28Feb / 2018

Rare Disease Day Spotlight on PLOS Authors: Open Data Repositories in Practice

0000-0002-8715-2896 Science increasingly involves collaborative research groups, program partnerships and shared learnings to encourage transparency, reproducibility and a responsible transition to a more open way of doing science. Open Science policies and best practices are

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22May / 2017

dbGaP 10th Anniversary Symposium June 9, 2017

dbGaP (the NIH database of Genotypes and Phenotypes) is celebrating its 10th Anniversary this year! We are proud to support over 850 studies and 1.6 million samples. We invite you to join us at the dbGaP 10th Anniversary Symposium to … Continue reading →

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13Dec / 2016

Replace Francis Collins as NIH Director

For decades the NIH has been the premier funding agency in the world, fueling the rise of the US as the undisputed powerhouse of global science. But in his eight years in charge of federal efforts to understand, diagnose and cure disease, current NIH Director Francis Collins has systematically undermined the effectiveness of the institution and overseen a decline of American science.

Biomedical research in the US has been driven by the creativity and industry of individual investigators and their trainees. Collins has systematically diverted funds from investigator initiated projects in favor of “big science” projects conceived in and managed from inside the Beltway.

The model for these initiatives is the well-regarded Human Genome Project. However Collins, who headed this project in its final years, learned all the wrong lessons from this effort, focusing on central planning and control, and the generation of massive datasets, while ignoring the importance of technology development. Hence his signature projects as NIH director have been ill-conceived and wasteful of precious research funds.

The NIH has always aimed to fund scientists based on their ideas and accomplishments, but under Collins’s big science paradigm, money is increasingly doled out based on researchers’ willingness to sacrifice their autonomy and creativity to Bethesda’s plans. Scientists are herded into consortia and spend endless hours on conference calls to produce data that are of fleeting value.

Collins’ has further corrupted the process of peer review by becoming too close to leaders of the major research institutions, who have had an outsized role in shaping billions of dollars of NIH initiatives, and then benefited disproportionately when funds from these projects were distributed.

The US has led the world in training biomedical scientists, attracting many of our most talented minds into science. Central to this was the expectation that they could build stable careers based on NIH funding. But under Collins this system has collapsed. “Young” PIs generally do not receive their first grants until they are in their 40’s, spend an increasing amount of time seeking funds, and no longer feel they can count on NIH funding.

American science has always enjoyed strong support from Congress and the public. This support depends on a high degree of trust. But Collins has repeatedly made unrealistic promises to Congress and the public to secure support for his signature initiatives. There is almost certain to be a public backlash against the NIH when these projects fail to deliver.

Scientific progress almost always begins with basic discoveries. But in his efforts to curry favor with Congress, Collins has consistently promoted translational research with a dubious track record over basic biomedical research. He has involved the NIH in massive translational projects that are either premature or that the NIH is ill-prepared to carry out.

Finally, science as an endeavor involved building on the research of others. However Collins’s NIH is mired in a serious reproducibility and reliability crisis. Confidence in NIH funded research is at an all-time low, and Collins has responded with bureaucratic measures that have little hope of correcting the problems, while leaving untouched the perverse incentives that lead to the production of unreliable research.

Fortunately, destroying the greatest scientific engine humanity has ever created takes time. The US remains the global leader in biomedical research, with a talented and creative scientific workforce eager to tackle pressing problems in basic science and public health, and a diverse array of commercial enterprises ready to turn their discoveries into products that improve the health and well-being of our citizens. There are many thousands of talented and dedicated people at the NIH. But more time with Collins at the helm would be a disaster.

The National Institutes of Health are an invaluable resource for the American people and our economy. But it is in serious need of reform if we are to benefit optimally from the opportunities of 21st century biomedicine. It’s time to replace Francis Collins and name a talented physician scientist with real vision and wisdom as NIH Director.

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16Nov / 2016

Antimicrobial resistance: What is it? Why is it a problem? What is being done to stop it?

By Kelly Wroblewski, director, infectious diseases, APHL

Antimicrobial resistance is arguably the most significant public health threat facing the world today. As resistance builds, the threat of severe illness or death from common infections becomes an increasing possibility for everyone.

What is antimicrobial resistance?

Antimicrobial resistance occurs when microbes, including bacteria, viruses, fungi and parasites, evolve or adapt to survive exposure to drugs or other treatments designed to kill them. Once the microbes have developed resistance, treatments used against them are rendered useless.

While all types of antimicrobial resistance are extremely concerning, antibiotic resistance – when bacteria become resistant to antibiotics – is often seen as posing the most serious health threat. Why is this?

Compared to other microbes, more bacteria are becoming increasingly resistant to treatment, and resistant bacteria can cause more adverse health outcomes in infected people. Antibiotics are also more commonly used than antiviral, antifungal or antiparasitic drugs.

How did antibiotic resistance become such a big problem?

While many complex issues have led to this urgent situation, three factors stand out:

1. The overuse and misuse of antibiotics in healthcare, agriculture and other aspects of day-to-day life is a significant contributor to antibiotic resistance. Simply stated, every time we use antibiotics inappropriately, we’re helping bacteria figure out how to outsmart and outperform them – to resist Inappropriate use includes taking antibiotics to treat viral infections, starting a course of antibiotics and not completing it, using antibiotics in agriculture to improve livestock survival and crop yields, and the liberal use of over-the-counter antibacterial soaps and ointments.

2. Development of new antibiotics and diagnostic tools to detect resistance has suffered due to a lack of investment. As bacteria develop resistance to existing drugs, scientists must work to develop new antibiotics to treat infections. However, for the past 30 years, antibiotic drug development has been stagnant and the prospects are not promising.

Prior to the drug development phase (bringing drugs to market) is drug discovery, the process of identifying candidate medications and active ingredients. This is a challenging and therefore incredibly expensive endeavor with few economic incentives. For companies that make it to the drug development phase, creating drugs that kill bad bacteria without killing good cells (including the host) is extremely difficult.

3. It is difficult to systemically detect, track and respond to new resistant pathogens and outbreaks without a comprehensive global surveillance system. To slow the spread of resistance, we have to know where to find it and have a plan to stop its spread. Though the United States has acted to counter resistant forms of diseases like TB and gonorrhea, it hasn’t taken a public health approach to diseases commonly found in health care settings like the superbug CRE. Failure to detect and stop the spread of these infections at the community level contributes to increased numbers of resistant infections, poor patient outcomes and increased healthcare costs. What’s more, aggressive detection and response efforts are needed to prevent local outbreaks from becoming pandemics.

What’s being done to slow or stop antimicrobial resistance?

The past few years have brought much needed progress. Finally, the US public health and health care systems have a comprehensive plan to combat this problem and resources to make it happen.

In 2014, the White House released the National Strategy on Combating Antibiotic-Resistant Bacteria and President Obama signed an Executive Order directing key federal agencies to take action to combat the rise of antibiotic resistant bacteria. In December 2015, Congress passed a budget providing $375 million to implement this strategy with $161 million going to CDC.

Since then, significant steps have been taken to move the dial in the right direction.

CDC has distributed approximately $67 million to local and state governments to improve their ability to detect and respond to existing and emerging resistance as well as implement strategies to improve antibiotic stewardship.
CDC has established the Antimicrobial Resistance Laboratory Network (ARLN) which will provide infrastructure and capacity for seven regional public health laboratories across the country to better identify and characterize some of the most significant antimicrobial resistance threats. In addition, the ARLN will provide resources to all state and several large local public health jurisdictions to improve their CRE surveillance capacity.
CDC, FDA and NIH have launched a comprehensive campaign aimed at improving antimicrobial stewardship in healthcare and reducing the frequency of antibiotic use in agriculture.
NIH and the HHS Office of the Assistant Secretary for Preparedness and Response (ASPR) launched the Antimicrobial Resistance Diagnostic Challenge, a $20 million prize competition that to stimulate innovation in the development of new, faster diagnostic tools.
CDC and FDA have collaborated to establish the Antimicrobial Resistance Isolate Bank, a repository of resistant pathogens that will be made available to companies developing new antibiotics and diagnostics.

These are significant and valuable steps forward. As these and future efforts get underway, collaboration across sectors will be critical to success. APHL is committed to supporting members and working closely with partners in the battle against antimicrobial resistance.

The post Antimicrobial resistance: What is it? Why is it a problem? What is being done to stop it? appeared first on APHL Lab Blog.

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17Dec / 2015

Precision Medicine Initiative – Ricki’s Pick for Breakthrough of the Year

‘Tis the season for Science magazine to name their Breakthrough of the Year, a designation that typically irks me because it implies that science happens suddenly and we all know that of course it doesn’t.

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15Sep / 2015

Pathogens and Defense: Speakers recap from the 6th EMBO Meeting

By Meredith Wright From September 5-8, scientists converged on Birmingham, UK for the 6th European Molecular Biology Organization Meeting. EMBO is an organization which aims to support multiple branches of science, by holding courses, workshops, conferences, and publishing the EMBO … Continue reading »

The post Pathogens and Defense: Speakers recap from the 6th EMBO Meeting appeared first on PLOS Blogs Network.

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10Sep / 2015

A Fourth Offering of A Librarian’s Guide to NCBI

This blog post is directed toward medical or science librarians in the United States who offer bioinformatics education and support services or are planning to offer such services in the future. The NCBI, in partnership with the National Library of … Continue reading →

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13Oct / 2014

NIH Director Francis Collins’ ridiculous “We would have had an Ebola vaccine if the NIH were fully funded” meme

Almost as soon as the African Ebola epidemic hit the headlines, NIH Director Francis Collins was making the rounds arguing that we would have had an Ebola vaccine by now, if only Congress hadn’t slashed the NIH budget.

Lest you think I’m taking his words out of context, here is what he said to a House Energy and Commerce Subcommittee on Health Roundtable Discussion on Health and Medicine Issues on September 10, 2014:

The NIH began working on a vaccine for Ebola in 2001. We have steadily pursued that effort over these last 13 years, hoping that by the time a big outbreak occurred we would be ready for it. That vaccine has now been in animal trials, shown to be highly effective. But as of this summer, when the outbreak really began to catch fire, had not yet quite reached the point of a phase 1 clinical trial.

We worked in record time with enormous assistance from our colleagues at FDA to speed up the process. And last week, the first volunteers at the NIH clinical center were injected with this vaccine in a phase 1 trial to determine whether in fact it is going to be safe. And in another two or three months we will know that, and then hopefully be in a position to begin a phase 2 trial in the places where it’s most needed in Africa.

But I have to tell you, if we had not gone through this 10-year decline in the support of biomedical research, we would be a year or two ahead of where we are now. And think about the difference that would make, had we in 2014 been in the position to distribute rapidly tens of thousands of doses, in collaboration with our colleagues at GSK, of this vaccine, how much different would this be and how many lives would have been saved.

I read this testimony at the time, and was taken aback by this statement, but I was a bit reluctant to undermine efforts to increase NIH funding, no matter how cynical they might be. It was, after all, Congressional testimony, and one can forgive a bit of exaggeration in pursuit of remedying the horrible financial situation the NIH (and, thus its grantees and would be grantees).

But now Collins has gone public with this claim, in an article in the Huffington Post, and so it’s time to call this for what it is: complete bullshit.

First, let’s deal with the most immediate assertion – that if there had been more funds there would be an Ebola vaccine today. Collins argues we’d be a few years ahead of where they are today, and that, instead of preparing to enter phase 1 trials today, they’d have done this two years ago. But last time I checked, there was a reason we do clinical trials, which is to determine if therapies are safe and effective. And, crucially, many of these fail (how many times have we heard about HIV vaccines that were effective in animals). Thus, even if you believe the only thing holding up development of the Ebola vaccine was funds, it’s still false to argue that with more money we’d have an Ebola vaccine. Vaccine and drug development just simply doesn’t work this way. There are long lists of projects, in both the public and private sector that have been very well-funded, and still failed.

It is a gross overtrivialization of even the directed scientific process involved in developing vaccines to suggest that simply by spending more money on something you are guaranteed a product. And, if I were in Congress, frankly I’d be sick of hearing this kind of baloney, and would respond with a long list of things I’d been promised by previous NIH Directors if only we’d spend more money on them.

Second, let’s assume Collins is right. That the only reason we don’t have an Ebola vaccine today was that the project wasn’t properly funded. If this is true, than one should rightly ask why this wasn’t given a higher priority. The potential for a serious Ebola outbreak has been there for a long time. And while money is tight at the NIH, they still manage to find funds to do a lot of stuff I would not have prioritized over an Ebola research program it it was really on the crux of delivering a vaccine. So there is an element of choice here too that Collins is downplaying.

But what really bothers me the most about this is that, rather than trying to exploit the current hysteria about Ebola by offering a quid-pro-quo “Give me more money and I’ll deliver and Ebola vaccine”, Collins should be out there pointing out that the reason we’re even in a position to develop an Ebola vaccine is because of our long-standing investment in basic research, and that the real threat we face is not Ebola, but the fact that, by having slashed the NIH budget and made it increasingly difficult to have a stable career in science, we’re making it less and less likely that we’ll be equipped to handle all of the future challenges to public health that we’re going to be face in the future.

Don’t get me wrong. I get what Collins is trying to do. I just think it’s a huge mistake. Every time I see testimony from NIH officials to Congress, they are engaged in this kind of pandering – talking about how concerned they are about [insert pet disease of person asking question] or that and how, if only they could get more money, we’d be able to take make amazing progress. But guess what? It hasn’t worked. The NIH budget is still being slashed. It’s time for the people who run the biomedical research enterprise in this country to make basic research the center of their pitch for funding. Collins had a huge opportunity to do that here, but he blew it.

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12Sep / 2014

Jack the Ripper, more poison at NIH, Rosetta & the comet

Ripped from the headlines

Scientists have greeted with hoots and catcalls the claim that Jack the Ripper, the near-mythical late-19th Century London serial killer, has been identified from DNA as an immigrant Polish baker named Aaron Kosminski.

The DNA …

The post Jack the Ripper, more poison at NIH, Rosetta & the comet appeared first on PLOS Blogs Network.

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30Aug / 2014

NIH Announces Revised Genome Data Release Policies

Just got notified of this by the UC Davis Med. School grants administration: NOT-OD-14-124: NIH Genomic Data Sharing Policy. Lots of interesting things in here including a summary of the comments that they received on the draft policy.

I have copied some of the more interesting and relevant bits below:

Sharing research data supports the NIH mission and is essential to facilitate the translation of research results into knowledge, products, and procedures that improve human health. NIH has longstanding policies to make a broad range of research data, in addition to genomic data, publicly available in a timely manner from the research activities that it funds.
The public comments have been posted on the NIH GDS website. http://gds.nih.gov/pdf/GDS_Policy_Public_Comments.PDF
The statement of scope remains intentionally general enough to accommodate the evolving nature of genomic technologies and the broad range of research that generates genomic data.
Several comments were submitted by representatives or members of tribal organizations about data access. Tribal groups expressed concerns about the ability of DACs to represent tribal preferences in the review of requests for tribal data.
The GDS Policy expects that basic sequence and certain related data made available through NIH-designated data repositories and all conclusions derived from them will be freely available. It discourages patenting of “upstream” discoveries, which are considered pre-competitive, while it encourages the patenting of “downstream” applications appropriate for intellectual property.
NIH expects investigators and their institutions to provide basic plans for following this Policy in the “Genomic Data Sharing Plan” located in the Resource Sharing Plan section of funding applications and proposals. Any resources that may be needed to support a proposed genomic data sharing plan (e.g., preparation of data for submission) should be included in the project's budget.
Large-scale non-human genomic data, including data from microbes, microbiomes, and model organisms, as well as relevant associated data (e.g., phenotype and exposure data), are to be shared in a timely manner.