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.

 

 

Webinar: Gender bias in academic publishing

Join Publishing Campus for this highly anticipated webinar in which three industry experts explore the issue of unconscious bias and its role in academic publishing.

About the webinar

Unconscious gender bias in academia can have a real impact on women’s careers. Whether it’s obtaining a job or publishing a paper, quick judgments made subconsciously by reviewers can have very tangible consequences. In this webinar, you’ll learn the ins and outs of identifying and avoiding the pitfalls of gender bias. You’ll come away with clear evidence of the influence of unconscious bias in peer review, and hear about some of the recent efforts by publishers to reduce it, making the publishing process fairer and more equitable for all.

Attend this event – Thursday 11 May, 2017 – 2 pm BST / 3 pm CEST / 9 am EST

Ask the experts

Join the Gender Bias in Academic Publishing Mendeley group to field your questions to the experts and engage in deeper conversation with other attendees.

Presenter bios

Joanne Kamens is the Executive Director of Addgene, a mission-driven nonprofit dedicated to helping scientists around the world share useful research reagents and data. She holds a PhD in Genetics from Harvard Medical School and founded the Boston chapter of the Association for Women in Science. In 2010, she received the “Catalyst Award from the Science Club for Girls” for her longstanding dedication to empowering women in the STEM fields.

Nicole Neuman holds a PhD in biochemistry from Tufts University, which was followed by a post-doctoral fellowship at Brigham and Women’s Hospital, studying cell signaling. She joined Cell Press in 2012 as Editor of Trends in Biochemical Sciences. Nicole has enjoyed engaging Cell Press in community conversations around gender in the STEM fields, first by organizing a symposium around gender and science and now by co-leading the “The Female Scientist,” a column in the Cell Press blog Crosstalk.

Kate Hibbert holds a degree in Earth Sciences from the University of Oxford and a PhD in Isotope Geochemistry from the University of Bristol. She joined Elsevier in 2015 as a Publisher for its Geochemistry and Planetary Science Journals and has been a true champion for women in STEM.

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.

 

 

Beyond ‘Download Science’: Or How to Not Drown in Data at the AGU

Topic-specific conferences are no longer just focused on research; Data sharing initiatives are now a major part of the discussions happening in research. With Mendeley Data and other Data Management initiatives, we are always looking to learn more, directly from the researchers. Anita DeWaard, Vice President of Data Research and Collaboration for Elsevier, shares how she learned data repositories often struggle with similar issues — and how collaboration can help address those issues.

Beyond ‘Download Science’: Or How to Not Drown in Data at the AGU

I attended my first AGU meeting in New Orleans last fall, with the intention to learn more about informatics, metadata and research data in the Earth and Planetary sciences. For a newbie, this meeting is an intimidating affair where over 25,000 scientists gather to discuss topics ranging from plate tectonics to probabilistic flood mapping, and from solar prominences to paleoclimatology.

Informatics and metadata played a huge role in the program sessions. The Earth and Space Science Informatics Section alone, for example, amounted a staggering 1,200 talks and posters on that topic alone. And that by no means comprises the full extent of sessions about informatics and metadata: for instance, the Hydrology Section has not one but two sessions (with 10 – 20 papers each) on  ‘Advances in Data Integration, Inverse Methods, and Data Valuation across a Range of Scales in Hydrogeophysics’, and the Public Affairs Section hosts ‘Care and Feeding of Physical Samples and Their Metadata’.

It is easy to feel overwhelmed. Yet once I stopped focusing on watching the endless streams of people moving up and down escalators to more and more rooms full of posters and talks (and once I finally retrieved my Flat White after the seemingly endless fleece-clad line at the Starbucks!) I learned that if you just jump in the stream and go with the flow, the AGU is really just a great ride.

I was involved in three events: a session about data discovery, one on Unique Identifiers, and the Data Rescue award, which Elsevier helped organize, together with IEDA, the Interdisciplinary Earth and Data Alliance (http://www.iedadata.org/).

Data Repository issues; Or, how to come up with a means of survival

In the Data discovery session, we had 8 papers pertaining to searching for earth science data. Siri Jodha Khalsa and myself are co-chairing a nascent group as part of the Research Data Alliance on this same topic, very is quite relevant to us in developing our Datasearch platform. It struck me how very comfortable and aware of various aspects of data retrieval the earth science community seems to be, compared to repositories in other domains, who are just starting to talk about this.

The data repositories that presented were struggling with similar issues; how to scale the masses of content that need to be uploaded, how to build tools that provide optimal relevancy ranking over heterogeneous and often distributed data collections, keep track of usage, provide useful recommendations, and offer personalisation services when most search engines do not ask for login details, all with a barebones staff an an organisation that is more often than not asked to come up with means for its own survival.

The end of download science

At the Poster session that evening, it was exciting to see the multitude of work being done pertaining to data discoverability. One of the most interesting concepts for me was in a poster by Viktor Pankratius from MIT, who developed a ‘computer-aided discovery system’ for detecting patterns, generating hypotheses, and even driving further data collection from a set of tools running in the cloud.

Pankratius predicted the ‘end of download science’: whereas in the past, (earth) scientists did most of their data-intensive work by downloading datasets from various locations, writing tools to parse, analyze and combine them, and publish (only) their outcomes, Pankratius and many others are developing analysis tools that are native to the cloud, and are shared and made available together with the datasets for reuse.

Persistent Identifiers

On Thursday, I spoke at a session entitled:“Persistent Identification, Publication, and Trustworthy Management of Research Resources”: two separate but related topics. The first three talks focused on trustworthiness, Persistent identifiers are a seemingly boring topic, that, however, just got their own very groovy conference, PIDaPalooza (leave it to Geoff Bilder to groovify even the nerdiest of topics!).

One of the papers in that session (https://agu.confex.com/agu/fm16/meetingapp.cgi/Paper/173684) discussed a new RDA Initiative, Scholix, which uses DOIs for papers and datasets to enable a fully open linked data repository that connects researchers with their publications and published datasets. Scholix represents a very productive collaboration, spearheaded by the RDA Data Publishing Group, involving many parties including publishers (including Thomson Reuters, IEEE, Europe PMC and Elsevier), data centres (the Australian National Data Service, IEDA, ICPSR, CCDC, 3TU DataCenter, Pangaea and others) and aggregators and integrators (including CrossRef, DataCite and OpenAIRE).

Persistent identifiers combine with semantic technologies to enable a whole that is much more than the sum of its parts, that surely points the way forward in science publishing; it allows, for instance, Mendeley Data users to directly address and compare different versions of a dataset (for some other examples see my slides here).

Celebrating the restoration of lost datasets

A further highlight was the third International Data Rescue Award. This award, the third so far, is intended to reward and celebrate the usually thankless task of restoring datasets that would otherwise disappear or be unavailable. This reward brings together (and aims to support the creation) of a community of very diverse researchers, who all have a passion for restoring data.

This year’s winners, were from the University of Colorado in Boulder. Over a period of more than fifteen years, they rescued and made accessible the data at the Roger G. Barry Archive at the National Snow and Ice Data Center, which consists of a vast repository of materials, including over 20,000 prints, over 100,000 images on microfilm, 1,400 glass plates, 1,600 slides, over 100 cubic feet of manuscript material and over 8,000 ice charts. The material dates are incredibly diverse and date from 1850 to the present day and include, for instance, hand-written 19th century exploration diaries and observational data. Projects such as these tell us the incredible importance of data, especially in times like these, where so much is changing so quickly. Looking at the pictures in the Glacier Photograph Collection shows the incredible extent of glacial erosion between, for instance, 1941 and today, when an entire glacier has simply vanished and offers a grim reminder of the extent to which global warming is affecting our world.

In short, there is a lot out there for all of us to learn from going to the AGU. Earth science is abuzz with data sharing initiatives: there are exciting new frontiers to explore, important lessons to be learned, and invaluable data to be saved.