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Prof. Rolf Georg Beutel: “The established data base will continuously grow and extend, integrating an ever increasing number of open access studies.”

In line with the recent beetle boom on ScienceOpen, a researcher led collection on Coleoptera has been created on ScienceOpen.  In the following interview founder and editor of the collection, Rolf Georg Beutel (Professor of Zoology at the Institut für Spezielle Zoologie und Evolutionsbiologie, Jena) will share a little background and gives us an insight on how it works in practice, how such thematic collections serve research communities. And of course, he will also reveal why beetles are cool.

Hi Rolf, thank you for joining. Can you first tell us a bit about your research background, and how you originally got interested in Entomology? Why did you choose to study Coleoptera?

I must admit that in contrast to many other entomologists I was not interested in insects at all as a child or later as a student of Zoology at the University of Tübingen. I was clearly inspired by an eccentric but outstanding academic teacher, Dr. G. Mickoleit, who suggested I should investigate the head and mouthparts of a very small and very cryptic beetle larva. Even though I had a hard time with my first objects of study, I obviously got hooked and continued studying beetles and other insects for the rest of my scientific career.

Why did you decide to build a ScienceOpen Collection on Coleoptera?

Dr. Stephanie Dawson, whom I have known for more than 10 years, mainly in the context of the Handbook of Zoology series, suggested to me to establish this ScienceOpen collection on beetles. My positive previous experience with her expertise and also with ScienceOpen was confirmed by the impressively efficient process of building and presenting this collection.

Coleoptera is one of the first automatically synchronized collections on ScienceOpen. What were the main principles of building the collection and how it develops?

Coleoptera is an immensely diverse and popular group. The intention was to go beyond the traditional fields of taxonomy and morphology, even though these have certainly their merits and are still very important in different contexts. The established data base will continuously grow and extend, integrating an ever increasing number of open access studies.

Do you have favourite pieces or lines of research in the collection that you find especially relevant to this field? 

Primarily I consider myself as a systematist, and therefore I am interested in articles on phylogeny and classification in the first place. Even though many publications in these fields are older and not available as electronic files (or not covered by open access), the new collection already provides an impressive number of relevant studies and will grow with an accelerated rate in the future.

As an evolutionary biologist dealing with beetles among other groups of insects, I appreciate that the data base covers multiple lines of research, as for instance genetics or physiology. This has the potential for reciprocal stimulation of researchers of Coleoptera, beyond the basic disciplines like systematics and taxonomy. These are indispensable tools in biodiversity research and provide an essential reference system for studies in other fields. Connected with topics like for instance the physiological and genetic backgrounds of feeding habits or reproductive biology, evolutionary biology of Coleoptera is getting really exciting. The very rapidly growing molecular data in the “age on phylogenomics” open fascinating perspectives in the investigation of beetles and other organisms.

In which ways your research community benefits from the collection?

The easy accessibility of open access articles on beetles is an obvious advantage of this collection.

Finally, tell us about what is the coolest thing in studying entomology?

Beetles are often very beautiful insects and have attracted attention very early, for instance as religious symbol (Scarabaeus sacer) or material for jewellery, or also simply as food source.  Among amateur collectors, who made valuable contributions over the last centuries, only butterflies enjoy a comparable popularity. Talking about what is cool about Coleoptera, it is hard to avoid a statement made by the geneticist and evolutionary biologist J.B.S. Haldane, who allegedly said that God had an “inordinate fondness of beetles”. This mainly refers to the incredible diversity of the group, which presently comprises approximately 380.000 described species, about one-third  of all known organisms. The question why Coleoptera was much more successful (in terms of species numbers) than other groups is an intriguing question in itself for evolutionary biologists. Aside from this, beetles are an integrative part of nearly all terrestrial and limnic habitats. Many species are important plant pests but others beneficial as natural enemies of harmful species.  What fascinates me most is that after centuries of research crucial phylogenetic issues are still unsolved, like for instance the interrelationships of the 4 extant suborders (“it is the glory of God to conceal things….”). Presently exponentially growing molecular data sets and improved analytical approaches (www.1KITE.org) provide new powerful tools to resolve these issues. This is definitely “cool” and exciting!

Thank you, Rolf, it’s been great getting your insight!

(Credit: U.Schmidt, Flickr. CC BY 2.0)

Got inspired? You can create your own thematic collection by following these steps.

 

Judicial Tyranny or American Justice? Guest post by Lisa Matthias

‘Research hasn’t been completed until it has been properly communicated.’ This is one of the great mantras of Prof. Sir Mark Walport, Chief Scientific Adviser to the UK government. What this means is that all research needs and deserves to be communicated to as wide an audience as possible, and published in an accessible format, in order to maximise its potential impact. To that end, we asked Lisa Matthias, who recently published her Master’s research with us at ScienceOpen, to tell us more about her work and what she found. Here’s her story!

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Recently, I published my Masters thesis all about the politicization of US Supreme Court by partisan media. The background behind my research is that partisan news outlets cater their reports to specific partisan groups that have distinct ideological beliefs. These channels broadcast one-sided coverage, which constantly reinforces and strengthens their target audience’s political beliefs, while adopting a hostile position towards opposing views at the same time. This is most deeply highlighted in the US because of the highly polarising nature of the two-party political system.

To achieve such one-sided reporting, news stories are framed. Framing refers to how a story is told, and involves selecting and highlighting certain aspects of it, while others are explicitly neglected. The goal is to encourage a particular interpretation or evaluation of the presented information. Let’s take the Supreme Court’s ruling of legalizing same-sex marriage nationwide as an example. By shifting the audience’s focus to specific pieces of information, such as equal rights, religion, or opposing groups, the decision can be framed in terms of equality, morality, or conflict, respectively.

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Framing (Source)

When people form an opinion they typically take into account all the information available to them. In the case of the Supreme Court, however, it is predominantly the media that provides that information, because the Court is generally detached from the public. This means the media has great control over the information that the public bases its opinion on about the Court and, therefore, the media also affects how the public perceives the Court. However, reporters are often left to interpret the Court’s decisions and to speculate about possible consequences, but they lack the intensive legal training that is essential to fully understand the Court’s highly specified rulings. In trying to make sense of the decisions, journalists might focus on the Justices’ personal and ideological views instead of on the legal reasoning behind the ruling. The consequence of all this is that media coverage of the Supreme Court has become increasingly politicized. On the other hand, the Court wants to convey an image of itself as an apolitical institution, which is described as being guided by legal principles, instead of personal interests, which is more characteristic of politicians.

Continue reading “Judicial Tyranny or American Justice? Guest post by Lisa Matthias”  

Open science stars: An interview with Dr. Gal Schkolnik

Last week, we kicked off a series interviewing some of the top ‘open ​scientists’ by interviewing Dr. Joanne Kamens of Addgene, and had a look at some of the great work she’d been doing in promoting a culture of data sharing, and equal opportunity for researchers. Today, we’re bringing you another open science star, Dr. Gal Schkolnik, who recently published a really cool Collection with us on the bacterium Shewanella. Here’s her story!

Hi Gal! So can you tell us a bit about your research background, and how you originally got interested in science?

I did my BSc in Chemistry at the Tel Aviv University and my MSc at the Weizmann Institute, analyzing  the chemical composition of deforestation-fire smoke from the Amazon, where farmers and corporations yearly set hectares of rainforest on fire for agriculture and pasture. For my PhD at the Technische Universitaet Berlin I measured the electric fields at protein surfaces and self-assembled monolayers. Now I’m researching Shewanella, an electroactive bacterium that can transfer electrons across its outer membrane. As you can see, I always start on a completely new field, because my greatest passion in life is acquiring knowledge – so learning something new is my favorite kind of challenge. I’m basically just a kid who never got over the “why” stage, haha. Plus I had some very inspiring teachers at school – two wonderful women who nurtured my natural tendency to go deep in pursuit of answers to the hardest questions.

People who have no access to journal subscriptions can use ScienceOpen to gain more knowledge about electroactive bacteria and their possible applications.

Continue reading “Open science stars: An interview with Dr. Gal Schkolnik”  

The catalyst for open clinical trials is the patient – Interview with Dr. Anula Jayasuriya

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Every year in May, I attend the Charité Entrepreneurship Summit, a unique event for international medical entrepreneurs and life science innovators organized by the Charité Foundation in Berlin. This ‘think-tank’ meeting connects sparkling ideas with pragmatic reality and facilitates a ‘one-of-a-kind’ scene for ‘let’s innovate and implement’ biomedical professionals and entrepreneurs from all over the world. This year, I had a special opportunity to meet and conduct an interview with Dr. Anula Jayasuriya, a wonderful personality and a talented scientist, physician, and investor. While contacting and talking with Anula Jayasuriya, I realized that she represents an amazing role model for every young scientist-entrepreneur. Here is some of food for thought from our conversation on entrepreneurship in medical sciences and open science.

Q1: The NIH has been one of the biggest forces behind the push towards increasing access to scientific information, but we are just at the beginning of the open science movement – open data being the next big hurdle. Do you see potential for an impact on the US health care system?

AJ: I think the NIH initiatives are very exciting, and open data will make a huge difference in the whole US health care system – but it will take time. At the end of the day, the NIH doesn’t make drugs, right? So we have to contend with industry. I wonder how it’s going to play out for pharma and biotech? Their business model is centered on protecting their innovations with IP and making money from products during the exclusivity period.

The moral imperative to share drug development data is that such information would greatly benefit patients and society. Let’s speculate that three big pharma companies working on development of the same category of drugs in their pipelines would be willing to share their failure results. This would be very important in preventing adverse reactions and health-related complications in patients. Perhaps these companies could form an industry consortium where every company was required to share their drug development failure data. There are many hurdles to be overcome before this can be a reality. For example, the first to fail is likely to benefit others but not itself. Money saved by averting future failures maybe eclipsed by lost revenues and compromised IP,  etc. Pharma has to see an economic incentive to share data. Perhaps there could be an attractive market for acquiring failure information? In any case, there would need to be a dramatic transformation and innovation around the existing IP-based “winner-take-all” industry business model.

Pharma has to see an economic incentive to share data

Q2: Do you believe that patient access to the clinical trial data and mandated data sharing will create a climate that could accelerate drug development and translational science research?

AJ: I believe that the biggest motivator and catalyst in this process of sharing clinical trial information will be the patient. We are entering a very exciting era of patient engagement. Going forward, I see patients playing active roles in clinical trials. As patient participation is essential to clinical drug development patients have the power to make the change. The passive patient is likely to become a memory of the past. Already today there is a US Government funded institute called PCORI (Patient Centered Outcomes Research Institute) that is making grants to investigators who engage patients in clinical trial design. I see patients challenging Pharma, Biotech and Regulators to adapt to a world where patients are active decision makers alongside industry and regulators. The FDA today is caught in the middle of a rapidly transforming ethos. All stakeholders will need to adapt to a new equilibrium. Let me give you some examples. In 1993, I was working for Roche pharmaceuticals. This was during the early days of the HIV outbreak where there was an urgent need to develop new drugs to fight the devastating epidemic. Patient advocacy groups had a huge impact on getting pharma companies to work together and also influenced the FDA to act quickly and really make a difference (read more about Act Up). I saw first-hand how powerful the cooperative approach was. By the way, physicians were very pleased to see collaborations, which led to effective treatment and greatly benefited patients. But that was one narrow case in the past.

Today, I see changes taking place across several diseases, especially in fighting cancer and rare diseases. Patients, together with their families, are building tight communities to share and disseminate knowledge about their diseases. In the USA, there is a popular movement called “hacking your body”. This is a different kind of open innovation – the innovations are ones that have been “opened”/discovered by patients. The drive is coming from patients and their families. Now, patients are playing active roles, often going around regulatory barriers and industry specifications and advocating for themselves.  As a physician, I am immensely pleased to see engaged patients. There are likely to be some hiccups and missteps along the way but I think that in the long run it will lead to accelerated drug development and, most importantly, better patient outcomes.

I believe that the biggest motivator and catalyst in this process of sharing clinical trial information will be the patient… This is a different kind of open innovation – the innovations are ones that have been “opened”/discovered by patients.

In the US, patients are entitled to free access to their medical records. If patients who participated in clinical trials were also entitled to access to their clinical trial records and were able to communicate with co-participants in the same trial I think they could “hack” the trial, by comparing adverse events and outcomes. And they are likely to share these aggregated data openly even if industry does not. I see patients, their families and society as the key actors in improving their health care.

There are two important ways to improve and accelerate drug development: understanding the science behind drug failures, and developing a process of sharing information openly within trial participant and disease the communities through the internet.

It is very encouraging that the NCI (the National Cancer Institute (NCI), part of the US National Institutes of Health) has successfully mediated a unique public-private partnership called the lung map trial, a multi-pharma collaboration in lung cancer. Five pharmaceutical companies (Amgen, Genentech, Pfizer, AstraZeneca, and AstraZeneca’s global biologics R&D arm, MedImmune) and Foundation Medicine (a cancer tumor genome analytics company) will collaborate to provide the treatment that is best suited to the individual patient – delivering personalized care.  Patients need to enroll only in a single trial to access drugs developed by five different pharma companies. This is a groundbreaking development – real progress.

In addition, there are many digital health start-up companies whose business models are based on selling anonymized clinical trial data. (Of course, there are several ethical, privacy and compliance considerations to be addressed, but let’s just put them aside for now.) The promise of “Big Data Analytics” as it applies to health care is that the aggregation of these data will lead to better outcome for patients. I am optimistic!

There are two important ways to improve and accelerate drug development: understanding the science behind drug failures, and developing a process of sharing information openly within trial participant and disease the communities through the internet.

(Read more here: Big data analytics in healthcare: promise and potential; Making Big Data Work: The Promise and Potential to …)

Q3: Do you think that big data, open science, and a worldwide network could in the future precisely tailor therapies to each patient’s individual requirement?

AJ: Precision medicine is the holy grail of health care. Tailoring cancer therapies makes a big difference in treatment outcomes today – cancer is the “low hanging fruit” due to easy access to the genomic analyses of tumors. Ultimately, delivering precision medicine relies on aggregating and analyzing data on a large number of areas: genomics, metabolomics, RNA, proteomics, behavior, environmental exposures, social and cultural milieus, etc. – this is a VERY big data play. I think the delivery of precision medicine will happen incrementally, in stages – with ever increasing degrees of precision as our understanding of the various contributing areas increase. Open science and data sharing are essential to generating the best data inputs from a multitude of sources to create a big data repository that serves as the basis for analytics.

Open innovation enables us to create products from a platform (repository) of information, which is freely available to everybody. For instance, having unrestricted access to scientific literature enables a company to develop their own algorithms for novel prognostic and diagnostic genomic screens – they could, for example, figure out which patients are sensitive/resistant to various drugs. Algorithms “learn” — the more patient data tested, the more an algorithm is refined and hence clinically informative. If, however, a company develops a screening or diagnostic test and patents it, thus excluding its use by others, it is no longer “open”.

The case of Myriad Genetics Inc. is interesting. They recently lost a lawsuit contesting the exclusivity of their BRCA test for breast cancer. The company used patient sequence information to develop and patent their screening test. Myriad claimed that they had exclusive rights to patients’ sequence information and to the test they derived from it. For several years Myriad was able to build a very profitable business by excluding others from duplicating their test, even though the actual sequence information the company used belonged to patients (http://www.the-scientist.com/?articles.view/articleNo/36076/title/Gene-Patents-Decision–Everybody-Wins/). Myriad’s claims were overturned and patent law is the US changed such that naturally occurring sequences can no longer be patented. I am in favor of this outcome as it greatly benefits patients who can now access BRACA tests from several companies at a much lower price.

I am excited about the concept of open innovation because it is a major step toward improving patient care. That being said, in a capitalist society, this has to be tempered by providing sufficient incentives to industry (on whom we are dependent unless we innovate a new model) to produce drugs, diagnostics, etc. I am confident that the “new normal” will result in better health care for society and the ability of industry to adapt and innovate novel and more productive business models.

I thank Dr. Anula Jayasuriya for the fascinating insights into the world of drug discovery and the role open innovation can play.

Non-Anon Post-Pub Peer Review in action!

Image attribution: Stop and Go, Nana B Agyel, Flickr, CC BY
Image attribution: Stop and Go, Nana B Agyel, Flickr, CC BY

One of the trickiest parts about launching anything new, also true for PLOS ONE too back in the day (hard to believe now!), is that the best way to explain what you do is to show it in action. Since we only officially launched in May, we’ve been watching some interesting use-cases develop, by which we mean ScienceOpen articles with Non-Anonymous Post-Publication Peer Review (PPPR). Even though we publish with DOI in about a week, it’s taken a little longer for the reviewers to have their say (reviews also receive a DOI), but we’re finding that what they say is well worth reading.

These articles and their associated reviews reassure us that PPPR, which some feel is still pretty radical, is a nascent but potentially healthy way to improve the way we review research. They also start to show that PPPR can benefit all sorts of research. If it can work for less spectacular, negative or contradictory research, then perhaps it will shine for once in a lifetime findings (which are of course far more rare).

Example 1. Professor Hugo Ten Cate (et al), a member of our Editorial Board, from Maastricht University, Dept of Internal Medicine, Maastricht, The Netherlands, published an article entitled “The anti-coagulants ASIS or APC do not protect against renal ischemia/ reperfusion injury” with us. It has received two PPPR from relevant experts, one by Professor Nigel Mackman and the other by Professor Ton Lisman. What really helps to tell the story of this article, from the author’s perspective, is that Hugo has made a video in which he explains that the results of this paper were not spectacular, in fact they were mostly negative, but that doesn’t mean that the article shouldn’t be published (and other journals did not want to do that) because it balances out other papers that show positive outcomes. Naturally, we agree with him!

Example 2.  Assistant Professor Nitika Pant Pai (et al), a member of our Editorial Board at McGill University in the Department of Medicine and a Scientist at the MUHC Research Institute, published an article entitled “Head to head comparisons in performance of CD4 point-of-care assays: a Bayesian meta-analysis (2000–2013)” with us. It has received a detailed review from Dr Paul Drain, a Medicine Resident at Stanford University.  Again, the author made a video in which she enthusiastically explains her support for Open Access and the concept of PPPR.

Example 3. Daniel Graziotin, a PhD student in Computer Science at the Free University of Bozen-Bolzano, Italy, published an article entitled “Green open access in computer science – an exploratory study on author-based self-archiving awareness, practice, and inhibitors,” with us which is an exploratory study of the awareness/practice/inhibitors of self-archiving among authors in an Italian computer science faculty. It has received two reviews, the first from Professor Stephen Curry (on our Editorial Board) and the other from Dr Alexandros Koulouris. In this case, the author gave us an interview to explain the background to this initial piece of research.

Example 4. Professor Nikos Karamanos (et al), a member of our Editorial Board from the University of Patras in Greece, published an article entitled “EGF/EGFR signaling axis is a significant regulator of the proteasome expression and activity in colon cancer cells” with us. It has received two reviews, one from Prof Dr Liliana Schaefer and the other from Assistant Professor Satoshi Tanida. Again, the author gave us an interview in which he explains the background to his article and his feelings on OA.

What do these use-cases tell us? Mostly that its early days, so meaningful observations are perhaps premature! However, here are some thoughts:

  • The reviewers that are being invited to the scientific conversation are participating and broadening the debate
  • The reviews are respectfully delivered with a straightforward tone, even when critical (probably because they are Non-Anon)
  • It’s good to see papers from the medical community, arguably the quintessential OA use-case for researchers, patients, their families and friends
  • The reviewers are appropriately matched to the content, authors can suggest up to 10 and anyone with 5 or more publications on their ORCID iD can review any content on the platform
  • The authors are largely, but not exclusively, from our Editorial Boards (no surprises here since they are usually the first to support a new publishing venture and are more senior so are freer to experiment)
  • Reading Non-Anon PPPR is a new skill requiring balancing a scholars background with their reviews and comparing/contrasting them with those of the others
  • None of these authors have yet used Versioning to revise their original articles in the light of reviewer feedback received (although this article is now on version 2)

Anyways, we hope you enjoy watching how PPPR at ScienceOpen evolves as much as we do! Feel free to leave a comment on this post to continue the conversation.

Welcome to author Nitika Pant Pai – impassioned OA advocate!

Today, we’re pleased to announce a new article entitled Head to head comparisons in performance of CD4 point–of-care assays: A Bayesian meta-analysis (2000-2013) by multiple award-winning researcher Nitika Pant Pai, Assistant Professor at McGill University in the Department of Medicine and a Scientist at the MUHC Research Institute and her co-authors Samantha WilkinsonTiago ChiavegattiBenedicte Nauche and Lawrence Joseph.

To mark the publication of her first ScienceOpen article, Nitika, who is also a member of our Editorial Board, prepared this video which is compelling both for what she says and how she says it – with a great deal of commitment!

Just 35 seconds into the video, a big smile spreads over Nitika’s face as she starts to talk about Open Access (OA) and her fist goes up as she says “more power to Open Access”! From then on, she discusses her real-life experiences of not having access to journals when she was training in India, wanting to spare others the same experience and why OA was therefore “the jewel for me”. Nitika’s enthusiasm for OA is infectious and energizing, she calls it a “pure movement”, says it is a way to “give back to the community” and believes it is going to permeate all sections of society, helping knowledge to spread. Continue reading “Welcome to author Nitika Pant Pai – impassioned OA advocate!”  

ScienceOpen Author Interview Series – Daniel Graziotin

ScienceOpen Author Interview Series – Daniel Graziotin

Today’s interview comes from another recent ScienceOpen author, Daniel Graziotin. In his ScienceOpen article, “Green open access in computer science – an exploratory study on author-based self-archiving awareness, practice, and inhibitors,” he analyses the results of an exploratory questionnaire given to Computer Scientists. It addressed issues around various forms of academic publishing, self-archiving of research, and copyright. In the following interview with ScienceOpen, Graziotin gives a unique perspective, as a young scientist and as a software and web developer coming to scientific publishing from the world of open software development. His ideas are bound to be interesting to emerging scientists in particular, as he represents a new globally engaged generation of scientific researchers making full use of open knowledge to further innovation. Continue reading “ScienceOpen Author Interview Series – Daniel Graziotin”  

ScienceOpen Author Interview Series – Miguel Andrade

Our interview series continues with a quick chat with ScienceOpen Editorial Board Member and recent ScienceOpen author Professor Miguel Andrade. His paper, entitled “FASTA Herder: A web application to trim protein sequence sets,” ( http://goo.gl/4qa7Ez ) presents a publicly available web application that uses an algorithm to identify redundant sequence homologs in protein databases.

Miguel Andrade received his PhD in Biochemistry at the Universidad Complutense de Madrid and trained at post-doctoral level at the European Molecular Biology Laboratory in Heidelberg and Cambridge. He has been Continue reading “ScienceOpen Author Interview Series – Miguel Andrade”  

ScienceOpen Author Interview Series – Nikos Karamanos

Today’s interview continues both the Author and the Editorial Board Interview Series with a conversation between ScienceOpen and Nikos Karamanos, Professor of Chemistry at the University of Patras in Greece. Professor Karamanos is one of the authors of the recent ScienceOpen publication, “EGF/EGFR signaling axis is a significant regulator of the proteasome expression and activity in colon cancer cells” ( http://goo.gl/XD9R0L ), and an established scholar, Editorial Board member for various journals, and chair and organizer of numerous conferences. He is principal investigator Continue reading “ScienceOpen Author Interview Series – Nikos Karamanos”  

ScienceOpen Author Interview Series – Carol Perez-Iratxeta

Today’s author interview comes from Carol Perez-Iratxeta ( http://goo.gl/fwloa7 ), a bioinformatics researcher based at the Ottawa Hospital Research Institute (OHRI) in Ottawa, Canada. Her research concerns data mining and computational genomic analysis applied to human disease.

Together with fellow OHRI researcher Caroline Louis-Jeune, as well as Dr. Miguel Andrade, based at the Max Delbrück Center for Molecular Medicine in Berlin, Germany, she has just published an article entitled, Continue reading “ScienceOpen Author Interview Series – Carol Perez-Iratxeta”  

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