A Karger Open Access Journal
The interdisciplinary ‘hub’ for researchers, clinicians and public health professionals
Cabezón Ruiz S. · Busoi C.-S. · Harkin M. · Gardini E. · Van Nistelrooij L. · Peterle A. · Pietikäinen S.
Horgan D. · de Braud F. · Jonsson B. · Vallone S. · Jagielska B. · Koeva J. · Geanta M.
Horgan D. · Kent A. · McMahon S.
Horgan D. · Baker M. · Riegman P. · Bernini C.
Horgan D. · Codacci Pisanelli G. · Esposito G. · Moch H.
Horgan D. · Henning G. · Banks I. · van der Wal T. · Hasurdjiev S. · Pelouchova J.
BioMedMix contains short reviews of interesting research and the latest trends in biomedicine and STM publishing, as well as interviews with leading and up-and-coming scientists.
Nowadays, there seems to be an app for everything. Health is no exception, and there are already tens of thousands of apps in the categories of “Health and Fitness” and “Medicine”. According to a German report, mHealth, as the field is known, is basically health care supported by mobile devices such as smart phones and wearables like smart watches.
mHealth incorporates mobile devices, such as smart phones, to support health care
One task health apps are being designed for is reminding patients to take their medicines at the proper times. For example, Janssen Healthcare Innovation developed Care4Today Mobile Health Manager, an app designed to keep patients on schedule with their medications and that sends reports to the patient’s family and health care provider. Such apps can increase patient adherence with drug regimens as well as keep their family and doctor informed as to how well they are doing in this pursuit, thus increasing the effectiveness of treatment.
In the realm of wearables, researchers at Oregon State University are working on monitoring our health via a contact lens. They are developing a lens with a transparent sensor that can measure glucose levels in diabetics. This data, in turn, could be sent to a smart phone, letting diabetic patients know when their glucose levels are too high or low. The researchers, however, want to go a step further. They are working on having the sensors send the glucose level information directly to a wearable pump that immediately releases insulin and glucagon to regulate the patient’s blood sugar. The Oregon State University scientists see other applications for the transparent contact lens sensors, such as measuring pulse and blood oxygen levels. They even see the technology being used for detecting cancer by recognizing biomarkers of cancer risk.
- “Can Treatment Adherence Be Improved by Using Rubin’s Four Tendencies Framework to Understand a Patient’s Response to Expectations?” in Biomedicine Hub discusses how the personality type of a patient influences adherence to treatment and how to use this knowledge to improve adherence.
- The new Karger journal, Digital Biomarkers, explores such topics as mHealth and big data in medicine and public health.
Many deadly diseases have been eliminated or at least made preventable by vaccines. Small pox – gone; diphtheria, tetanus, and pertussis – can be prevented with one shot. The childhood scourge of chicken pox has been decreased by almost 90% with the varicella vaccine. In addition to the obvious benefits of longer healthier lives, the success of vaccines also translates into real money savings. Below is a sampling of numbers showing the costs of preventable diseases and the savings vaccines can create.
Many deadly diseases have been eliminated or at least made preventable by vaccines.
- In the campaign to eradicate small pox, it is estimated that the US recaptures its domestic investment (ca. USD 92 million) for the vaccination program every 26 days (Science of Eradication: Malaria, Basel, 2017).
- A review last year estimated that vaccine-preventable diseases in US adults cost USD 9 billion in direct costs for hospital, outpatient care, medication and indirect costs like lost work and productivity, with unvaccinated individuals accounting for 80% of these costs (Source).
- The Centers for Disease Control and Prevention in America estimates that more than USD 10 are saved for every USD 1 spent on childhood vaccinations (Source).
- A 2008 outbreak of measles in California resulted in eleven unvaccinated children contracting the disease. The cost to treat each case totaled more than USD 10,000, whereas giving them the vaccine would have cost between USD 20 and 60 – not to mention lost wages if the parents taking care of them had to miss work (Source).
- The Bill and Melinda Gates Foundation estimate the following costs are avoided through global vaccination efforts: USD 1.4 billion in treatment costs, USD 300 million in lost wages for caretakers, and over USD 60 billion in lifetime productivity lost due to disability and death (Source).
“Science is a way of thinking much more than it is a body of knowledge.” Carl Sagan
The work of Andreas Vesalius, a 16th century anatomist, is still relevant for today’s scientists.
Professor Arthur English’s prolific career has focused on regeneration of nerves following injury and trauma, which he has also pursued as the editor of the journal Cells Tissues Organs (CTO) for the last 25 years. However, enter his office and you may be surprised to see Vesalius’s The Fabric of the Human Body in pride of place. What can a 16th century anatomist, with a passion for taking bodies apart, teach a cutting-edge scientist trying to put them together again? We had to ask.
What fascinates you most about Vesalius?
First, his tremendous ability to make many precise observations from dissections of human bodies, many under less than ideal conditions. All of the anatomical details of what he observed are there, in full view, and that by itself constitutes an impressive contribution. Second, his skill in synthesizing these observations into an organizational plan of human anatomy. It is this latter skill that is particularly impressive for me.
Is the spirit of Vesalius alive in today’s science?
As the co-editor of CTO, a journal devoted to publications related to regeneration science at all levels of biological organization, I revere papers that include Vesalius’s application of the scientific method. Our best papers in CTO do not stop at describing elements of experimental regeneration biology, but synthesize multiple observations, often made at more than one level of biological organization, into an explanation.
Can you give an example?
There are many examples in our CTO issues devoted to special topics. Papers seek to fuse published findings in the recent literature with original observations in the context of those topics. There are some nice examples in the context of stem cells and peripheral nerve regeneration.
However, in the spontaneous submissions we receive, we keep a careful eye out for papers going beyond mere description and into explanation. In their widely cited study of the matrix composition and mechanics of decellularized lung scaffolds, Petersen et al. made precise observations using histochemical staining and mechanical testing of decellularized lung tissues. Then, much as Vesalius incorporated his precise anatomical observations to a plan for the fabric of the human body, these authors used their findings to develop a model that enables the study of lung matrix biology and mechanics.
What can today's scientific authors learn from Vesalius's approach?
This amalgamation of multiple observations reflects an approach to scientific endeavor that is not often emphasized in today’s world of experimental biology. Some might even argue that Vesalius’s precise cataloging of human structure has but a small place in contemporary biology. I would disagree. A hallmark of the best scientific papers published today, those that we all are impressed to read in high impact factor scientific journals, is the bringing together of multiple observations, often made using different and sometimes really novel technologies, into an organizational plan that serves to explain a biological phenomenon. For me, what separates a good paper from a great paper is one that includes such an explanation, not merely a description of experimental results.
Vesalius was one of the first to go beyond scientific description to tell us how all of his detailed observations had more far-reaching significance. The examples from CTO provided above are, to me, clear evidence that this tradition is alive today. Most working scientists today do want to go beyond a description of their findings to explain the significance of those findings. I believe that far too few of us appreciate the intellectual debt that we owe Vesalius. For that reason, I believe that his place in modern biology ought to be front and center.
Your article’s title and abstract are the keys to getting your research its well-deserved attention, and in fact are the first things readers see when they search databases such as PubMed and ScienceDirect. The title and abstract are what persuade a reader to invest time (and perhaps money) to read (and maybe even cite!) your research and findings.
Get Noticed: Short Titles and Solid Abstracts Are Your Friends
The title needs to be catchy and capture the essence of the article so that a reader can quickly determine if it will be of interest to them. Research has shown that articles with shorter titles tend to get cited more often than those with longer titles, and articles with question marks in the title seem to get cited less. However, including colons can be beneficial: it basically lets you include two messages to hook the reader. Remember, since the title is the first thing anyone sees, it is extremely important that is describes your article accurately, quickly, and in an interesting manner. You also want to avoid using technical jargon and abbreviations, as too much will narrow your audience to your specialized field, reducing its cross-disciplinary appeal and scaring away a more general public readership. Another thing to consider is using words such as “randomized” in the titles for articles dealing with a randomized controlled trial – the same is true for reviews and meta-analyses. Doing so will easily identify what type of article it is, as indexers don’t always do this.
Your abstract needs to explain the main points of your paper briefly and clearly. 150 to 250 words are usually enough to give an overview and not scare away potential readers with too much text. Avoid using excessive jargon and abbreviations, as this makes it hard for people from other disciplines to get a grasp of what your paper is about, thus narrowing your audience and the reach of your findings. A structured abstract is often a good idea as it provides clarity and structure by briefly summarizing the background, methods, results, and discussion/conclusion, and is often required by many journals. Finally, you need to use several good keywords that are often searched for, so that your article will be easily found in Internet searches.
For further reading, see:
- “What Are Structured Abstracts?”
Drug repurposing (also known as repositioning) is an important and promising part of translational medicine. This involves identifying or finding new uses and/or targets for existing drugs or compounds. There are a number of benefits of drug repurposing, ranging from ethical considerations to reducing costs and speeding up delivery to the market. By identifying drugs that have already been deemed safe, costly preclinical and early-phase trials don’t have to be repeated, thus sparing unnecessary animal and human testing, not to mention lots of money and time.
Drug repurposing is an important and promising part of translational medicine.
There are different ways researchers go about finding drugs to repurpose. One is by basically stumbling upon a new indication. A famous example is sildenafil (Viagra). Originally developed with hypertension and angina in mind, early-phase trials found penile erection to be a side effect, leading researchers to repurpose it for treating erectile dysfunction.
Recently, more systematic approaches using big data have been developed for identifying drugs that are good candidates for repurposing. Gaining access and analyzing the ever-increasing amount of information the science world is compiling on gene sequences, biomarkers, and drug effects and indications hold a lot of promise for finding new uses for old drugs and will continue to increase in importance. One researcher, Dr. Jan Baumbach, believes utilizing big data can shave off up to five years from the drug development cycle. He and his team are using big data analytics to sift through large amounts of pharmaceutical data and have found a lot of needles in the proverbial haystack – in fact, they have identified more than 30,000 drugs that hold potential for repurposing. Such efforts are sure to cut down on development costs and will hopefully speed up getting new old drugs to patients who can benefit from them.
Related: see the post “Citizen Scientists” from Mark2Cure to learn about efforts using crowd sourcing for data mining in medical and scientific literature.
With each step, the effectiveness is decreased since a certain percentage is always lost.
(Graphic: Marcel Tanner)
How can a drug with high efficacy have a low effectiveness rate? This may sound counterintuitive, but is actually quite simple. Marcel Tanner recently explained to the Biomedicine Hub team some factors that contribute to this phenomenon.
As the drug leaves the “laboratory bench” and makes its way to the “patient’s bedside,” no step is done with 100% perfection, with the result that each step whittles away at the total number of people that can be helped by the medication, as is well illustrated in the chart below. Not everyone who needs it will have access to the drug (access), and not every doctor will recognize who could benefit from the drug (targeting accuracy). If the drug makes it past these first two hurdles, the issue of compliance will also come into play: the provider may not prescribe it correctly (provider compliance) and the patients won’t all follow the instructions exactly for taking it (consumer adherence). Altogether, these factors add up and take their toll on the effectiveness of a drug, with the result that drugs that appear very promising in clinical trials fail to live up to their expectations in the real world.
Translational medicine strives to smooth these transitions from “bench” to “bedside” by optimizing procedures, sharing knowledge, and looking for ways to improve delivery of drugs and treatments, and thus improve the overall global health picture.
What’s the point of doing research if nobody finds out about it? The University of Basel has an innovative program – the so-called WIMO (Wissenschaftsmonat) – that teaches its medical students how to effectively communicate their research and findings. For one month, WIMO participants learn the basics of scientific writing, work on writing up their own research, and practice presenting their findings in the setting of a congress. The best presentations are awarded the Karger Prize. One of this year’s winners was Lukas Bock (3rd place), who researched the biomarker troponin. In the interview below, he tells us a little about his topic, what he sees as his next steps, and what he learned during WIMO 2017.
Your work was honored with the Karger Prize. Could you tell us a little bit about your topic and what led you to it?
Cardiac troponin is a molecule that can only be found in the heart and can be measured in the blood if heart muscle cells are destroyed, for instance during a myocardial infarction. I was part of a research team that investigated troponin levels in patients who underwent surgery. Any surgery is a huge stress for the body and particularly the heart, so it is quintessential to be able to judge the risk of a surgery before starting.
Therefore, we investigated whether this biomarker, troponin, can predict cardiac risk in patients before they undergo surgery and which of its subunits are better suited to be measured in this context. We found that troponin can in fact be used to predict the risk of surgery, and we also found that the different subunits also do well, but differently depending on which surgery is performed.
What do you see as the next step in your research? What would you like to investigate further with this topic?
I plan to focus on improving my clinical skills as a treating physician and will only return to the bench after seeing how medicine works in day-to-day practice. I feel proper research requires understanding how research findings can be implemented in clinical routine, and that this can only be done after seeing illnesses in real life.
If I were to continue researching troponin, I would be interested in its molecular background, as there are still many gaps to be filled. For instance, we still don't completely understand how troponin is eliminated from the body or how exactly it is released from heart muscle cells. A better understanding of its physiology would certainly represent a huge leap forward in the use of troponin as a diagnostic marker.
You took part in the WIMO 2017. What did you take away from it? What did you find to be challenging? What was the most helpful?
WIMO made me aware of how crucial it is to present science in a simple, yet appealing manner to your audience. Working on a subject for a long time in an area where no other research group has been before inevitably transforms you into a partly nerdish person, and it is hard to imagine how people not working on your subject might find it difficult to follow your reasoning. By showing my presentation to other colleagues, I realized how often we tend to make things more complicated than they actually are. Their feedback was extremely valuable to me to avoid this trap.
The problem of overweight and obesity is nothing to take lightly – the WHO reports that overweight/obesity is responsible for more deaths than being underweight, and that obesity in the world has doubled since 1980. In fact, it can lead to serious health repercussions such as cardiovascular disease (heart disease and stroke), diabetes, musculoskeletal disorders (osteoarthritis), and cancer (breast, prostate, colon, etc.).
The primary cause is no big mystery: more calories are consumed than are burned off. It probably doesn’t help matters that globally we are eating more high-fat energy-dense foods like potato chips, fast food, and ice-cream. Stress may also be a part of the problem, especially when we think about the consequences of “emotional eating,” i.e., eating not out of hunger, but instead in the search of comfort. However, the role stress plays in obesity is poorly understood, and this was the topic of a recent study from Finland which sought to investigate this relationship. The researchers conducted a case-control study of people in a stressful situation, and found that they tended to me more overweight/obese than controls, and that they had a higher prevalence of stress in their lives. The authors also identified stress factors that affect obesity. You can read their article in full on Biomedicine Hub.
What do you eat when you are stressed? What “comfort food” do you reach for? Below you will find some examples of comfort food from the Karger team.
- Koski M, Naukkarinen H: The Relationship between Stress and Severe Obesity: A Case-Control Study. Biomed Hub 2017;2:458771.
This week, we shine a light on George Patrinos, one of the Senior Editors of Biomedicine Hub, an Associate Editor of Public Health Genomics, and an Associate Professor of Pharmocogenomics of the University of Patras School of Health Sciences in Greece. He tells us about some of his current projects, such as pharmacogenomics and building up genetic databases; how translating genomics from bench to bedside is like an ancient Greek temple; and the Golden Helix Conferences®, which he is active in.
George Patrinos outside of the lab.
What are some exciting developments your field is experiencing?
Our group is active in the field of pharmacogenomics, which aims to customize drug dosing according to one’s genetic profile, and the most important and exciting developments at the moment are the translation of pharmacogenomics findings and implementation of pharmacogenomics in the clinic. This is particularly important since successful implementation of pharmacogenomics in the clinic, especially if performed pre-emptively, will not only improve the quality of life of the patients by increasing drug efficacy and minimizing adverse drug reactions that are often life-threatening, but is also expected to reciprocally reduce the overall national health care expenditure. This can be particularly important for health care systems in countries with economic constraints, for example in Europe and Southeast Asia, where certain genome-guided treatment modalities have already been demonstrated to be cost-effective.
What would you like to see happen in your field?
Although there have been major leaps in pharmacogenomic research, facilitated by the genomic technology revolution, the pace of these discoveries and the generation of pharmacogenomics knowledge has not met with reciprocal advances in the translation of these findings into the clinic. To this end, there are often significant barriers that hamper the smooth incorporation of pharmacogenomics research findings in the daily medical practice, which have to do more with disciplines related to public health genomics than pharmacogenomics research itself. If we view the translation of genomics from research to the clinic as an ancient Greek temple, with genomics and pharmacogenomics research representing the foundation and genomic medicine the roof, the various public health genomics subdisciplines can be metaphorically represented as the supporting pillars that must be carefully erected for the superstructure of genomic medicine to hold. As such, although the foundations of genomic medicine are presently becoming stronger and being ascribed ever-increasing hopes and expectations, the pillars themselves are still weak and largely under construction. Hence, we should ensure that the various public health genomics subdisciplines are properly developed, such that they can contribute towards paving the way for a smoother transition from genomics research to genomic medicine.
What are you currently working on?
Our group is one of the few worldwide that is involved in multidisciplinary work in pharmacogenomics. This work includes genome discovery work, genome informatics analysis, and public health research. In particular, we are working on establishing the role of cis- and trans-regulatory elements in the reactivation of fetal hemoglobin production and the role of several genomic loci in the individualization of hydroxyurea treatment in β-type hemoglobinopathy patients. We are also involved in elucidating the genes involved as pharmacogenomic biomarkers in lithium treatment efficacy in bipolar disease patients and the role of TPMT promoter variants in 6-MP treatment toxicity. Since 2010, we have been engaged in a pan-European project to determine the prevalence of clinically relevant (actionable) pharmacogenomic biomarkers in 18 European populations and the application of whole-genome sequencing in pharmacogenomics. We have also conceived and successfully implemented the notion of microattribution as a means to incentivize genomic data sharing in the public domain. In 2005 we established the National Genetic Database concept and developed software for its development and curation. We have also developed FINDbase, a global National Genetic Database, documenting clinically relevant genomic variation allele frequencies in over 100 populations worldwide and a Web-based tool to help translate pharmacogenomics information into a clinically meaningful format. Finally, we have been working on expanding the concept of public health genomics in pharmacogenomics, bridging the notions of stakeholder analysis, economic evaluation in pharmacogenomics, and ethics in genomics, and we have been very active in increasing genomics awareness to the general public and pharmacogenomics education for health care professionals.
The Afea Temple as a symbol of the translation of genomics from research to the clinic.
Tell us about the Golden Helix® Conferences. How did they get started? What topic is planned for this year?
The Golden Helix® Conferences are international meetings on genomic medicine and consist of The Golden Helix Symposia, The Golden Helix Pharmacogenomics Days, and The Golden Helix Summer Schools. These conferences are named after the house of Francis Crick (“The Golden Helix”; 19/20 Portugal Place, Cambridge, UK) to emphasize their focus on human genomics and personalized medicine. The themes of these conferences revolve around the fields of genomics, pharmacogenomics, and personalized medicine. The conferences were launched in 2008 and take place in developing countries in Europe, the Middle East, Asia, and Africa, attracting very high-profile academics and researchers from research centers of excellence and large corporate entities. Pharmaceutical and biotechnology companies as well as charitable entities have sponsored the series, which over the years have helped to reduce the costs for participants. The conferences are a well-orchestrated effort to enrich genomics education among health care professionals and to increase genomic literacy among patients and the general public, specifically addressing the needs of participants from developing countries. This year, the major Golden Helix Conference will be held again in Athens, Greece jointly with the Global Genomic Medicine Collaborative (G2MC), on April 27–29, 2017 with the theme “Implementing Genomic Medicine into Practice”.
The list of health benefits from breastfeeding is long. According to the Cleveland Clinic in the USA, breastfed babies have stronger immune systems; less cases of serious illnesses such as pneumonia, whooping cough, and bacterial meningitis; and are just overall healthier. It’s not just the babies, though – mothers also enjoy many positive effects from nursing their infants: faster weight loss after giving birth (making the baby’s milk burns up about 500 calories a day), and a decreased risk of several diseases such as breast cancer, cardiovascular disease, and osteoporosis are just a couple of them.
Breastfeeding has many health benefits for infants and mothers. Picture by pexels.com/unsplash.com
The World Health Organization recommends starting breastfeeding within one hour after birth. It also encourages the mother and baby to be in skin-to-skin contact shortly after birth, citing evidence that such contact is important for initiating breastfeeding and increases the likelihood that it will be successful for several months.
Of course, complications can arise during birth and with infants, interfering with breastfeeding. This was the topic of a popular Biomedicine Hub article that reported on neonatal hypoglycemia, which can affect up to 15% of newborns and require a trip to the neonatal intensive care unit (NICU) for intravenous dextrose. The researchers noted, however, that asymptomatic hypoglycemic infants are also transferred to the NICU at significant cost and loss of mother-baby contact at this critical time when breastfeeding patterns are just beginning to get established. They conducted a review of cases and found that using a dextrose gel supplement with feeds, which is already used in adults to treat hypoglycemia, reduced the need for intravenous dextrose therapy in newborns affected by asymptomatic hypoglycemia. This in turn reduced the need for transfer to the NICU and the ensuing high costs, and resulted in more mother-baby time, thus promoting breastfeeding.
This Biomedicine Hub article has created a lot of attention, earning a high Altmetric Attention Score. In outputs of similar age, the article ranked 8,083 out of 233,772 – that means it scored higher than 96% of articles that came out about the same time. Such a ranking shows good resonance and the high interest the public has in this topic.
After months or years of research, nobody wants to spend untold hours writing up their hard work only to find it has gone unnoticed and unread. To combat this, there are ways to create buzz about your work and track the attention it receives.
Kudos, the UK-based provider of author services, dedicates itself to getting authors the attention they deserve. It’s an easy process that all authors should take advantage of. First the author explains his/her work in easy-for-anyone-to-understand language and highlights the important bits. Then there is the sharing step: of course e-mail and social media figure prominently in this stage, but Kudos also brings it to a wider audience by sharing content and placing links across search engines and subject indexes. And as everyone wants to see the fruits of their labor, Kudos makes it possible for authors to measure their efforts with a number of metrics including downloads, citations, and altmetrics.
Altmetric, famous for its attention score that looks like a “donut,” is also a valuable resource for researchers. This company provides information on the online attention and engagement published works are generating, and keeps authors up to date on what others are saying about their research. Altmetric monitors a variety of sources, such as public policy documents, blogs, social media (e.g., Facebook, Twitter, and LinkedIn), Wikipedia, YouTube, citations, and many others, to track articles. One of the advantages of this is that it lets researchers demonstrate the impact their work is making on the scientific world, i.e., show where important people in the field have commented on it, where it has been mentioned in public policies, or when it has resonated in specific localities, which in turn could be instrumental in securing grants and funds for further research.
Now go out and see what impact your research is making – you might discover some new bragging rights.
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Karger Publication Manager Paul Lavender
Although most biomedical scientists did not enter the world of clinical research out of a desire to write, publishing their findings and results so the scientific community can read about them is important. We asked Paul Lavender, a Publication Manager at Karger and former medical writer and editor, how to approach the task of writing up a study or case report and what he thinks are some important things to remember. Below is a summary of what he had to say.
- Do good research. If you are clearly presenting sound data in an interesting field then it will be published. It is really that simple. However, if the methodology or analyses are questionable, then it is very difficult to be published – regardless of how well the paper is written.
- Have a target journal before you write – know what section it can appear in and what the editors look for. Write specifically for this journal. Don’t try to make a one-size-fits-all piece to shop around. In the end, you might not get the audience you want to reach.
- Consider the impact factor (IF) of a journal. This does not mean, however, to choose the journal with the highest IF. Such journals sometimes only choose articles they think will receive a lot of citations to protect their IF, with the result that highly specialized, even if high-quality, research is rejected in favor of something that appeals more to the researching masses. How many times would you honestly expect (not hope!) your paper will be cited in the next 2 years? That can give you an idea of your target IF.
- Use a checklist before you start writing. There is no need to reinvent the wheel, so follow established and recognized checklists to give your paper a solid structure that does not leave out any important aspects. You can find information about checklists on the EQUATOR Network website.
- Finally, don’t try to be too clever – keep your language simple. You want to make it as easy as possible for a peer reviewer to say ‘yes’ to your paper. If the reviewer has to spend a lot of time struggling through dense or unclear language, he/she might reject it regardless of the science. Think of the times you have struggled to read papers and other times you have glided through. How grateful do you feel when a paper is easy to understand?
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Knowledge network created from the data mined by "citizen scientists" (reproduced with permission from the Su Lab, The Scripps Research Institute)
It is no easy task for scientists and researchers to stay up-to-date with the latest biomedical news in their fields, and even harder to keep up with what is going on in other areas that may also be of interest to them. The volume of published works is breathtaking. PubMed already boasts more than 26 million entries from the body of biomedical literature, and adds 1 million more each year.
Bioinformatics scientists from the Scripps Translational Science Institute (STSI) in La Jolla, CA (USA), have started a project, Mark2Cure, which they hope will provide researchers some much needed help in sifting through the vast reams of literature and perhaps uncover some hidden gems. Mark2Cure is a web-based platform that utilizes crowdsourcing, i.e., volunteers or "citizen scientists" as they call them, to mine data from the biomedical literature.
The only requirement for becoming a "citizen scientist" is the ability to read texts in English. Most of these volunteers are motivated to “advance science” and for “learning” purposes, while others come from the communities of those affected by rare diseases. Aspiring “citizen scientists” take a short online tutorial that familiarizes them with the platform. After this, they first identify relevant concepts, e.g., genes, diseases, and medicines, in a text and then secondly look for relationships between these concepts, e.g., drugs that are used to treat certain diseases. A simple example would be coding the key terms from a text as: axitinib (drug) treats cancer (disease). This is then fed into computers which use algorithms to organize the data into more useful and manageable forms. Hopefully, researchers can then use this pool of knowledge to discover new connections between diseases and treatments, and perhaps make new discoveries or form new hypotheses. Ultimately, the stated goal of Mark2Cure is to “identify key terms in all biomedical research abstracts enabling researchers to identify new relationships and ideas that would otherwise remain hidden.”
Mark2Cure performed a small trial to test the effectiveness of the “citizen scientists” against experts. Overall, the volunteers were very accurate in highlighting mentions of diseases, comparable to the experts. Now, the platform is being used in its first project to search for material related to N-glycanase 1 (NGLY1) deficiency, an extremely rare disease with few published reports. The "citizen scientists" have already uncovered 10,000 documents of interest.
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- Experimental and Clinical Pharmacology Unit CRO-National Cancer Institute, Aviano, Italy
- Doctoral Course in Pharmacological Sciences, University of Padova, Padova, Italy
- Clinical pharmacology
- Pharmacogenomics, primarily related to oncology
- Pharmacogenomic and outcome research
- Public health policy and regulatory research
- Pharmacoepidemiology and drug safety
Rossana Roncato is a pharmacogenetics researcher at the National Cancer Institute of Aviano, Italy. She recently took part in the 2016 Golden Helix Summer School, held on Syros Island, Greece, where she won the Golden Helix Prize for presenting her research on predicting the prognosis of epithelial ovarian cancer through tumor genetic signatures. This program of the Golden Helix Foundation and the Genomic Medicine Alliance is designed to give researchers from around the world a forum to expand their knowledge in the exciting field of genomic medicine. This year’s theme was “Cancer Genomics and Individualized Treatment” and included such topics as genomics and pharmacogenomics, public health, informatics, and drug design. You can read the abstract of Rossana Roncato’s work here.
Rossana Roncato presenting at the 2016 Golden Helix Summer School.
How did you come to your chosen field?
My field is the study and development of innovative strategies to personalize therapy for oncologic patients based on their genotype. My “first steps” were as a visiting master’s student at the University of California, San Diego, where I worked on an experimental research project focused on the study of protein kinase C signaling in cancer. However, it wasn’t until I had to choose the subject for my PhD that I considered moving from molecular to clinical pharmacology. From all the possible projects, I chose one in pharmacogenetics because of a seminar I attended as an undergraduate student at the University of Padova. The lecturer, Erika Cecchin, is now my supervisor at the National Cancer Institute of Aviano.
As a PhD student, I had the opportunity to research the different stages of pharmacogenetic marker development: from the exploratory setting related to both the colorectal and ovarian fields to the clinical implementation of genetic screening of well-acknowledged markers for severe chemotherapy-related toxicities in everyday practice at our hospital.
Who or what inspires you in your profession?
I have found inspiration in the brilliant women scientists I have met throughout my studies and career, from the principal investigator of my former lab, Alexandra Newton, a visionary scientist and role model both personally and professionally, to Corina Antal, my former supervisor who, through her endless dedication to science, taught me the discipline, precision, and rigor that I still carry with me. My current supervisor and mentor, Erika Cecchin, challenges me on a daily basis to see where I cannot. I am grateful to all of them.
How can your research offer hope to cancer patients?
Pharmacogenetics aims to make drug use safer: someone may need a lower dosage, while another patient needs the standard dose and others perhaps a double dose -- all still being equal in response and toxicity. Chemotherapeutic-related toxic effects may be severe and life-threatening, endangering the adherence of cancer patients to therapy as well as their possibility to get cured. However, tailored medicine has the potential to motivate more patients to adhere to their treatment since a personalized regimen increases their involvement in their own care. This is also important in the context of the increasing usage of complementary and alternative medicine among cancer patients over the years. Furthermore, with the constant rise in oncology treatment costs, the use of chemotherapeutic drugs needs to become more targeted and focused on where they have the best chances of producing an effective clinical benefit.
What are the most exciting changes you see for cancer patients in the next 20 years?
Considering that genotyping costs will drop in the near future, becoming increasingly inexpensive and widely accessible, the introduction of pharmacogenetics profiling in clinical practice could deliver an efficient and personalized care that ultimately cuts public health costs.
What are the biggest challenges in oncology research?
The introduction of next-generation DNA sequencing machines has exponentially increased the rate of biological data generation. The management of “big data” in genomics is, in my opinion, the greatest challenge that researchers in oncology will have to face in the near future. Knowledge of statistics and bioinformatics together with genomics will make the difference.
- President of the Swiss Academy of Sciences
- Professor of Epidemiology and Medical Parasitology, Faculties of Science and Medicine, University of Basel
- Director emeritus, Swiss Tropical & Public Health Institute, Basel, Switzerland
- Infection biology, primarily neglected tropical diseases
- Basic research in cell biology and immunology on malaria, schistosomiasis, trypanosomiasis, and filariasis
- Epidemiological and public health research on risk assessment, vulnerability, health impact, and district health planning
- Extensive work in Africa and Asia
Prof. Tanner has worked extensively in developing countries in Africa and Asia, and feels at home both in the lab and in the field. He is a senior editor for Biomedicine Hub and tells us a little about his background, what he would like to see happen in public health, and why crosstalk between science disciplines is important.
What is your field and what led you to it?
Infection biology is my field, primarily diseases of poverty and neglected tropical diseases. In 1979, I went to Cameroon as a young post-doc, with the goal of isolating new antigens from worms that cause river blindness. We went to some villages and took nodulectomies out of the skin of the villagers, and we also treated them. Being there showed me that the local people also had other health issues, not just the disease we were investigating, which made a big impression on me. That’s how I came to be more interested in epidemiology and public health and made the decision to focus on field work and leave the lab.
Marcel Tanner and Omari Juma of the Ifakara Health Institute, Tanzania, (photo: Peter Jaeggi, 2014).
What are some exciting developments in your field?
In 2015, the Nobel Peace Prize in Medicine was awarded to three researchers for their work in developing new treatments for malaria and combating infections caused by roundworms. From discoveries like these, we’ve been able to drastically alleviate the burdens caused by malaria, lymphatic filariasis, and river blindness. It’s even conceivable that we will be able to eliminate some of these diseases in some areas.
What would you like to see happen in infection biology?
While the development of new medications and therapies is, of course, important, it isn’t the only part of the equation. The local social and health systems that deliver these treatments are equally crucial to combating these diseases, and it would be nice to see this important work in setting up and running these systems also be recognized.
Biomedicine Hub is an interdisciplinary journal – how has crosstalk between different disciplines of medicine been important for your research?
In our research portfolio, we aim to cover the whole value chain from innovation to the validation of scientific findings towards application. Clearly, our goal at the Swiss TPH and all organizations that strive for inter- and transdisciplinary approaches is to combine research, teaching/training, and direct applications in public health practice. This approach and the prerequisite that we undertake our science endeavors in the spirit of mutual learning for change will ensure a high degree of harmoniously created inter- and transdisciplinarity, thus leading to a comprehensive impact in health and social systems.
Nature has long been a source of inspiration to scientists, artists, and everyday people. Recently, Ashton et al., bioengineers from the University of Utah, have found their muse in the caddisfly larvae, which tapes together the armor it needs for the fast-flowing streams in which it lives. What’s amazing is that this 'tape' can be applied underwater. An Internet video from NPR recently explained the work they are doing and the promising applications it has for the medical world.
Caddisfly larvae are able to ‘tape’ together a protective case made out of small pebbles underwater. The ‘tape’ is actually silk, and is incredibly sticky and resilient. Although the researchers are only just beginning to understand its structure and how it works, uncoding its secrets will hopefully show us how to create strong synthetic adhesive materials that work in wet environments, such as inside the human body. The implications for medicine are huge – in the future, surgeons may be able to add tape to their armamentarium of stitches and screws to put us back together again.
Read the original research article from Ashton et al.
M. Großmann / pixelio.de
Is your attention to detail impeccable? Does nothing get past you? Click on the following link and test your skills: https://www.youtube.com/watch?v=IGQmdoK_ZfY.
If you are one of the 50% who missed the gorilla, then chalk it up to ‘inattentional blindness’. When given a demanding task that requires our full attention, we tend to focus on the matter at hand and are not on the lookout for the unexpected. However, since few of us are professional gorilla counters, it could also just be a rookie mistake.
To see if professionals also miss gorillas, Trafton Drew, from Harvard Medical School, and his fellow researchers did a similar test with radiologists. Drew put a small picture of a man dressed in a gorilla suit on CT slides of lungs, gave the slides to a group of radiologists, and asked them to look for nodules. Most of them (83%) missed the gorilla. So how can the experts miss something so obvious? One explanation is simple -- they weren’t asked to look for gorillas, they were looking for small nodules.
Drew and his colleagues stress they are not implying radiologists are not good at what they do. Instead, they want to show that even highly trained professionals are not immune to the limits of human attention and perception. They feel the results show that medical search tasks should be optimized to account for these limitations.
Trafton Drew spoke to NPR about his research earlier in the year. The transcripts and article can be found at http://www.npr.org/…/why-even-radiologists-can-miss-a-goril…. The original paper can be found at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964612/.
CT scan picture by tushchakorn/123RF
While we all know that chocolate does have some health benefits, for many of us chocolate is still a guilty pleasure. A new study recently published in Pulse http://www.karger.com/Article/FullText/445876 , however, might give chocolate lovers cause to pat themselves on the back.
In a 5-year study, Crichton et al. investigated the long-term effects of chocolate consumption on arterial stiffness. The authors looked at pulse wave velocity, a good predictor of cardiovascular disease, in people who never or rarely eat chocolate, those who eat moderate amounts (defined as once per week), and frequent consumers (more than once a week). Chocolate intake was ascertained via questionnaire. The researchers found that the never-eaters had the highest pulse wave velocity, followed by the frequent eaters. The group that practiced moderation in their chocolate pursuits had the lowest levels of PWV, and was thus seen to be at lower risk for arterial stiffness.
Crichton et al. view their findings as novel as their results suggest a threshold effect of chocolate, i.e. moderate amounts are better than none, but that higher chocolate consumption does not necessarily increase the benefit.