Why do people Mark2Cure?

Why do people Mark2Cure? | The Su Lab.

Mark2Curators have been busy! Over the weekend, our volunteers brought the current beta experiment from about 28% completion to over 50% completion. We’ve gotten excellent feedback from you and are working to improve on the issues and suggestions you’ve sent us! Thank you and keep them coming!!!

We're at 56% complete as of this morning--double where we were last Friday Morning!
We’re at 56% complete as of this morning–double where we were last Friday Morning!

We now have over a hundred registered Mark2Curators who have shared compelling reasons as to why they Mark2Cure.

If we categorize the reasons, they look something like this:

Why do people Mark2Cure? If we categorized it, people Mark2Cure because...
Why do people Mark2Cure? If we categorized it, people Mark2Cure because…

We know all of our Mark2curators are altruistic, else they wouldn’t be contributing, but many have their reasons for doing so. For over half of our Mark2Curators, the primary motivation for contributing is to help others! How awesome is that? About half of our Mark2Curators were motivated by their interested in health and science. About 25% of our Mark2Curators were motivated by disease ties, with >70% of the disease ties being rare diseases. If you’re wondering why the sum of the percentages is over 100%, it’s because many reasons cannot neatly be contained by a single category.
 
If a picture is worth a thousand words? What's a picture formed from the words of our Mark2Curators worth?  ...priceless!
If a picture is worth a thousand words? What’s a picture formed from the words of our Mark2Curators worth? …priceless!

This post was originally written for Mark2Cure and can be viewed in its entirety here.

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A Veterans Day Tribute

Re-blogged from: http://directorsblog.nih.gov/2014/11/11/a-veterans-day-tribute/

    Today, we celebrate Veterans Day. On this special day, let us pause and salute all who have served and honor the tremendous sacrifices made by members of the U.S. armed forces and their families to preserve our freedom.

    This occasion also gives us an opportunity to acknowledge the many important contributions of the veterans who are now working here at NIH. Currently, our agency employs about 1,000 veterans and is making a concerted effort to add even more to our ranks. As a result of these outreach and recruitment efforts, NIH hired 122 veterans during fiscal year 2014… 48 of whom were disabled veterans, I’m proud to report.

    As is the case for everyone who works at NIH, these veterans are using their knowledge, skills, and experience to help advance NIH’s mission. In fact, I’d like to share a thought from one of these veterans, Jayne Lura-Brown, a program analyst at our National Institute of Dental and Craniofacial Research. In her profile on the “Jobs at NIH” web site, this Navy veteran says: “No matter what level or type of career we find ourselves in, NIH has something for us—that something that we all want, which is the chance, or another chance—to do something meaningful and to continue to be a part of something GREAT.”

    For Jayne and other NIH veterans, their next chance includes pursuing medical, hospital, dental, and public health careers. Their new mission is to fight cancer, diabetes, Alzheimer’s, and other common disabling disorders, bringing their unique military training and resolve to help turn scientific discoveries into better health for all. For any veteran interested in joining us at NIH, I’m including links at the bottom of this post to help you get started.

    Last week, Jayne helped to organize the fourth annual NIH Veterans Day Celebration. I participated in the event and was inspired by the life story of the keynote speaker, Retired Commander Everett Alvarez, Jr. Fifty years ago, as a young man based on a Navy aircraft carrier in the South China Sea, Alvarez became the first pilot shot down and held as a prisoner of war in North Vietnam. After eight grueling years of captivity, he returned home as the second longest-held POW in U.S. history. Today, you would never know it. His quick sense of humor and successful career in business speak volumes about a life well served, inside and outside of the military.

    But we must never forget that not all return. As a reminder, the Setting of the Missing Man Table was performed during the NIH ceremony. This moving military tradition pays special tribute to a soldier missing, fallen, or imprisoned. I’d like to share a video of the Setting of the Missing Man Table in special appreciation on this Veterans Day.

    Veterans, I know that I speak for all of us at NIH in offering sincere thanks for your personal sacrifices, past and present. We will continue to open our doors to you at NIH, and we look forward to working alongside more veterans in the future.

See the original post here.

More on the scientific/medical contributions of the military here:

A History of Military Contributions. Source: The Phoenix Patriot, Winter 2012

Neat Science Thursday – Perpetuating Pseudoscience

The myths touched on in a previous Thursday post are extremely persistent, but aren’t usually very harmful. In contrast, the pseudoscience perpetuated by many supplement peddlers, like Dr. Oz, can have serious adverse effects. Hence it was no surprise that many in the scientific community applauded the congressional grilling of Dr. Oz, and John Oliver’s informative yet bleakly entertaining follow up.

While John Oliver did an excellent job highlighting the issue, no one actually believed that something would be done about the use of pseudoscience in selling dubious dietary supplements.

Proving everyone right, Business Insider just published an article on a new trendy supplement–Activated Charcoal:
With the change of the seasons (in this case, summer to fall), it always seems like people feel the need to detox their bodies.

A lot of the recent detox buzz is around activated charcoal. Charcoal, however, isn’t really new – it’s been around since long before the 19th century, when both the ancient Egyptians and Greeks used it as a multi-purpose poison and disease antidote.

Today, it’s most commonly used in emergency settings to treat accidental poisonings or drug overdoses. Well, that’s until someone decided it would make a great supplement for a detox program, anyway.

Seriously? Activated Charcoal as a dietary supplement? Disturbing. And just when you though the pseudoscience nonsense can’t get any worse, it turns out that Consumer Reports has may be pandering to Dr. Oz too, adding to existing concerns about Consumer Reports steady slide into promoting pseudoscience.

The Genetic Literacy project received a memo regarding Dr. Oz’s visit to Consumer Reports from a former senior editor who parted ways with CR after getting “fed up with the woo”. ‘Woo’ refers to pseudoscience, magical thinking, or quackery.

Neat Science Thursday – Scientific communication is hard

For my dissertation research, I studied the mechanisms of viral persistence in the central nervous system using an in vitro model consisting of picornavirus infections of differentiated and undifferentiated murine neural progenitor and stem cells.

To some of my non-science friends and family, that explanation sounds something like, “I studied blah blah blah, miscellaneous pretentious scientific jargon, blah blah.”

Of course, they would still have no idea what I studied, and any further attempts to explain would be met with that kind, patient look that people give you when they’re bored but are too polite to walk away.

So I would tell non-science people that I studied “how a virus hides in the brain for a long time, and the consequences of having a virus hiding in the brain using mouse stem cells”.

This explanation will elicit much more interest, but can sometimes get distorted when described second-hand to others since it’s not as accurate. Also, there may be some fellow scientists who will think you lack professionalism, or don’t know what you’re talking about if you use this sort of description.

If you think about it, there is so much jargon specific to each field of study, it’s actually pretty impressive how well scientists have been able share information across disciplines. Of course, there is always room for improvement in that arena, especially since researchers primarily disseminate their findings via scholarly articles, keying them for easy search amongst fellow researchers in their discipline. The differences in jargon sets contributes to the difficulty in finding research articles outside your field of research which contain research findings that could have important impacts in your own work. It’s also why there has been a lot of interest in annotating research literature and making it more searchable (Go! Go! Mark2Cure) as well as creating an open database where information contained in research literature can be formally structured around a set of shared ontologies (Go! Go! Wikidata.

It’s also great that these findings are becoming more available as funding agencies help to drive open access policies enabling the public to finally access the research paid by tax/donation dollars. But open access does not mean accessible if we consider the sheer volume of jargon that must be learned in order to read and understand scholarly articles. How can we expect tax payers to support research if they are locked out on so many levels? Now before you argue that ‘people need to take personal responsibility for their own education’ or ‘the articles aren’t really hard to read if you actually put in the effort,’ ask yourself this, ‘Am I dismissive of people science communicators that communicate science via non-traditional channels (ie- non-academic journals)?’ If your answer is ‘yes’, you waive all rights to complain about the scarcity of research funding.

If your answer is ‘no’, consider contributing your expertise to a truly accessible knowledge-base/medium like Wikipedia. Efforts are already under way to make information on every human gene of interest publicly available on Wikipedia (the Gene Wiki initiative), and greater participation is needed from scientific community.

For those of you, researchers or not, who ARE able to communicate science with such elegance, enthusiasm, poignancy, and precision–especially those of you on non-traditional channels like Science 2.0, twitter, etc.–thank you for using your talents to engage the public so they can see how their money is being spent. You are awesome! The rest of us will just have to keep trying.

Neat Science Thursday – Too Much Information

Personalized medicine has been a goal for a growing number of biomedical researchers over the last twenty years. Considering the fact that biomedical research literature on personalized medicine has grown from 5-10 articles/year in the 1980’s to over 2500 articles per year since 2013, incredible progress has been made towards this extremely challenging goal. For personalized medicine to happen, at least two elements are necessary: 1. A means of acquiring personalized data is needed, and 2. A means of integrating, analyzing, and applying that data. The explosive improvements in the amount, quality, efficiency, and cost-effectiveness of obtaining personalized data , creates a huge challenge in the integrating, analysis, and application of that exponentially growing body of data available. Thus, the challenge of personalized medicine primarily lies in the integration and analysis of ‘Big Data.’ Yes, there is always room for improvement in data acquisition, but all the growing data is problematic if it cannot be effectively utilized. Researchers from all over the world have been working on analysis tools in order to better extract useful information from the growing available sets of omics data, and [Warning: shameless plug alert] The Su lab’s Omics Pipe is one attempt to automate the best practice multi-omics data analysis pipelines. [End shameless plug]

Barbour Analytics published a fascinating post on the N-of-1 problem in Big Genomics. It is a great read for anyone interested in personalized medicine, rare diseases, big data, and bioinformatics. Here is a teaser to encourage you to take a look at the original post:


    How do we assess the impact of a single novel mutation, or a set of novel mutations, unique to an individual? This is the N of 1 problem in Big Genomics. Statistics, and statistical genetics rely on summary, on binning the patterns of populations of individuals into categories of adequate size that we can compare groups using standard metrics like mean, median, mode, standard error, and in more elaborate frameworks use more sophisticated metrics like moments, edges, vectors and ridges.

    The N of 1 problem in Big Genomics will require modeling approaches, to construct models of the genome, and make projections on the likely function of single de novo mutations, and suites of these private mutations. Robust modeling efforts in this area will be a major challenge in the era of genomic medicine, and personalized medicine. At present we are effectively constrained to study mutations that have recurred throughout evolution. As our population grows, as the number of persons under care, and participating in genomic medicine increases, we will need to address the private mutation issue head on.

    We can look to cancer genomics for some guidance. Cancers are a genomic disease, with both inherited and de novo elements, and direct sequencing of genomes often reveal unique mutations that lead to unique cancer profiles. This field has the advantage of seeing a clear disease manifestation in the form of tumor growth, often restricted to a tissue or cell type. This helps make more direct inferences about the likely function of the novel mutation.

    That said, we face the inherent limitation that a mutation may be unique, or at least rare, and for this reason it is difficult to use traditional statistical approaches, approaches that rely on summary, on the behavior of groups of instances. While the genotype information may be limited to one person in these instances, we can assist ourselves in this effort by capturing more information about clinical and biological phenotype. Detailed phenotypic characterizations of a tumor or affected tissue – extending to the transcriptome, kinome, metabolome, cytokine profiles, cell morphology and indeed clinical status itself, can help us perform a sort of reverse interpolation to infer the function of the single N of 1 de novo mutation. While the mutation may be unique or rare, the disease manifestation itself may be common, or at least share key features with other maladies.

Now go read the original post here: ‘Private Mutations’: The N of 1 in Big Genomics — Barbour Analytics.

Neat Science Thursday – Science communication matters

Tweets about science flooded twitter feeds again yesterday when Science released its list of the top 50 scientists on twitter and their corresponding K-index. If you haven’t heard of the K-index, you’re probably not on very high on it. The top 50 list received an enormous (and rather negative) response in the twittersphere. Why? Aside from obvious flaws of only relying on twitter followers and neglecting to include a lot of great female scientists, the top 50 list revived the reviled K-index!

Scientists that use twitter already took the k-index out of its self-imposed isolation, slapped it with a failing grade as a joke, highlighted its egregious mistakes, directed it to use real data before injecting it with a lethal dose of reality and leaving it to die. Many scientists that use twitter lambasted the K-index because they knew how useful it could be especially for sourcing articles (#icanhazpdf anyone) that are NOT open access and for outreach.

Contrary to popular belief, many scientists spend a lot of energy and effort in outreach because they understand and acknowledge the importance of scientific communication. Don’t think science communication is important? Consider how it affects the parent’s decision on whether or not to vaccinate a child. Science communication isn’t exactly easy either.

Don’t do enough of it (it being sci-comm, of course), and someone else will step in with grossly misleading headlines on how your research shows that aspirin cures cancer. Do too much of it, and fellow scientists will disrespect you and remind you that your place is back at the bench (K-index anyone). Do it poorly and you will have the same results as not doing enough, or you will be ignored to the point that when someone confirms your findings it will look completely like a huge discovery rather than an incremental one.

Those in science that are able to communicate science with elegance, enthusiasm, poignancy, and precision are praiseworthy. Hats off to those of you who do it so well–that means you, GeneoTW writers, Science 2.0 and other science bloggers. You are all awesome! For the rest of us, we’ll just have to keep trying.

Now go back to tweeting great science, people.

Neat Science Thursday – Growing Science with Games

Gamification has become increasingly useful in getting people involved in science. Everyone can now contribute to science or learn more about science by playing fun and interesting games. Fortunately, you do not have to search very hard in order to find these awesome citizen science games because Chandra Clarke has already compiled them into an extensive list on her site. Here is just a small sample of the games that are available:

Astro Drone – Created by the European Space Agency, fly your Parrot AR drone in virtual space and compare yourself with real-life astronauts. Data from your successful flights will be used to train robots on how to navigate their environment. Website: http://www.astrodrone.org/.

Apetopia – Run over a landscape and then choose the door with the colour that best matches the sky at that moment. Collect coins and avoid obstacles too. The game helps determine perceived color differences; player choices are used to model better color metrics. Website: http://colors.htw-berlin.de.

Beat the Bots – Are you smarter than a spambot? VouchSafe has built an anti-spam program that uses the way humans think to try to outsmart spammers. Draw a line with your mouse to join an object to its best match, or circle the object that doesn’t belong. Yeah, okay, this isn’t really citizen science, but defeating spam is definitely for the greater good, don’t you think? Facebook: https://apps.facebook.com/beatthebots/

Cell Slider – Join the effort to defeat cancer by reviewing images to spot cancer cells. http://www.cellslider.net/

Collabio – Participate in social psychology research. Collabio is a Facebook application that wants you to guess tags that other friends have used to describe an individual. Points are awarded according to the number of other friends who have agreed with each tag. Facebook: http://apps.facebook.com/collabio/

Cropland Capture – Want to help improve the world’s food security? Help to improve basic information about where cropland is located on the Earth’s surface. Website: http://www.geo-wiki.org/games/croplandcapture/

Dizeez – Help researchers link various genes to diseases. The game is very simple: You are shown one gene name, and five diseases. Pick the disease that is linked to the gene to get points, and get as many points as you can in one minute. Website: http://sulab.scripps.edu/dizeez/

There are loads and loads more games so check out her Ultimate list of Citizen Science Games

More citizen science games can also be found on the Games for Change website which seeks to use gamification to catalyze social impact. Look under the STEM category, though science-related games can also be found under the other categories like ‘Environment.’ Many of these games are more on the science educational side rather than citizen science, but citizen science games like Foldit are sprinkled around the site.

If you prefer RPGs, try “Citizen Science” or “Oncology” on <a href="http://www.brainpop.com/"the BrainPop site.

Finally,