provide the opportunities for them to grow into their role. If the person seems unwilling to change, perhaps they are one of the 5 percent that are intentional uncivil, and it might be time to let them go.

 

 

Beware the Banana Killer! The future of food: A Pint of Science Preview

We’re bananas about our latest Pint of Science post! Sarah Schmidt is previewing her research on Fusarium wilt of bananas and how engineering resistance in bananas is a crucial part of our future food security.

Mendeley is proud to be partnering with Pint of Science for the third year running.

As an introduction to the great talks on offer we’re going to be previewing some of the most interesting here on the Mendeley Blog, featuring speakers from across all Pint of Science themes. You can follow along on our blog under the tag PintofScience17 or on Twitter under the hashtag #pint17.

You can book tickets to hear Sarah live in Norwich on 15 May or follow her on Twitter @bananarootsblog.

The banana killer – How to engineer resistance to a devastating fungal disease of bananas

Every morning, I slice a banana in my breakfast cereals. And I am not alone. On average, every person in the UK eats 100 bananas per year. In other countries, it’s even more. In Uganda, people consume between 3 and 11 bananas per day!

Bananas are the most popular fruit in the world and the fourth most important food staple after wheat, rice and maize. The most traded banana cultivar is called Cavendish. This is the banana you find in supermarkets around the world – medium size with nice curves and a fresh yellow skin. Almost 50% of the bananas grown worldwide are Cavendish. Curiously, the Cavendish variety originates from England. A keen gardener at the Chatsworth estate grew the exotic plant in the greenhouse and named it after his employer Lord Cavendish.

The Cavendish banana became popular in the 1960s, when a devastating epidemic of Fusarium Wilt wiped out banana plantations in Middle America. This Fusarium Wilt epidemic almost led to a complete collapse of the banana export industry. Only the Cavendish banana was resistant and could be grown on the infested plantations.

Take a close look at your bananas!

Unfortunately, a new Fusarium wilt race appeared in the 1990s in South East Asia and this new race is able to infect Cavendish bananas and many other cultivars. Breeding bananas is incredibly time and space-consuming, because edible bananas don’t have seeds. They are so-called virgin fruits that can only be propagated clonally. If you have a close look at your Cavendish banana at home, you will notice the little black dots within the tasty fruit pulp. These little dots are the remnants of the stone-like seeds of wild bananas. Without seeds, breeding new varieties is painfully slow and certainly not fast enough to save the Cavendish.

That’s why I am exploring new ways of combating Fusarium wilt disease by taking leads from the causal agent: the soil-borne fungus called Fusarium oxysporum f. sp. cubense. The fungus infects the plants through the banana roots and grows within the plant’s water transporting system. Banana plants sense this attack and respond by the formation of gummy-like substances that block the transport system and eventually lead to wilting and collapse of the whole plant. This is an overreaction of the immune system that is similar to the fever attacks of a Malaria patient.

Like the Malaria pathogen, the Fusarium fungus secretes small proteins to manipulate the immune system of the host. These proteins are similar to secreted proteins of other Fusarium species that infect, for example, tomato plants. In tomato, some of these secreted proteins are recognized by immune receptors, which results in disease resistance. Using biotechnology, we can transfer the tomato immune receptors into banana to make them resistant against Fusarium wilt in banana. I am also employing the genes coding for small secreted proteins to develop diagnostic tools to identify the fungus in non-symptomatic banana plants. These diagnostics are important to halt the worldwide spread of Fusarium wilt and to prevent its entry to the export plantations in Middle America.

If we don’t prevent it, it will be the end of bananas in the UK.