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Real Time Coverage @BIOConvention #BIO2019:  Issues of Risk and Reproduceability in Translational and Academic Collaboration; 2:30-4:00 June 3 Philadelphia PA

Reporter: Stephen J. Williams, PhD @StephenJWillia2

Derisking Academic Science: The Unmet Need  

Translating academic research into products and new therapies is a very risky venture as only 1% of academic research has been successfully translated into successful products.

Speakers
Collaboration from Chicago area universities like U of Chicago, Northwestern, etc.  First phase was enhance collaboration between universities by funding faculty recruitment and basic research.  Access to core facilities across universities.  Have expanded to give alternatives to company formation.
Half of the partnerships from Harvard and companies have been able to spin out viable startups.
Most academic PI are not as savvy to start a biotech so they bring in biotechs and build project teams as well as developing a team of ex pharma and biotech experts.  Derisk as running as one asset project.  Partner as early as possible.  A third of their pipeline have been successfully partnered.  Work with investors and patent attorneys.
Focused on getting PIs to get to startup.  Focused on oncology and vaccines and I/O.  The result can be liscensing or partnership. Running around 50 to 60 projects. Creating a new company from these US PI partnerships.
Most projects from Harvard have been therapeutics-based.  At Harvard they have a network of investors ($50 million).   They screen PI proposals based on translateability and what investors are interested in.
In Chicago they solicit multiple projects but are agnostic on area but as they are limited they are focused on projects that will assist in developing a stronger proposal to investor/funding mechanism.
NYU goes around university doing due diligence reaching out to investigators. They shop around their projects to wet their investors, pharma appetite future funding.  At Takeda they have five centers around US.  They want to have more input so go into the university with their scientists and discuss ideas.
Challenges:

Takeda: Data Validation very important. Second there may be disconnect with the amount of equity the PI wants in the new company as well as management.  Third PIs not aware of all steps in drug development.

Harvard:  Pharma and biotech have robust research and academic does not have the size or scope of pharma.  PIs must be more diligent on e.g. the compounds they get from a screen… they only focus narrowly

NYU:  bring in consultants as PIs don’t understand all the management issues.  Need to understand development so they bring in the experts to help them.  Pharma he feels have to much risk aversion and none of their PIs want 100% equity.

Chicago:  they like to publish at early stage so publication freedom is a challenge

Dr. Freedman: Most scientists responding to Nature survey said yes a reproduceability crisis.  The reasons: experimental bias, lack of validation techniques, reagents, and protocols etc.
And as he says there is a great ECONOMIC IMPACT of preclinical reproducability issues: to the tune of $56 billion of irreproducable results (paper published in PLOS Biology).  If can find the core drivers of this issue they can solve the problem.  STANDARDS are constantly used in various industries however academic research are lagging in developing such standards.  Just the problem of cell line authentication is costing $4 billion.
Dr. Cousins:  There are multiple high throughput screening (HTS) academic centers around the world (150 in US).  So where does the industry go for best practices in assays?  Eli Lilly had developed a manual for HTS best practices and in 1984 made publicly available (Assay Guidance Manual).  To date there have been constant updates to this manual to incorporate new assays.  Workshops have been developed to train scientists in these best practices.
NIH has been developing new programs to address these reproducability issues.  Developed a method called
Ring Testing Initiative” where multiple centers involved in sharing reagents as well as assays and allowing scientists to test at multiple facilities.
Dr.Tong: Reproduceability of Microarrays:  As microarrays were the only methodology to do high through put genomics in the early 2000s, and although much research had been performed to standardize and achieve best reproduceability of the microarray technology (determining best practices in spotting RNA on glass slides, hybridization protocols, image analysis) little had been done on evaluating the reproducibility of results obtained from microarray experiments involving biological samples.  The advent of Artificial Intelligence and Machine Learning though can be used to help validate microarray results.  This was done in a Nature Biotechnology paper (Nature Biotechnology volume28pages827–838 (2010)) by an international consortium, the International MAQC (Microarray Quality Control) Society and can be found here
However Dr. Tong feels there is much confusion in how we define reproduceability.  Dr. Tong identified a few key points of data reproduceability:
  1. Traceability: what are the practices and procedures from going from point A to point B (steps in a protocol or experimental design)
  2. Repeatability:  ability to repeat results within the same laboratory
  3. Replicatablilty:  ability to repeat results cross laboratory
  4. Transferability:  are the results validated across multiple platforms?

The panel then discussed the role of journals and funders to drive reproduceability in research.  They felt that editors have been doing as much as they can do as they receive an end product (the paper) but all agreed funders need to do more to promote data validity, especially in requiring that systematic evaluation and validation of each step in protocols are performed..  There could be more training of PIs with respect to protocol and data validation.

Other Articles on Industry/Academic Research Partnerships and Translational Research on this Open Access Online Journal Include

Envisage-Wistar Partnership and Immunacel LLC Presents at PCCI

BIO Partnering: Intersection of Academic and Industry: BIO INTERNATIONAL CONVENTION June 23-26, 2014 | San Diego, CA

R&D Alliances between Big Pharma and Academic Research Centers: Pharma’s Realization that Internal R&D Groups alone aren’t enough

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Peer Review and Health Care Issues

Larry H. Bernstein, MD, FCAP, Reporter

https://pharmaceuticalintelligence.com/12/1/2014/Peer-Review-and-Health-Care-Issues

(Medscape – Dec 1, 2014)

Peer-reviewed journals retracted 110 papers over the last 2 years. Nature reports the grim details in “Publishing: the peer review scam”.

When a handful of authors were caught reviewing their own

papers, it exposed weaknesses in modern publishing systems.

Editors are trying to plug the holes.

 

The Hill reports that the FDA may lift its ban on blood donations from gay men. The American Red Cross has voiced its support for lifting of the ban.

Advisers for the Food and Drug Administration (FDA) will meet this week to decide whether gay men should be allowed to donate blood, the agency’s biggest step yet toward changing the 30-year-old policy.

If the FDA accepts the recommendation, it would roll back a policy that has been under strong pressure from LGBT advocates and some members of Congress for more than four years.

“We’ve got the ball rolling. I feel like this is a tide-turning vote,” said Ryan James Yezak, an LGBT activist who founded the National Gay Blood Drive and will speak at the meeting. “There’s been a lot of feet dragging and I think they’re realizing it now.”

Groups such as the American Red Cross and America’s Blood Centers also voiced support of the policy change this month, calling the ban “medically and scientifically unwarranted.”

The FDA will use the group’s recommendation to decide whether to change the policy.

“Following deliberations taking into consideration the available evidence, the FDA will issue revised guidance, if appropriate,” FDA spokeswoman Jennifer Rodriguez wrote in a statement.

This reporter has more than 20 years of Blood Bank experience.  The factor in favor of the recommendation is that the HIV 1/2 and other testing is accurate enough to leave the question of donor lifestyle irrelevant.  However, it remains to be seen whether the testing turnaround time is sufficient to prevent the release of units that may be contaminated prior to transfusion, which is problematic for platelets, that have short expirations. In all cases of donor infection, regardless of whether units are released, a finding leads to not releasing the product or to recall.

 

Democrats made a strategic mistake by passing the Affordable Care Act, Sen. Charles Schumer (N.Y.), the third-ranking member of the Senate Democratic leadership, said Tuesday.

Schumer says Democrats “blew the opportunity the American people gave them” in the 2008 elections, a Democratic landslide, by focusing on healthcare reform instead of legislation to boost the middle class.

“After passing the stimulus, Democrats should have continued to propose middle class-oriented programs and built on the partial success of the stimulus,” he said in a speech at the National Press Club.

He said the plight of uninsured Americans caused by “unfair insurance company practices” needed to be addressed, but it wasn’t the change that people wanted when they elected Barack Obama as president.

“Americans were crying out for an end to the recession, for better wages and more jobs; not for changes in their healthcare,” he said.

This reader finds the observation by Senator Schumer very perceptive, regardless of whether the observation in hindsight might have had a different political outcome.  It has been noted that President Obama had a lot on his plate.  Moreover, we have not seen such a poor record of legislation in my lifetime.  There are underlying issues of worldview of elected officials that also contribute to the events.

 

THE PEER-REVIEW SCAM

BY CAT FERGUSON, ADAM MARCUS AND IVAN ORANSKY

N AT U R E |  2 7 N O V  2 0 1 4; VO L 5 1 5 : 480-82.

Most journal editors know how much effort it takes to persuade busy researchers to review a paper. That is why the editor of The Journal of Enzyme Inhibition and Medicinal Chemistry was puzzled by the reviews for manuscripts by one author — Hyung-In Moon, a medicinal-plant researcher then at Dongguk University in Gyeongju, South Korea.

The reviews themselves were not remarkable: mostly favourable, with some suggestions about how to improve the papers. What was unusual was how quickly they were completed — often within 24 hours. The turnaround was a little too fast, and Claudiu Supuran, the journal’s editor-in-chief, started to become suspicious.

In 2012, he confronted Moon, who readily admitted that the reviews had come in so quickly because he had written many of them himself. The deception had not been hard to set up. Supuran’s journal and several others published by Informa Healthcare in London
invite authors to suggest potential reviewers for their papers. So Moon provided names, sometimes of real scientists and sometimes pseudonyms, often with bogus e-mail addresses that would go directly to him or his colleagues. His confession led to the retraction of 28 papers by several Informa journals, and the resignation of an editor.

Moon’s was not an isolated case. In the past 2 years, journals have been forced to retract more than 110 papers in at least 6 instances of peer-review.

PEER-REVIEW RING
Moon’s case is by no means the most spectacular instance of peer-review rigging in recent years. That honour goes to a case that came to light in May 2013, when Ali Nayfeh, then editor-in-chief of the Journal of Vibration and Control, received some troubling news. An author who had submitted a paper to the journal told Nayfeh that he had received e-mails about it from two people claiming to be reviewers. Reviewers do not normally have direct contact with authors, and — strangely — the e-mails came from generic-looking Gmail accounts rather than from the professional institutional accounts that many academics use (see ‘Red flags in review’).
Nayfeh alerted SAGE, the company in Thousand Oaks, California, that publishes the journal. The editors there e-mailed both the Gmail addresses provided by the tipster, and the institutional addresses of the authors whose names had been used, asking for proof of identity and a list of their publications.ew rigging. What all these cases had in common was that researchers exploited vulnerabilities in the publishers’ computerized systems to dupe editors into accepting manuscripts, often by doing their own reviews. The cases involved publishing behemoths Elsevier, Springer, Taylor & Francis, SAGE and Wiley, as well as Informa, at least one of the systems — could make researchers vulnerable to even more serious identity theft. “For a piece of software that’s used by hundreds of thousands of academics worldwide, it really is appalling,” says Mark Dingemanse, a linguist at the Max Planck Institute for Psycholinguistics in Nijmegen, the Netherlands, who has used some of these programs to publish and review papers.

A 14-month investigation that came to involve about 20 people from SAGE’s editorial, legal and production departments. It showed that the Gmail addresses were each linked to accounts with Thomson Reuters’ ScholarOne, a publication-management system used by SAGE and several other publishers, including Informa. Editors were able to track every paper that the person or people behind these accounts had allegedly written or reviewed, says SAGE spokesperson Camille Gamboa. They also checked the wording of reviews, the details of author-nominated reviewers, reference lists and the turnaround time for reviews (in some cases, only a few minutes). This helped the investigators to ferret out further suspicious-looking accounts; they eventually found 130.

SAGE investigators came to realize that authors were both reviewing and citing each other at an anomalous rate. Eventually, 60 articles were found to have evidence of peer-review tampering, involvement in the citation ring or both. “Due to the serious nature of the findings, we wanted to ensure we had researched all avenues as carefully as possible before contacting any of the authors and reviewers,” says Gamboa. When the dust had settled, it turned out that there was one author in the centre of the ring: Peter Chen, an engineer then at the National Pingtung University of Education (NPUE) in Taiwan, who was a co-author on practically all of the papers in question.

PASSWORD LOOPHOLE
Moon and Chen both exploited a feature of ScholarOne’s automated processes. When a reviewer is invited to read a paper, he or she is sent an e-mail with login information. If that communication goes to a fake e-mail account, the recipient can sign into the system under whatever name was initially submitted, with no additional identity verification. Jasper Simons, vice-president of product and market strategy for Thomson Reuters in Charlottesville, Virginia, says that ScholarOne is a respected peer-review system and that it is the responsibility of journals and their editorial teams to invite properly qualified reviewers for their papers.

ScholarOne is not the only publishing system with vulnerabilities. Editorial Manager, built by Aries Systems in North Andover, Massachusetts, is used by many societies and publishers, including Springer and PLOS. The American Association for the Advancement of Science in Washington DC uses a system developed in-house for its journals Science, Science Translational Medicine and Science Signaling, but its open-access offering, Science Advances, uses Editorial Manager. Elsevier, based in Amsterdam, uses a branded version of the same product, called the Elsevier Editorial System.

Usually, editors in the United States and Europe know the scientific community in those regions well enough to catch potential conflicts of interest between authors and reviewers. But Lindsay says that Western editors can find this harder with authors from Asia — “where often none of us knows the suggested reviewers”. In these cases, the journal insists on at least one independent reviewer, identified and invited by the editors.

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Reporter: Aviva Lev-Ari, PhD, RN

 

 

READ THE HISTORY OF PeerJ

https://pharmaceuticalintelligence.com/open-access-scientific-journal/peerj-model-for-open-access-online-scientific-journal/

 

From: PeerJ <newsletter@peerj.com>
Date: Wed, 12 Jun 2013 18:10:54 +0000
To: AvivaLev-Ari <Avivalev-ari@alum.Berkeley.edu>
Subject: PeerJ turned One today – help us celebrate by entering our competition

PeerJ
Hi Aviva,
We are very pleased to announce <http://blog.peerj.com/post//celebrating-the-one-year-anniversary-of-peerj>  that this is the one year anniversary of PeerJ – it was on June 12th, 2012 that we first announced ourselves and started the process towards becoming a fully-fledged publishing company. Today, just 12 months later, PeerJ is completely up and running; we are publishing high quality peer-reviewed science; and we are doing our very best to change the world by pushing the boundaries of Open Access!

To briefly overview what has been achieved in the last year – we announced ourselves on June 12th 2012 and opened the PeerJ doors for submissions on December 3rd. We published our first PeerJ articles on Feb 12th 2013, and followed up by launching PeerJ PrePrints on April 3rd 2013. This last year has been spent recruiting an Editorial Board of 800 world renowned researchers; building cutting edge submission, peer-review, publication and pre-print software from scratch; establishing ourselves with all the major organizations who archive, index, list and certify new publications; and building an entirely new type <http://blog.peerj.com/post/46261563342/6-reasons-to-publish-with-peerj>  of publishing company from the ground up.

Some of the highlights have included:

* the fantastic reception <http://svpow.com/2012/08/30/peerj-sorted/>  to our membership model <https://peerj.com/pricing/&gt;  which means that authors now have a way to publish for their lifetime for a single low price payment (starting at just $99);

* the fact that we have been processing submissions with extreme speed and effectiveness <http://blog.peerj.com/post/45340534713/peerj-is-fast> ;

* the fact that our Open Peer Review process has been so well received <http://blog.peerj.com/post/43139131280/the-reception-to-peerjs-open-peer-review>  with over 40% of reviewers now providing their name and almost 80% of authors making their reviews public;

* being named by the Chronicle of Higher Education as one of the “Top 10 Tech Innovators in the Education Sector <http://chronicle.com/article/The-Idea-Makers-Tech/138823/> ” and by Nature as “a significant innovation <http://www.nature.com/news/journal-offers-flat-fee-for-all-you-can-publish-1.10811> ”;

* and of course the fact that the journal has turned out to be so innovative <http://blog.peerj.com/post/42920094844/peerj-functionality> , beautiful and aesthetically pleasing <http://theseamonster.net/2013/05/peerj-awesomeness/> .

The giveaway

We are celebrating this milestone with a new PeerJ Competition. On June 19th, we will give away 12 “complimentary publication” passes (the ability to publish one paper with us at no cost to you or any of your co-authors) + a PeerJ Charlie T-Shirt + a pin + a fridge magnet (!) to a random selection of 12 people (one for each month of our first year) who publicly post some variation of the following message:

“PeerJ just turned one! Open access publishing, for just $99 for life – check them out and submit now!”

Please include a link to us as well (you choose the best one!).

The last year has been an intense journey, and to be honest we have been so busy we almost missed the anniversary! We would like to take this opportunity to thank the many thousands of researchers who have signed up as PeerJ Members; all those who have authored or reviewed articles; all those who have joined our Editorial Board; and anyone who have simply expressed their support – without the involvement and enthusiasm of these people we would not be where we are today. Of course, we must also thank our dedicated staff (Alf Eaton, Patrick McAndrew and Jackie Thai) and Tim O’Reilly, who collectively took a chance on a brand new publishing concept, but who have been irreplaceable in making us what we are today!

Please encourage your colleagues to look into PeerJ, and make sure they consider submitting their next article to us. The future of academic publishing is here, right now <http://blog.peerj.com/post/46261563342/6-reasons-to-publish-with-peerj> .

The PeerJ Founders
and the PeerJ Team

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Reporter: Aviva Lev-Ari, PhD, RN

Publishing’s Gender Gap

Female scholars are gaining ground in publishing, but cluster in sub-disciplines and tend not to be listed as first or last authors.

By Beth Marie Mole | October 23, 2012

Marie Curie, Wikimedia, UnknownThe percentage of women authors in academic publishing has risen to 30 percent since 1665, but women are still less likely to be first or last author, and tend to cluster in sub-disciplines, according toresearchers at the University of Washington who analyzed two million academic papers published from 1665 to 2010 by 2.7 million scientists, social scientists, and humanities scholars.

“The results show us what a lot of people have been saying and many of my female colleagues have been feeling,” environmental scientist Jennifer Jacquet of New York University, who was involved in the study, told The Chronicle of Higher Education. “Things are getting better for women in academia,” despite the fact that they are still not publishing at the same rate and level as their male counterparts.

Mining JSTOR, a digital archive of scholarly publications, the researchers tagged articles by field and subfield of research, then used data from the Social Security Administration to identify author age. Most importantly, they also tagged authors by gender, assuming that if a name was used 95 percent of the time for one gender it was probably accurate. Publications with androgynous author names were left out of the analysis.

In 2010, when women scholars reached 30 percent of published authors, women made up 42 percent of full-time faculty, 34 percent of which were tenured professors. This suggests that although women are continually gaining ground in publishing—only 27 percent of authors publishing between 1990 and 2010 were women—they are still not publishing at the same rate as men. Moreover, women are under-represented as the coveted first author, the lead author on the research, as well as last author, considered the senior researcher on the study. In molecular and cellular biology, for example, women made up 30 percent of the authors but only 16.5 percent of the last authors. And only about 19 percent of women were first author overall, with the majority falling in the second, third, or fourth author listed.

When the researchers looked at the gender distribution among sub-disciplines, they found additional disparities. For example, although women comprised 30 percent of authors overall, some subfields, such as paleontology, had only 16.6 percent female authors.

Despite the gaps in publishing, the data don’t necessarily provide evidence for gender discrimination. “The international literature show that when women submit work, there is no bias in it being accepted, but the likelihood of women submitting work may be lower,” human development professor Wendy Williams of Cornell University, who studies women’s role in science, told The Chronicle. Still, most believe the results warrant further study.

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