Bookkeeping or science: what’s behind a paleo data compilation?

Guest blog by Darrell Kaufman, Northern Arizona University, US

Here Professor Kaufman talks about the importance of community-endorsed data compilations for accelerating discovery in paleoclimate science. He helped coordinate an international consortium that assembled “A global multiproxy database for temperature reconstructions of the Common Era”, which was published on 11 July in the journal Scientific Data. You can read it here

A respected colleague of mine once told me that compiling data was a task better left to bookkeepers. He’d rather focus on ‘science.’ Granted, that was before the term ‘informatics’ had appeared on the scene, and prior to the massive buildup of data we now face. But his sentiment still rings in the inevitable criticism of my grant applications in which I propose to assemble a database of existing data: rehashing other people’s old data is one rung down on the intellectual ladder. If one needs to borrow data from a previous study, one just contacts the public data repositories.

I contend, however, that there’s more scientific ingenuity to a well-crafted ‘data compilation’ and more coordination behind a ‘community endorsed’ data product than meets the eye.

My experience with the development of the Past Global Change’s (PAGES) 2k paleo-temperature dataset, which was just released through the journal, Scientific Data, is a case in point. PAGES aims to improve understanding of past climate variability; within this program, PAGES2k focuses on the past 2000 years—the Common Era (CE)—a period when climate was relatively similar to today and for which records based on ‘paleo’ records (evidence from natural archives that attest to climate change prior to the instrumental period) are relatively abundant. But to start, I first need to define a ‘paleo data compilation’ and to provide some background to the topic.

Motivations for a paleo data compilation

The first step to securing data resources for any scientific community is to establish a long-term, well-organized data repository. Fortunately for the paleoclimate community, several first-rate data repositories actively curate relevant data.

The theoretical next step is to mine the archives to extract the data needed to address a particular research question, such as the pattern of surface temperature change over the planet during past two millennia, the purview of the PAGES2k project.

When doing so, however, my data-hungry colleagues and I have discovered that the repositories contain an uneven and incomplete sampling of the huge variety and long legacy of observational datasets that have been interpreted in terms of past climate. We also found that key metadata and other data needed to assess uncertainties are missing in many cases, hampering the reuse of the data.

The high proportion of unavailable, inconsistently formatted or incompletely documented data motivates some paleoclimate researchers to assemble datasets that target a particular scientific question. They might start with data from existing archives, but then add missing records, fill in fundamental information, provide quality control and standardize the format and vocabulary so the contents can be easily ingested by computers.

These paleo data compilations accelerate scientific discovery on several fronts. For example, they often point to future scientific priorities through recognition of crucial gaps. They enable us to avoid over reliance on select records while proving an objective means to recognize aberrant or misinterpreted records through systematic comparison against the full body of other available recordsAnd, they lend themselves to quantitative analyses by multiple researchers who can apply a suite of different approaches to solve a research question, all using the exact same set of records.

Maximizing its scientific value

Such data compilations have great utility in paleoclimate science, but considering the enormous amount of work involved, how do we make the best use of limited resources to maximize the scientific outcome? Addressing this question has been one of the most rewarding scientific challenges of my career.

The iterative process involves identifying the most substantial scientific questions, then adapting them according to what can actually be answered based on the existing data, which isn’t known at the outset, and also fitting them to what is doable given the person power available to assemble the data, which is a major limitation. Additional questions, including those that are lurking beyond the scientific horizon, are brought into the mix, especially if they could be tackled through an incremental additional effort to expand the dataset.

The endeavor becomes more scientifically challenging in light of the large variety of information sources about past climate, including tree rings, coral, glacier ice, and marine and lake sediments, not to mention the complicated array of data that are used to establish the timelines that underlie the paleoclimate records. Organizing a disparate assortment of data into a uniform and unified database requires a wide-ranging appreciation of the variety of data and the questions that they might usefully address, now and into the future. It requires a coordinated community of collaborative specialists.

Promoting it as a community product

A bone fide ‘community endorsed’ data product, especially one that seeks to gather evidence about worldwide phenomenon, is based on an extended international effort. The process must be open, but not a free-for-all. Participants need avenues for genuine engagement and explicit credit for their contributions.

The PAGES2k paleo temperature database project was coordinated through the PAGES International Project Office in Switzerland. PAGES is a core project of Future Earth and is funded jointly through the US National Science Foundation and Swiss Academy of Sciences.

PAGES actively maintains a large directory of paleoclimate scientists, all of whom were invited to participate in the data compilation. This process gathered 98 volunteers from 22 countries to represent the paleoclimate community. Most of the authors contributed new data and many certified records as appropriate for inclusion in the database, including whether they met some basic quality criteria.

Some authors also annotated individual records according to their expert judgment and, in some cases, included cautionary notes about alternative or evolving interpretations. Their expertise and their identity will travel along with the data, in hopes that the data will be used wisely. In my view, the inclusion of expert’s comments and other documentation needed for intelligent reuse of paleo data is the most important development in the PAGES2k database.

To incorporate these and other innovative features, the PAGES2k database is contained in the highly flexible Linked Paleo Data (LiPD) format, which was developed along with the database itself. LiPD can accommodate the unlimited variety of data types used by paleoclimate scientists, including chronological data. A systematic version scheme has been established to track revisions as new data are added or existing records are modified. The data have also been loaded onto the LinkedEarth data-management platform, which enables transparent discussions of the evolving interpretation and versioning of individual records, and is supported by the first paleoclimate ontology.

It’s difficult to foresee how data-handling practices will evolve in the rapidly changing, cyber-based, data-management landscape. Yet one thing is for certain: it will be in the direction of taking better care and making better use of our scientific data assets, regardless of whether it’s considered tedious bookkeeping or challenging science.

Looking back: Toxic PCB levels in European orcas and other dolphins

Guest blog by Paul Jepson, Institute of Zoology at the Zoological Society of London (ZSL), UK

Earlier in 2016 Scientific Reports celebrated its fifth anniversary. You can view our interactive infographic and blogs marking this occasion here.

As this fifth anniversary year draws to a close, we’ve got back in touch with authors from two popular papers from recent years.

Now that some time has passed, we wanted to know about their experience publishing with the journal, what impact they felt their research has had and if there’s been any surprises along the way.
Last week we posted an interview with Alex Greenwood, author of the study “Anti-NMDA Receptor Encephalitis in the Polar Bear (Ursus maritimus) Knut”.

In this blog, we’ve spoken another Scientific Reports author: Paul Jepson. In January 2016, Dr Jepson and his colleagues published the study “PCB pollution continues to impact populations of orcas and other dolphins in European waters” in Scientific Reports.

Here’s what he had to say about the research.

Could you give a brief overview of your study?

The few remaining killer whale populations in European waters have very low, or zero rates of reproduction, and are close to extinction in industrialised parts of Europe. Polychlorinated biphenyls (PCBs) are chemical pollutants which were banned in the EU in the mid-1980s, but after an initial drop in concentrations following the ban, they have now stabilized across Europe in humans, fish and wildlife.

The goal of the study was to assess the exposure to — and likely effects of — specific chemical pollutants including PCBs in European whales, dolphins and porpoises (cetaceans). We found that PCBs were at excessively high concentrations in the blubber of several marine apex predator species across Europe, including killer whales and bottlenose dolphins, and were associated with long-term and on-going population declines.

Our results suggest that much more work is needed to mitigate PCB contamination of the marine environment, and to comply with the Stockholm Convention that requires the reduction and eventual elimination of large sources of PCBs and other persistent organic pollutants.

What impact would you say your paper has had?

The paper was only recently published but it has been widely reported in newspapers and by other media, globally. The PCB issue — as based on our paper — also featured on the BBC current affairs programme Newsnight.

A public meeting about PCBs in killer whales and dolphins in Europe was held at the Zoological Society of London (ZSL) in March, where I spoke along with two other speakers. The meeting had the second largest audience for a ZSL public meeting ever and, after a lively Q&A session, Professor Ian Boyd, Chief Scientific Adviser at the Department of Environment, Food and Rural Affairs, closed the event.

This new cetacean PCB data has quickly fed into various international scientific and policy forums, including the Working Group for Marine Mammal Ecology (WGMME) of the International Council for the Exploration of the Seas (ICES). The recent ICES WGMME report (2016) concludes that PCBs pose the greatest threat to bottlenose dolphins and killer whales throughout the Northeast Atlantic region. The ICES also provide rigorous scientific advice to the Convention for the Protection of the Marine Environment of the North-East Atlantic (OSPAR) — including EU compliance with the Stockholm Convention.

Were any of your findings unexpected?

The main finding that very high PCB concentrations still persist in Europe — over three decades after the EU ban on PCB use / manufacture — has surprised a lot of people, including scientists who thought the ban would result in a gradual decline in PCBs in all biota. In fact, Europe has the highest PCB exposures in the marine environment globally. The very low reproductive rates in some of the highly PCB-contaminated resident/coastal bottlenose dolphins and killer whales are highly consistent with known PCB effects on reproduction. This is a very depressing finding, because if an apex predator population effectively stops reproducing, it will eventually disappear.

Another surprise was the very high PCB exposures in bottlenose dolphins and killer whales around the Iberian Peninsula. We have known that the Mediterranean Sea has been a pollution hotspot for many years, but the very high PCBs levels in bottlenose dolphins and killer whales on the Atlantic side of the peninsula also rather surprised us. Clearly action is urgently needed to dispose of large stocks of PCB-contaminated materials, especially in France and Spain.

Was there a particular reason you chose to publish in Scientific Reports?

The journal is highly respected and open access.  It also takes longer papers and so we were able to include more results and a longer discussion. After submission, the Scientific Reports review process was very rigorous but fair. The referee’s comments improved the final manuscript, including the statistical treatment of the data. Shortly before publication, the journal Press Office held an international telephone conference for science journalists to attend — this undoubtedly helped the paper to obtain the excellent and high-quality media coverage that followed publication.

Dr Paul Jepson is a Reader at the Institute of Zoology at the Zoological Society of London (ZSL) and is the main grant holder for the UK Cetacean Strandings Investigation Programme (CSIP) funded by the UK Government. He is a European Veterinary Specialist in Wildlife Population Health and has worked on pathological and other investigations into stranded marine mammals since 1993 and stranded marine turtles and basking sharks at ZSL since 2002.

Looking back: The mystery of Knut, the famous polar bear

Guest blog by Alex Greenwood, Leibniz Institute for Zoo and Wildlife Research (IZW), Germany

Knut the polar bear

Berlin Zoological Garden

Earlier in 2016 Scientific Reports celebrated its fifth anniversary. You can view our interactive infographic and blogs marking this occasion here.

As this fifth anniversary year draws to a close, we’ve got back in touch with authors from two popular papers from recent years.

Now that some time has passed, we wanted to know about their experience publishing with the journal, what impact they felt their research has had and what’s surprised them.

First up, here is an interview with Alex Greenwood, an author of the study in Scientific Reports that suggested Knut, the famous hand-reared polar bear from the Berlin Zoological Gardens, suffered from anti-NMDA receptor (NMDAR) encephalitis. The study “Anti-NMDA Receptor Encephalitis in the Polar Bear (Ursus maritimus) Knut” is available here.

We spoke to Professor Greenwood about the research.

Alex Greenwood

Could you give a brief overview of your paper in Scientific Reports?

Our study in Scientific Reports was the culmination of our efforts to determine what caused the death of Knut, the world famous polar bear. A necropsy performed at the Leibniz Institute for Zoo and Wildlife Research (IZW) determined that Knut had inflammation of the brain (encephalitis) and suggested the cause was an infectious agent. However, intensive, cutting-edge pathogen diagnostics immediately after necropsy did not identify any causal pathogen. The negative results required completely new thinking and approaches; among the candidates was an autoimmune disease.

Similar to Knut’s case, many human medical cases went undiagnosed for decades because a causative pathogen could not be linked to the symptoms of encephalitis. In 2007 it was revealed that many of these patients suffered from an autoimmune disease (where the patient’s antibodies attack their own brain as foreign material). The most common among these diseases is anti-NMDA disease — where the patient’s antibodies attack the N-methyl-D aspartate receptor in the brain, leading to severe inflammation. The team of Dr. Harald Prüß at Charité/German Center for Neurodegenerative Diseases (DZNE) Berlin, who are experts on these diseases, reasoned that this could potentially explain Knut’s case. After extensive testing, the teams at the IZW and Charité determined that this in fact is what explained Knut’s encephalitis.

What sort of impact have your findings had?

Anti-NMDA disease is now more broadly recognized among the public because of its association with Knut. This will hopefully lead to improvements in diagnosis of this and related diseases, particularly because in humans the presentation of the disease can be quite variable.  Zoo and wildlife veterinarians have realized that not all diseases, even those where a pathogen is suspected, will necessarily be the result of infectious diseases and that management practices may have to take this into consideration. For example, the counterintuitive management strategy in such an encephalitis case would be to suppress the immune system — not a therapeutic intervention one would necessarily consider in the case of a pathogen caused disease. At the very least, it is quite likely that new cases in more species will be identified, expanding this disease’s occurrence to mammals in general. Others have already seen rarer neuronal receptor diseases in domestic cats. These diseases are unlikely to be restricted to cats and polar bears.

Was there anything surprising about this research?

Upon taking on Knut’s case, the flood of expert opinions, all supporting an infectious pathogen as the cause of Knut’s symptoms, was deafening. It was interesting to see how this guided so many of the contributions from collaborators and spectators. In many ways this narrowed the number of avenues initially investigated. We tried to keep an open mind but some of the ideas we had — including an aberrant immune reaction — were beyond what we thought is amenable to study in wildlife diseases, given that so much less is known about wildlife biology than human or laboratory animal biology.  Many of the techniques we considered would have likely yielded data difficult to interpret, without the fundamental knowledge of, for example, which proteins are expressed where in a polar bear.

Their sharp eyes and the constructive collaboration with Dr. Harald Prüß and his team made it possible to consider the improbable — and demonstrate that the improbable was in fact the answer. The ability to transfer the techniques from human medicine to a polar bear case was both unusual and extremely fortunate.

Was there a particular reason you chose to publish in Scientific Reports?

The study performed, in essence, represents a case report. Scientific Reports recognized that the findings in this case go well beyond Knut as an individual and allowed it to be peer reviewed. The identification of this disorder, which before Knut was only recognized as a human disease, must now be considered a disease of mammals with consequences for diagnosis and management in veterinary medicine in particular. Because Scientific Reports is open access this means anyone who is confronted with a similar case and suspects an autoimmune disease can refer to our study and our methods with no barriers to access. This was an important element in our consideration of where to submit the manuscript.

Professor Alex D. Greenwood is the Head of the Department of Wildlife Diseases at the Leibniz Institute for Zoo and Wildlife Research (IZW) and Professor of Wildlife Diseases in the Department of Veterinary Medicine of the Freie Universität Berlin, both institutions in Berlin, Germany. His work has focused on evolutionary virology, primarily on retroviruses and more recently herpes viruses in wildlife. He integrates ancient DNA, evolutionary and ecological analyses in most of his work and also has an interest in high throughput diagnostic methods. His work with Knut the polar bear intersected with the latter interest.

On Friday (23 December) we will post a second guest blog from another Scientific Reports author. 

Genetic variants in ‘red hair gene’ associated with increased number of skin cancer mutations

Carla Daniela Robles Espinoza, author on the Nature Communications paper

Carla Daniela Robles Espinoza

Mamun Rashid

Melanoma patients with genetic variants in the ‘red hair gene’, MC1R, have more mutations in their cancers compared to patients without such variants, found a study published in Nature Communications last week. Carla Daniela Robles Espinoza, one of the authors on the paper, takes us through the findings.

What were your main findings?

In this study, we wanted to investigate whether having common genetic variants in the red hair gene (called MC1R) can influence the number of mutations found in melanoma tumours. It has long been known that redheads are more prone to developing melanoma.

A woman with red hair using a camera, taking a photograph, adjusting the lens.

Melanoma patients with genetic variants in the ‘red hair gene’, MC1R, have more mutations in their cancers.

Getty Images

This is thought to be because they burn more easily in the sun, as exposure to UV light is one of the main risk factors for developing this cancer. However, there seems to be more to the story of how MC1R genetic variants increase the risk of developing melanoma. For example, previous studies have shown that, in mice, there is a sunlight-independent contribution to melanoma risk via the synthesis pathway of the red pigment1, and that there is an association between MC1R and melanoma risk which occurs independently of sun exposure in humans2.

Here, we analysed the melanoma tumours from more than 400 patients and observed an increase in the number of mutations in patients carrying variants in MC1R. This effect was observed also in individuals that are not necessarily red-headed (those with only one variant copy of the MC1R gene as opposed to two), which means that these people might also be highly susceptible to the mutagenic effects of UV light. However, we observed this increase in all types of tumour mutations, not only the ones associated to UV damage.

We could also quantify this contribution, noting that the expected number of sun-related mutations associated with an MC1R variant is comparable to the number gained in about 21 additional years of age. Therefore, our study provides evidence of the existence of additional mutagenic processes in melanoma patients with MC1R variants, which make up about 26-40% of the patient population3.

How does this work link melanoma and the gene MC1R?

Many studies had noted that people carrying MC1R variants are more susceptible to developing melanoma, but only recently we have started to fully understand the reasons. We provide evidence that there may be additional mechanisms, beyond the effects of UV alone, that contribute to elevating the risk of melanoma in patients with MC1R genetic variants. MC1R has important roles in DNA repair and cell survival; thus, processes that increase the risks of developing cancer might include the generation of DNA-damaging stress when making up the red pigment or a decreased ability to repair DNA in carriers of MC1R variants.

In this study we also report that primary melanocytes (the cells where melanoma originates) with incomplete MC1R function show defects in survival and DNA repair, suggesting this might be one of the mechanisms through which MC1R function impacts melanoma risk.

The distribution of mutation counts in melanoma tumours grouped by the presence of MC1R variants.

The distribution of mutation counts in melanoma tumours grouped by the presence of MC1R variants.

Carla Daniela Robles Espinoza et al., Nature Communications

What is the significance of this research for melanoma patients and for the general population?

The conclusion of our study is important because it has relevance for people who are MC1R carriers (for example, about 21% of the British and Irish population, 10% of the French population and 16% of the population in the United States4). This means that the majority of these people, who will not have red hair, are still more susceptible to the effects of melanoma mutagens than people with no MC1R variants, with UV light the most established environmental risk factor.

The results suggest that MC1R carriers should take care in the sun following established guidelines (for example: http://www.cancerresearchuk.org/about-cancer/causes-of-cancer/sun-uv-and-cancer/ways-to-enjoy-the-sun-safely).

Can you outline any future research steps?

Future research will aim to understand the different processes through which MC1R can increase the risk of developing melanoma, and also to look for other genetic contributors to skin cancer predisposition. This will hopefully help us to identify the people who are at increased melanoma risk and allow us to better inform patient management and public health campaigns.

References:

1. Mitra D et al. An ultraviolet-radiation-independent pathway to melanoma carcinogenesis in the red hair/fair skin background. Nature. 2012 Nov 15;491(7424):449-53. doi: 10.1038/nature11624. Epub 2012 Oct 31.
2. Wendt J et al. Human Determinants and the Role of Melanocortin-1 Receptor Variants in Melanoma Risk Independent of UV Radiation Exposure. JAMA Dermatol. 2016 Apr 6. doi: 10.1001/jamadermatol.2016.0050. [Epub ahead of print]
3. Williams, P. F., Olsen, C. M., Hayward, N. K. & Whiteman, D. C. Melanocortin 1 receptor and risk of cutaneous melanoma: a meta-analysis and estimates of population burden. Int. J. Cancer 129, 1730–1740 (2011).
4. Gerstenblith MR et al. Comprehensive evaluation of allele frequency differences of MC1R variants across populations. Hum Mutat 2007 May;28(5):495-505. doi:10.1002/humu.20476

Celebrating impact: How multidisciplinary One Health research produced results for real change in the real world

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Guest post by Naomi Marks, project communications manager at the Institute of Development Studies. She managed the communications for the Dynamic Drivers of Disease in Africa Consortium and now works with two other multidisciplinary zoonoses-related projects, the Myanmar Pig Partnership, and Livestock, Livelihoods and Health.

With the end of a large research project, there can be a certain sense of bathos. All that ambition at the beginning culminating in … what? Published papers in scientific journals, conference presentations on Slideshare, a website that you hope will continue to be updated and, well, the move on to the next project.

None of this is to put down traditional academic outputs, only to acknowledge the desire of most scientists to see science really make its mark.

This is particularly true when it comes to research in developing countries where there is not just a real pressure from the funders, but also a strong desire from the researchers to contribute to real change in the world—or “impact“, as we all now know it.

And so it is with real pleasure that at the end of the large research project that I’ve been working with that I can report that we seem to have avoided that plummeting feeling.

Dynamic Drivers of Disease

The Dynamic Drivers of Disease in Africa Consortium focused on diseases that pass from animals to people—those such as Ebola, Zika and avian flu that have led to so many headlines in recent years. It sought to explore the links between these diseases (known as zoonoses), ecosystems and poverty, and, in particular, how wider global patterns such as climate and land-use change affect how diseases emerge and spread.

A multidisciplinary undertaking, the project included environmental, biological, mathematical, social, political, and animal and human health researchers from 21 partners across three continents and eight countries—working not just alongside each other but also integrating their findings in new and exciting ways.

As if this wasn’t enough of an endeavour in its own right, other challenges came up over the four years of the project—some welcome (our lead researcher became Director of the Institute of Development Studies, adding to her workload considerably); some expected—or at least expectant (our pivotal research manager went on maternity leave); and one truly unexpected and ghastly: our Sierra Leone team, researching Lassa fever, had to stop work when the Ebola epidemic of 2014/15 resulted in movement restrictions in that country, and laboratory and clinical facilities were turned over to crisis Ebola work.

Despite all this, the project can claim to have contributed to real notches on the impact post.

Particularly notable is the creation of new, detailed risk maps for Rift Valley fever (RVF). These have already been put to use, forming an essential element of the Kenyan government disease monitoring and containment strategy when an epidemic threatened late last year. In the past, RVF epidemics have led to the deaths of millions of animals and hundreds of people with huge poverty impacts for pastoralists.

Also of note has been the identification of the patches of land to which tsetse flies are increasingly being confined in the Zambezi Valley in Zimbabwe. Tsetse are the insect vector of the trypanosomiasis parasite which causes disease in animals (with major knock-on effects on the farmers who are financially dependent on their livestock), and sleeping sickness in people (fatal when not properly treated). This has major implications for Zimbabwe’s tsetse control measures which have, in the past, targeted huge swathes of landscape. The research shows more targeted efforts will not only be more effective but also cheaper—and these findings are now being fed into the policy process.

Tseste sampling in Zimbabwe

Tseste sampling in Zimbabwe (credit: Prof. Vupenyu Dzingirai)

Even in Sierra Leone where much of our work was necessarily curtailed, the anthropological research carried out pre-Ebola epidemic into the socio-cultural beliefs and practices surrounding infectious diseases found unexpected application during the epidemic. Much of it fed into an online platform delivering real-time evidence-based advice to organisations such as the World Health Organization, Department for International Development (DFID) and the UN Mission for Ebola Emergency Response (UNMEER).

To note all this is wonderful—and please do look at our other success stories—but some provisos are important. Impact is non-linear, takes time and can be hard to measure; some of our most compelling impacts (including those above) weren’t necessarily those we anticipated, while others—such as our original hope to facilitate more joined-up “One Health” interventions—require ongoing stakeholder engagement that will inevitably take time to filter through.

Also—and importantly—impact doesn’t happen on its own. The Dynamic Drivers of Disease in Africa Consortium, which was supported by the Ecosystem Services for Poverty Alleviation programme, had impact at its heart. It was stressed throughout the research process from conception workshop to final symposium.

So much science, both of the natural and social variety, is intrinsically fascinating. To make it worth celebrating too is a wonderful thing.

The impact stories from the Dynamic Drivers of Disease in Africa Consortium can be viewed at: bit.ly/One_Health_stories

Connecting patients and clinicians: Why patient perspectives matter in research

Vanessa-Smith-headshot

Vanessa Smith is a patient activist working to raise awareness of chronic obstructive pulmonary disease (COPD) and the importance of the patient voice within the medical and research community. Vanessa has severe COPD and recently wrote a patient perspective which was published in npj Primary Care Respiratory Medicine, an online-only, open access journal devoted to the management of respiratory diseases in primary care. She writes about living with COPD on her blog, COPD in Focus, and can be found on Twitter @vancopd.

Tell us about your experience with chronic obstructive pulmonary disease (COPD).

I was diagnosed with severe COPD during the winter of 2008/2009. Although I’d had chest infections over the last ten years, I’d never heard of COPD, so the diagnosis came as a real shock: “It’s caused by your smoking. There’s no cure and you’ll get worse. You may have only another two years.”

It was a bleak time. I was 53, recently widowed, and had a 13-year-old daughter who was still in school. I had no idea what the future would hold and was terrified of leaving her an orphan. The burning thought in my head was that whatever happens, I have to stay around long enough to see my daughter reach adulthood and finish university with a good starting point in life.

That was what really drove me online to find out anything and everything I could about COPD. The NICE guidelines were a starting point in telling me what I needed—the flu jab, pneumonia jab and pulmonary rehabilitation to learn how to breathe with my condition—but there wasn’t much else. I used to stay up until four in the morning, looking for scientific research that could offer me clues on how to cope with the disease. I read everything I could get my hands on and made a point of putting into practice what I found—if I read about the most effective exercises to prevent muscle wasting, I started doing those every day.

“I used to stay up until four in the morning, looking for scientific research that could offer me clues on how to cope with the disease.”

This was seven or eight years ago when research was far less open access than it is now. Sometimes I found older papers to download, but the most up-to-date research was always behind a paywall. It wasn’t just the cost of paying for articles that was the trouble—many journals required subscription, which I’d do, but some would ask which hospital I worked for and I wouldn’t be able to access those papers as a result.

Having access to the most up-to-date scientific research is very important to me, because it was through reading the latest research that I discovered my prognosis—two to five years’ life expectancy—was based on old information. By taking measures such as the flu shot and exercising regularly, people are living 10, 20, even 30 years these days. The science showed me ways to cope with my disease that I didn’t otherwise know about.

npjPCRM_banner_1000px

You recently wrote a patient perspective in npj Primary Care Respiratory Medicine on the practicalities of living with oxygen as a COPD patient. What prompted you to write this?

I completed the European Lung Foundation’s European Patient Ambassador Programme, which taught me how to represent people living with my condition when interacting with healthcare professionals, policymakers, researchers and journalists. The ELF passed on a request from one of the editors who was looking for someone willing to write on what it’s actually like to live with oxygen. Writing the patient perspective wasn’t any harder than other things I’ve done, like an event summary or a blog post—the hardest part was really keeping it so simple and short!

Why do you think the patient perspective is important?

The patient perspective is an opportunity for healthcare professionals to get feedback on things they don’t always hear. A GP could prescribe the best inhaler for you, but not know how you live with it and if you’re complying with it. If you’re not complying with it, is it because you have a swallowing or breathing issue? Do you have trouble handling the inhaler because you have rheumatoid arthritis in your hands, but don’t like to say?

By prioritising patients in research, doctors will know better what matters most to the people they are treating. In the arena of lung cancer, breast cancer and heart disease, there are some fantastic patient organisations which give voice on behalf of their patients, but for disorders like COPD which don’t have a specific organisation in the UK, patient perspectives offer a space for us to speak up.

What do you want COPD researchers to keep in mind when researching and publishing?

Be as generous and as open as possible with your work—the more you share information with your peers, patients and fellow healthcare professionals, the sooner we’ll be able to move forward in treating and curing COPD, which is the most underfunded disorder based on disease burden.

Clinical trials need to better reflect the real COPD population. Too often, trials focus on men with moderate COPD and no comorbidities. Very few patients are as lucky as I am and have only COPD—many will also have heart disease, diabetes, or lung cancer. We need more representative patient populations in the research: male and female, those with severe COPD or not, and a range of comorbidities.

What can publishers do to support and engage patients?

Make more research open access so that more people can benefit from the findings, from individual patients like me, to patient organisations that don’t have a budget for journals subscription. Developing countries like India have high levels of COPD so open access also helps doctors and patient organisations working there who otherwise wouldn’t be able to read the research.

Publishers should raise awareness of patient perspectives; most patients probably don’t know these even exist. It would also be good to have more diversity of voices. The patient perspectives I’ve seen in science journals are often written by well-educated, working professionals, but patients often get diseases like COPD in later life when they’re no longer working. They may not have advanced degrees, but they do have real knowledge about living with their disease. We need to see patient perspectives as opportunities for both patients and researchers to learn from each other.

Do you have any tips for other patients on writing patient perspectives?

  1. Only write about what you know about.
  2. If you have a brief, stick to it. It will keep you focused and make the article so much easier to write.
  3. Don’t go over the suggested word count.
  4. Be confident in your ability. Remember you’re writing as a patient from the patient perspective. This gives valuable insight to academics and researchers and healthcare professionals. They’re not expecting you to write an academic article.
  5. Remember it’s OK to ask for help. While you know your illness, no one expects you to know about the publishing process.

What’s next for you?

The European Lung Foundation is starting a new module on patient involvement in research within the next month. I’m looking forward to taking that and finding out how patients can be more involved with research—it’s something I’d like to do more of.

Vanessa-greatnorthrun

Completing the Great North Run half marathon for COPD