Sep
20

Progress Through Partnership: The NINDS 2016 Nonprofit Forum

Last tuesday and wednesday (Sept 13-14th)  I was very honored to be an attendee at the “Progress Through Partnership: The NINDS 2016 Nonprofit Forum“. My role was to provide an industry perspective on several panels (alongside Dr. Ronald Marcus, Cerecor). There were a large number of rare disease (patients or parent) advocates, academic scientists and of course a large number of NINDS attendees. Going into this with no previous experience of the meeting I was a little unsure what I could add. But then as I sat there listening I think I had a unique perspective. I sit in an uneasy space as a scientist, a rare disease advocate and also someone that sees how small business can help. I am also impatient, so any hint that the science is not moving or that perhaps something is being missed, then I was on it. Apologies if it comes across as blunt but frankly with many diseases the progress has been too darn slow because of some key opinion leaders basically owning diseases and not having the ability to embrace new technologies or approaches that have been used elsewhere and could make the difference as outcome measures for clinical trials, for example. Below are some simple notes that I made – apologies if I missed anything while also on the panels on day 1, I also happened to live tweet which I have now storified.

Key points from Dr. Walter Koroshetz’s introduction – there were 161 registrants at this 10th non profit forum. He suggested we need to empower patients and power trials. He mentioned a vibrant translational program with Dr. Amir Tamiz. While the average number of grant applications increased by 25%, the average cost of grant is $379k. He mentioned one of the key policy issues being reproducibility. NINDS needs to support basic research (27% of budget). Some of the NINDS programs were mentioned including IGNITE, CREATE , BLUEPRINT as well as specific RFAs such as the Parkinson’s biomarkers program and the accelerated medicines partnership for Parkinson’s Disease.

Panel 1 – Lessons learned and case studies in natural history databases

Steve Kaminsky (International Rett Syndrome Foundation) their foundation saw 4 clinical sites would not be enough for recruiting and therefore built travel clinics (4-11 sites). He described the need for partnerships with NIH programs. Now other rare diseases are in the program, up to 15 sites using the infrastructure. The data created belongs to the nation,  is protected, and the 15 sites have access. Pharma has to go through PI to get access, and the general public can interface with investigators who can study it (what if the patients wanted to study it – he did not seem to allow for this scenario?). The database was part of RDCRN. He mentioned it was too expensive to keep the database going. Over 7000 data fields for 1234 patients has resulted in publications of impact on sleep, effectiveness of drugs, diagnostics, anxiety etc. all from analysis of 12 yrs of data. He suggested the future is through the past and the past is natural history studies.

Michael Shy (University of Iowa) described Charcot-Marie-Tooth and the more than 90 genes identified. The INC RDCRN is in its 8th yr.  They partner with advocacy groups. MDA, CMTA, and groups in the UK and Asia. They have 20 centers involved. He then focused on the CMT neuropathy score, described natural history studies as a science and how with CMT1A, measuring change that’s detectable is important He described frequent calls with researchers (I wondered are the calls with the RDCRN open to any advocacy groups or just close collaborator groups?).

Steve Roberds (Tuberous sclerosis alliance)  owned their database. He discussed the difference between clinic entered vs patient entered data and getting input from scientists for data collection. Getting information from clinical data and electronic medical records was also described. There was some discussion around what happens after the end of a grant and who owns data, the long term sustainability of a database. Such databases present opportunities whether that is partnering with industry, (e.g. he described a collaborations with Novartis), who can fund changes to the database. They can also access without having to build the database. The alternative was Novartis Europe who collected their own data in Europe via a CRO, and learnt what they had so the elements matched with the US database. Steve also mentioned linking to biosamples and how with highly variable diseases e.g. Epilepsy, tumors, etc. this can add value to the database. He also described how custom built databases could be made simpler and facilitate analysis in order to get finding and papers out to in turn encourage utilization. You have to start a NHS sometime and it is a longtime commitment.

Petra Kauffman (NCATS) discussed disease registry vs NHS, and the need for forward looking data management coordination so that surveys can go out fast. She also mentioned that NCATS is launching a Toolkit for rare disease foundations as an Online portal.

Panel 2. Data integration and data management: challenges and opportunities

Paul Gross (Hydrocephalus association) raised questions to be answered and discussed how to engage clinicians and partner with sites that lead in electronic medical/health records. Find clinicians on Epic’s (steering) board. These board clinicians  advocate for inclusion of data sets.

Greg Farber (NIMH) described the national data archive at NIMH which houses data from 130,000 human subjects. Researchers can submit an application and summary data is available to anyone with a browser. Data on  800TB of image data. NINDS has FITBAR database. Holds data funded by other groups and uses common data elements in data dictionary. Every 6 months they request data from NIH grantees and validate data. They use a global unique identifier which is a hash code that can aggregate data on the same subject from multiple labs. Their database makes data potentially discoverable. Greg also mentioned the challenge of professional clinical research subjects and how to identify them and remove from clinical trials. The database is also citable and linked to the literature.

Shawn Murphy (Harvard Medical School) described how to get large sample size for trials by creating a large warehouse in the EHR. 6.7 million patients in such a database relates to 2.5 billion facts. Data in EHR is not very accurate, e.g. you can test for diagnosis using codes and notes in medical records. Finding patients by query construction in the database was also described. He mentioned that there were over 5000 registered users of tool. He had a NIH grant for i2b2 to create a community of developers, the Hive develops new tools. He also described using phenotyping algorithms to define cohorts of treatment resistant responsive. His goal was to create gold standard training sets. Such that the data could be used to build a classification algorithm to predict depression and improve detection. The CTSA at each site forms networks to combine the data and perform big data queries. For example, what is a normal child? Normal MRI provide visual guides and can be used to make new clinical decisions. He mentioned SHRINE and SMART software also.

Tamara Simon (University of Washington) described using databases to look at CSF shunt complications. She used the PHIS database used across 40 children’s hospitals. She mentioned the hydrocephalus core data project which provided a comprehensive, prospective study. This involved detailed data with 15 forms and 413 questions. This also enabled her to address what patient factors were associated with shunt failures, infection etc. PEDSNet database was also mentioned.

Panel 3. Strategies for biomarker identification

Shahshi Amur (FDA) described resources and tools, and different categories for biomarkers , risk, prognostic etc. biomarkers used in drug development and surrogate endpoints. Enablers for endpoints included data quality , assay imaging protocols. She also stated the difference between qualification and validation, To date 13 unique biomarkers have been qualified by the FDA, and 28 submissions. (She did not mention how long to process qualifications – and what it the cost). She did describe natural history data as useful for prognostic biomarkers using strength of evidence.

Other speakers in this session included Dr’s Katrina Gwinn (NINDS), Hao Wang (NINDS) and Petra Kaufmann (NCATS) who discussed agreeing on biomarker terminology and the need to make sure you are going after the right things for biomarkers. The heterogeneity of patients with disease was mentioned. Consortia were described for bringing groups together to look into them,  how to stop reinvention. Standardizing and training staff to decrease noise in order to get the right treatment for the patient was also brought up. Standardization for bio specimens was thought important as well as the need to improve the quality of publications and the data that has to be associated with it. There was some mention of precompetitve efforts for biomarkers and the need overall for teamwork.

NIH101: priority setting, decision-making, NIH basics and discussion

Alan Willard (NINDS) presented on program considerations and the need to fund early stage investigators, concept clearance for proposed solicitations and influencing what they solicit through RFI.  He also alerted us to how people could volunteer for peer review and go to the CSR website to volunteer expertise. There was also some mention of OnPAR as a way to alerting other foundations of applications that were not funded but may be useful for funding by others.

Panel 4. Developing Better Clinical Outcome measures

Ron Bartek (Friedreich’s Ataxia Research Alliance) moderated this session which included Michael Shy (Univ Iowa)  who described outcome measures such as CMTNSv2, CMTPEDs (But did not describe how or if the scores are accepted by FDA). He also described the disability severity index, PCMT-QOL CMT health index and a recent paper that developed an MRI biomarker as published in Lancet neurology in 2016. Carsten Bonnemann (NINDS) again mentioned GAN and the importance of  using outcome measures from other disorders and combining known outcome measures with exploratory measures. Ray Dorsey (Univ Rochester) suggested the need for novel outcome measures.
He illustrated this as we still use a 100 yr old plus method for scoring Parkinson’s disease. He proposed novel sensors, remote monitoring, wearables, implantables etc. as alternatives. Another example was how voice recording can detect Parkinson’s, Parkinsonism and related disorders from 2015. 15,000 people took part in mobile app based study. It is also possible to measure pharmacological improvement in an app. Huntingtons disease and step time was yet another example. He also mentioned the importance of measuring patients function in the home environment. He made an excellent comment at the end of his presentation about some thought leaders embracing technology (and yet there are many others that do not).  Jacob Kean (University of Utah) discussed improving precision in patient reported outcomes, using and adaptive approach for using measures and short form selection. He also described how the NIH invested in PROMIS and the importance of tracking registry participants. Matthew Goodwin (Northeastern Univ) gave a very animated presentation which alerted the audience to the stickiness of technology and how wearables could give very clear kinematic signatures. Examples he used included tracking heart rate in autism, repeated measures which you can see groups clustering in. Also described were differences in hyper vs hypo aroused patients, and in epilepsy you can detect onset with wearable devices that can differentiate tonic and clonic signatures. There was also the potential to get devices to combine information with elements of citizen science for engagement. Some of the drawbacks include the cost of data analysis, in which case sampling might be good to find the signal. There is also the need for researchers that can do the modeling and the health sciences. Increasingly clinical companies are wanting to use mobile technologies.

Other elements are captured in the tweets used in the storify below.

Aug
16

Collaborations Pharma, Inc. And Rutgers Announce NIH Award to Develop Treatments for Tuberculosis

To follow up my last post .. I can now announce some recent funding from NIAID for the TB work with Dr. Joel Freundlich ! Here is the PR –

Fuquay-Varina, North Carolina – The National Institute of Allergy and Infectious Diseases (NIAID) recently awarded $149,388 to Collaborations Pharma, Inc. (CPI) to initiate a partnership with Rutgers aimed at developing a series of compounds for treating tuberculosis (TB), an infectious disease generally affecting the lungs in humans and caused by the bacterium Mycobacterium tuberculosis (Mtb).

One-third of the global population is understood to be infected with TB and the disease continues to kill 1.5 million people every year and to infect approximately 9 million. Despite the availability of effective treatments for the disease, the combined impacts of drug resistance and morbidity of patients co-infected with HIV/AIDS have stimulated research on new quicker acting (less than the current six-month minimum) treatments efficacious against drug-resistant infections that are less toxic when used with anti-retroviral regimens for HIV/AIDS.

“We initially used Bayesian machine learning models to rediscover a class of compounds which seems to have been neglected for over 40 years ago. The compound we found has activity against drug-sensitive TB as well drug-resistant forms” said Sean Ekins, CEO CPI.

“To date my lab has made many analogs of the initial active compound we co-discovered with Dr. Ekins. Our plan is to focus on addressing limitations using computational models developed by CPI to see if we can arrive at a compound with good activity in an acute mouse model of the disease” said Dr. Joel S. Freundlich, Associate Professor of Pharmacology, Physiology & Neuroscience and Medicine at Rutgers University–New Jersey Medical School.

Dr. Freundlich has a chemical biology lab of eleven scientists that utilizes a multi-disciplinary approach to study infectious diseases, with a specific focus on tuberculosis. His lab will aim to identify potential drug candidates as well as the mechanism of action of this antitubercular class. Ultimately their goal is to optimize this compound class to develop a commercially viable new series of antibacterials.

“This work is a wonderful example of our efforts to involve outside companies in our search for novel antibacterials” said Dr. David Perlin, Executive Director, Professor at the Public Health Research Institute Center at Rutgers and Principal Investigator, NIH/NIAID Center of Excellence in Translational Research.

“We are very grateful to NIAID for funding this project as CPI is focused on collaborations with academia so that we can apply our computational approaches to real world applications that can impact research on neglected diseases” said Dr. Ekins.

About Rutgers New Jersey Medical School
Founded in 1954, Rutgers New Jersey Medical School is the oldest school of medicine in the state. Today it is part of Rutgers, The State University of New Jersey, and graduates approximately 170 physicians a year. Dedicated to excellence in education, research, clinical care and community outreach, the medical school comprises 22 academic departments and works with several healthcare partners, including its principal teaching hospital, Newark University Hospital. Its faculty consists of numerous world-renowned scientists and many of the region’s “top doctors.” New Jersey Medical School hosts more than 50 centers and institutes, including the Public Health Research Institute Center, the Global Tuberculosis Institute and the Neurological Institute of New Jersey. For more information please visit: njms.rutgers.edu

About Collaborations Pharmaceuticals, Inc.
Collaborations Pharmaceuticals, Inc. performs research and development on innovative therapeutics for multiple rare and infectious diseases. We partner with academics or companies to identify and translate early preclinical to clinical stage assets. We have considerable experience of preclinical and computational approaches to drug discovery and toxicity prediction. For more information, please visit http://www.collaborationspharma.com/

Aug
04

Gearing up the new company

Well, its been quiet for several weeks as I had a few projects to complete. One was the final report for an SBIR and in addition I have been curating a special edition of Drug Discovery Today focused on Tuberculosis as well as writing grants (I am always writing grants). So lots of writing basically interspersed with some science and collaborations on new projects.

August marks the start of a clean break. I am going to mostly focus on my own company Collaborations Pharmaceuticals, Inc. which started over a year ago but has been in stealth mode. I have been putting together a number of collaborations and writing grants and doing preliminary work. The goal is to use this as an opportunity to address several rare and neglected diseases. It builds on the work Jill Wood, collaborators and I have been doing at Phoenix Nest Inc for Sanfilippo Syndrome. I reasoned what we have done for a single disease could be applied much more broadly. I have been approached by several families with children with rare diseases over the years and I am sure this will continue. What if there was a way to use the Phoenix Nest model to apply to their disease. Namely, provide a means to get STTR grants with collaborator academics working on the disease of interest. So it is pretty simple, as a business model. Identify the diseases, collaborators, write and win the grants and then ultimately license the science. I feel like this is the ultimate experiment. Twenty plus years of collaboration in the industry in various positions have lead to this. Start small, win grants, hire people and build business.

The challenge is continuing to build up Phoenix Nest and also serve as CSO of the Hereditary Neuropathy Foundation which are my major responsibilities as well as my many ongoing collaborations with scientists at many academic groups. This is a good opportunity to evaluate and plan for the future. One of the challenges will be managing a growing number of collaborations and I think this will create new opportunities for software development too. If there is anyone that wants to help me to find excellent academic collaborators then please get in touch. I am always open to new ideas!

I really enjoy the challenge of doing something that is new or a different topic, and in the past decade I have been successful in obtaining small business grants to help build other people’s companies. Now its time to use this ability for something which I started myself. I know it will require dogged persistence and patience (which I don’t have much of). The focus on rare diseases came from a single meeting while that of neglected diseases has built on collaborations initiated over the past 8 years or so and I hope it can build a second sustainable business and create jobs and treatments. As always, I will endeavor to document the process here as I can.

 

Jul
11

Experience with Reddit Science AMA

Today I took part in a Reddit Science Ask Me Anything (AMA). I had been invited to do this by the nice folks at Springer so I chose rare diseases as my topic and had 100s of questions to answer.

This naturally took far longer than 1hr to answer. Generally a good mix of topics from people introducing their rare disease of interest as well as people asking career advice. I would recommend it as a form of outreach and who knows it will likely lead to new connections. As scientists we should definitely be exploring methods like this to get the word out. Thank you for all the questions!\

(PS – I should add by the end of the day I probably spent 5hrs answering questions..debating how frequently to follow up and check in and respond. The format is not something I have a lot of experience with.)

 

 

Jun
27

MM4TB and a trip to a new Miro Exhibit

 


OIMG_0999 (2)ccasionally I take a bit of a diversion from my usual science focused postings, this one has an artistic flavor.

I am in beautiful Brataslava in the Slovak Republic for a few days for the final More Medicines for Tuberculosis (MM4TB) meeting. Every 6 months for the past 5 years we have had meetings of the members in this EU FP7 funded project working on developing new treatments for TB. To me these meetings have been a wonderful example of global collaboration with over 20 academic or company labs working on various elements from high throughput screening to X-ray crystallography.

IMG_0961
This afternoon we had a little break from the science presentations and took a tour of a new exhibit at the Danubiana Meulensteen Art Museum. I was pleasantly surprised by the museum which is very modern and displays an extensive array of modern art from local artists.

The exhibit we came to see is yet to open to the public and it is called “Miro and Cobra” and it runs until the 13th November 2016. We were very honored to have a treat of an exclusive guided tour from the director Vincent Polakovič . I should say the museum itself is a national treasure, but this exhibit is a must see for any Miro fan. I will not spoil it for you but I include only a few photos to whet the appetite!

IMG_0979

Having the Miro exhibit is a huge coup for this Museum and the light airy space really does the art a lot of favors, making the colors pop and shining a spotlight on the various sculptures.IMG_0959

My favorite part of the exhibit was the room that replicated Miro’s studio, complete with easels, split cane chairs. It felt like Miro was there and had just walked out for a breath of fresh air in between painting.

So although the MM4TB is coming to a close this trip will be remembered as a highlight. Thank you Katarína Mikušová for organizing the meeting and the magnificent hospitality of your country.

I would recommend a vacation to Bratislava and I will be back in future.

Next we have a little wine tasting before resuming the science tomorrow!   IMG_0962 (2) IMG_0958

Jun
24

BIO2016 and getting Big Pharma to listen to the patient’s voice..

Its hard to believe that a couple of weeks ago BIO2016 was coming to an end. After 5 days in San Francisco my legs were tired, my voice was rough, and I was tired of boxed lunches and eating dinner at crazy irregular times – generally very late. Its a hard life!

I was at the meeting thanks to the nice people at BIO who invited a whole array of patient advocates / disease foundations for the Patient pavilion. Don Gibbons from CIRM did a really nice blog on this and has some photos so you can see Allison Moore from the Hereditary Neuropathy Foundation and I in action. A big thanks to Gautami Inamdar for inviting us.

We used the opportunity to network with companies big and small and find out which ones might have potential therapeutics for Charcot-Marie-Tooth. We also used this as a platform to highlight the upcoming patient centered CMT summit.

Frankly BIO treated all the groups in the patient pavilion like VIPs, we could apply for front row seating to all the key notes, we had our own social event and had a tour of Genentech. This was pretty special, being bused to their site, escorted around a couple of labs, meeting scientists and getting wined and dined. Genentech really rolled out the red carpet. At one point we were in the high throughput screening (HTS) lab and in front of us was an ECHO being used to dispense solutions !  Of course the complete Genentech small molecule collection was also there too, just waiting to be screened in an assay. Many of the patient groups I am sure were thinking, in that 1.5 million or so compounds is a potential treatment for [insert name of their]  disease. Lots of questions were asked here and the scientists involved showed just how passionate they could be about the science. In the social hour afterwards we met several other Genentech employees and heard about what the company was doing. I have to say I know a few friends that work for the company so it was great to learn a bit more about the history behind the company.

After the first day or so we spent time in meetings, attending presentations (mitochondrial diseases stood out here) and walking what seemed long distances around the halls. BIO also gave us the opportunity to give a short presentation on HNF and the research we are involved with and funding.

It was not all rosy though, I happened to meet another rare disease parent at the meeting who has a foundation that has funded some research which had started using an FDA approved drug and shown some promising results in vitro. The parent wanted to meet with someone from the company that marketed the drug and so we went along to their booth. We were met with looks as if we were talking a foreign language. Clearly a huge disconnect with people at this big pharma and rare disease parents/ patient advocates. We went to another company who also has a drug in the same class. Again we were brushed off.. It does not have to be this way. We know from the way Genentech treated us, they listened, they seemed open. It appeared as if some of the companies still have much to learn about the importance of rare diseases.

I also had chance to do a bit more networking with additional rare disease foundations and came away from the meeting thinking what if BIO could organize a much small version of the meeting just focused on Rare diseases and at the same time they brought in some of the big pharma to educate them and build collaborations.. would it work..?

 

 

 

 

 

 

May
31

New grants for Phoenix Nest Inc. and LABioMed for Sanfilippo Syndrome treatment development

I can now report some very good news for Phoenix Nest Inc  in our efforts with our wonderful collaborators at LABioMedwe now have a couple of grants to work on treatments for Sanfilippo B and D. 
It would be great if we could find VC or angels that would help us get these treatments to the clinic even faster alongside our work on Sanfilippo C. Please get in touch and help us find more families with this disease
Here is the press release!
Public Release: 

Phoenix Nest and LA BioMed receive over $1.7 million in grant funding

Working together to develop treatments for devastating childhood disease

Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center (LA BioMed)

IMAGE
IMAGE: Patricia Dickson, M.D., LA BioMed lead researcher and director of the institute’s MPS Research Laboratory, will lead the studies seeking new therapies a for devastating childhood disease, MPS III…. view more

Credit: LA BioMed

LOS ANGELES – The National Institute of Neurological Disorders and Stroke recently awarded over $1.7 million in grant funding to Phoenix Nest, Inc. to continue its partnership with the Los Angeles Biomedical Institute (LA BioMed) to research the development of therapies for treating different forms of a devastating inherited genetic disorder, Sanfilippo disease, also known as MPS III.

MPS III disease is a progressive neurological disorder that is generally diagnosed in childhood and can lead to premature death. The new grants are for therapies to combat devastating brain disease due to MPS III types B and D.

Funding for work in MPS IIID is for recombinant enzyme therapy and is a Phase 2 Small Business Technology Transfer (STTR) award, following a successful $223,102 Phase 1 award. Phoenix Nest and LA BioMed were also awarded a Phase 1 STTR grant to develop a novel stem cell therapy for MPS IIIB syndrome. Both treatments have the potential to completely transform the care of children with MPS III disease, as no approved treatments currently exist for any type.

“We are pleased to continue our partnership with Phoenix Nest, Inc. in this important research to help children living with MPS III B and D. After promising results obtained in our first preclinical studies for an enzyme replacement for MPS IIID, we will next look at efficacy in a disease model with a goal of moving towards the clinic as quickly as we can,” said Patricia I. Dickson, MD, LA BioMed lead researcher and director of the institute’s MPS Research Laboratory.

Dr. Dickson has specific expertise in the development of intrathecal enzyme replacement therapies for treating MPS by replacing the missing enzyme through the patients’ spinal fluid.

“We are very grateful to the National Institute of Neurological Disorders and Stroke for continuing to fund this project to find more effective therapies for MPS IIID, which is so debilitating to the patients and causes enormous stress for the families involved,” said Sean Ekins, PhD, chief executive officer of Phoenix Nest, Inc. “The additional funding will be used to manufacture an enzyme for further testing. The research is seeking to develop a therapy that will limit or reverse the neurological damage caused by MPS IIID by delivering an enzyme, recombinant human alpha-N-acetylglucosamine-6-sulfatase (rhGNS), intrathecally to effectively treat the underlying causes of the neurologic symptoms of MPS IIID.”

The National Institute of Neurological Disorders and Stroke also provided funding for development of a treatment for MPS IIIB. “This represents a novel approach to use stem cells to make the enzyme alpha-N-acetylglucosaminidase that is needed to achieve therapeutic benefit,” said Dr. Dickson.

“Phoenix Nest, Inc. is solely focused on Sanfilippo syndrome, and we are honored to continue collaborating with Drs. Dickson, Tsui-Fen Chou, Michelina Iacovino and their teams so that we can develop multiple treatments for MPS IIIB and MPS IIID,” said Dr. Ekins.

###

About LA BioMed

Founded in 1952, LA BioMed is one of the country’s leading nonprofit independent biomedical research institutes. It has approximately 100 principal researchers conducting studies into improved treatments and therapies for cancer, inherited diseases, infectious diseases, illnesses caused by environmental factors and more. It also educates young scientists and provides community services, including prenatal counseling and childhood nutrition programs. LA BioMed is academically affiliated with the David Geffen School of Medicine at UCLA and located on the campus of Harbor-UCLA Medical Center. For more information, please visit http://www.LABioMed.org

About Phoenix Nest, Inc.

Phoenix Nest, Inc. is a biotechnology company focused on Sanfilippo Syndrome founded by and solely owned by several Sanfilippo Syndrome families. They actively collaborate with academic researchers to fund and commercialize their technologies. Phoenix Nest, Inc. also licenses assets from companies and universities that may have utility for Sanfilippo Syndrome. For more information, please visit http://www.phoenixnestbiotech.com.

For further information, please contact Jill Wood, Co-Founder and Chief Financial Officer, Phoenix Nest, 347-689-2186 jwood@phoenixnestbiotech.com

May
23

France faults Bial and Biotrial over fatal drug trial – but what caused it?

New posts appeared yesterday and today on the Bial drug (Bial 10-2474) failure in France.
What follows is the Google translate of this article in Le Figaro

“Biotrial the laboratory, who led the fatal clinical trial in Rennes, committed “three major shortcomings,” the final report of the General Inspectorate of Social Affairs (IGAS), animal health, which confirms its preliminary findings February, according to news reports Sunday. “The mission considers that the responsibility for Biotrial (…) such as Bial laboratory trial sponsor, are engaged,” wrote Le Monde on its online edition, adding having obtained the final report.

“She blames Biotrial ‘three major shortcomings” in the conduct of the trial and Bial a’ delay information of the health authority ‘and a choice insufficiently cautious’ to move to the 50 mg dose in multiple ascending doses, “the paper said. The first “is the lack of research information in a timely manner on developments in the health status of the first volunteer.” The second “no confirmation of their consent to the other volunteers Monday, January 11, before administration of the product.” The third common to Bial and Biotrial: Disregarding the duty to inform without delay the competent health authority.

Biotrial has strongly disputed these findings Sunday in a statement, saying IGAS had breached the principle of contradiction. It further claims that the investigators tried to exert “pressure” on its staff. Finally, it regrets that the investigators did not record the hearings in the minutes. Finally, it “reserves the right to seek the French courts the nullity of the report.” For its part, Liberation, who also had access to the document notes that the National Security Agency of Medicines (ANSM) “is in large part cleared.” As in its preliminary report, IGAS believes that “there is no need to challenge the authorization” to conduct the test.”

“The Biotrial center must commit to better protect healthy volunteers after the fatal clinical trial in Rennes, today ordered the Health Minister, Marisol Touraine, at a press conference. “I demand that Biotrial provide a major action plan to ensure that the deficiencies observed will not happen again,” said the minister. “This action plan will put myself without delay,” she added.

The General Inspectorate of Social Affairs (IGAS), animal health, confirmed, in its final report issued four months after the accident, the three major deficiencies identified in its preliminary report in February. The first is the lack of time and information search time on the evolution of the first voluntary health. The second on the absence of confirmation of their consent to the other volunteers Monday, January 11, before the administration. The third, common to the Portuguese pharmaceutical company Bial and Rennes test center Biotrial, concerns having been slow to inform the health authorities.

“The Inspectors believe that the responsibility of the laboratory and Bial Biotrial is engaged in several ways,” said the minister who decided to resume “full” the recommendations of IGAS. Biotrial has its side yesterday strongly disputed these findings considering that IGAS had breached the principle of contradiction. It further claims that the investigators tried to exert “pressure” on its staff. He regretted that the investigators did not record the hearings in the minutes. Finally, it “reserves the right to seek the French courts the nullity of the report.” ”

What appears to have been missed in this and the earlier report is that we are still no closer to understanding why the drug resulted in the death of one person and the injury to several others. Its seems at least from the science side that we have the same question as in January. All these reports have done is blame both parties rather than get to the bottom of it. This is not science. It is a bureaucratic nightmare.

May
19

Zika Open becomes ‘OpenZika’ on IBM World Community Grid

Logo-openika-blackAmazing to think that in January I was attending the SLAS meeting and over dinner conversations about Zika, I realized that this was one of ‘those defining moments’. I had never worked on the virus, but could I learn anything from the Ebola work that would help? What could we do with the data available at that time? Basically there was nothing more than the sequence of the virus. I would not have predicted what has unfolded since then. A more detailed version of events appears on the AAPS blog later today from me.

The little project that started as #ZikaOpen and resulted in a couple of open papers in the first few months of the year here and here ..has now become a fully fledged international project called OpenZika under the leadership of Dr Carolina Horta Andrade and co PI of Dr. Alexander Perryman (who is in The Joel Freundlich group at Rutgers) and has the IBM World Community Grid behind it. A press release is shown below and I will highlight more as they come out.

(IBM press release: http://www-03.ibm.com/press/us/en/pressrelease/49778.wssWorld Community Grid news article: https://secure.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=480(available in Spanish and Portuguese also) – Citizen IBM blog post: http://citizenibm.com/2016/05/andrade_zika_wcgrid.html )

 

The goal of OpenZika is to help find molecules which we can test against the virus. There are obviously millions of molecules but which ones will work? That is the challenge – can we find/predict them?

We will be docking large libraries of commercially available molecules and known drugs against the crystal structures, homology models of Zika proteins as well as template structures for other viruses. This will create lots of data for analysis that will be made public so others can use it to seed their own research efforts.

Zika presents us with both challenges and opportunities. Lets see what discoveries we can make through collaboration and the work of the community. Everyone contributing their computer or Android phone is basically a willing collaborator in this project. The more people we can get involved, the more computers, and he faster we can complete this project.

I would like to gratefully acknowledge the many people that have helped get us to this point and the continued support of IBM World Community Grid. Lets see where this can go.  I am hopeful we can find something of value for Zika and other viruses.

Here is the press release

Zika Treatment Search Launched, Fueled By IBM’s World Community Grid Crowdsourced research project aimed at helping scientists cure debilitating disease 
ARMONK, NY – 19 May 2016: IBM’s (NYSE: IBMWorld Community Grid and scientists are launching an international study to identify drug candidates to cure Zika, a fast spreading virus that the World Health Organization has declared a global public health emergency.

IBM and a global team of scientists are inviting anyone with a computer or Android device to join the #OpenZika project. Volunteers don’t need to provide time, expertise or money to help; they simply run an app on their Windows, Mac, Linux or Android devices that automatically performs virtual experiments for scientists whenever the machines are otherwise idle.

Through the OpenZika project, World Community Grid will power virtual experiments on compounds that could form the basis of antiviral drugs to cure the Zika virus, which has been linked to serious neurological disorders. With dramatically more speed than possible in a traditional lab, the project will screen compounds from existing molecule databases against models of Zika protein and crystal structures. Screening results will quickly be shared with the research community and general public. Promising compounds would then be tested in the collaborators’ laboratories.

For the OpenZika project, World Community Grid is working with an international team of researchers led in Brazil by the Federal University of Goias, and with support from Brazil’s Oswaldo Cruz Foundation (Fiocruz); Rutgers University’s New Jersey Medical SchoolCollaborations Pharmaceuticals, Inc.; and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California San Diego.

“Enlisting the help of World Community Grid volunteers will enable us to computationally evaluate over 20 million compounds in just the initial phase and potentially up to 90 million compounds in future phases,” said Carolina H. Andrade, Ph.D., professor at the Federal University of Goiás in Brazil and the lead researcher on the OpenZika project. “Running the OpenZika project on World Community Grid will allow us to greatly expand the scale of our project, and it will accelerate the rate at which we can obtain the results toward an antiviral drug for the Zika virus.”

The need for a treatment is acute as warmer weather approaches North America, creating an environment more conducive to Zika-carrying mosquitoes, and as international travelers contract and transmit the virus.

Other anti viral research efforts also hold promise. For example, IBM Research and Singapore’s Institute of Bioengineering and Nanotechnology announced that they have identified a macromolecule that could help prevent deadly viral infections such as Zika. IBM has provided its expertise and resources for other disease outbreaks, such as Ebola. For instance, IBM’s World Community Grid launched a project on Ebola research.

In addition, IBM has helped governments track diseases outbreaks.The company provided a citizen engagement and analytics system in Sierra Leone that enables communities affected by Ebola to communicate their issues and concerns directly to the government. For that pubic health emergency, IBM Research also created opinion-based heat-maps which correlated public sentiment to reported outbreak locations. IBM scientists have created a free, open source tool that helps scientists and public health officials create, use and study spatial and temporal models of emerging infectious diseases such as Zika.

As part of its citizenship program focused on innovative solutions to societal problems, IBM created World Community Grid in 2004 to address researchers’ critical need for supercomputing power. Partially hosted on IBM’s SoftLayer cloud technology, World Community Grid provides massive amounts of supercomputing power to scientists, free of charge. It does this by harnessing the unused computing power of volunteers’ computers and Android devices. More than three million computers and mobile devices used by nearly three quarters of one million people and 470 institutions across 80 countries have contributed virtual supercomputing power for more than two-dozen vitally important projects on World Community Grid over the last 11 years, at a value of more than $500 million.

World Community Grid has helped researchers identify new potential treatments for childhood cancer, identifying new materials for more efficient solar cells, and helping to identify how nanotechnology can filter water more efficiently. Many of these efforts might not have even been attempted without the free supercomputing power provided by IBM’s World Community Grid.

To perform such computational experiments, OpenZika researchers are using a widely used virtual screening tool called AutoDock VINA, developed by the Olson laboratory at The Scripps Research Institute. At its core, World Community Grid is enabled by Berkeley Open Infrastructure for Network Computing (BOINC), an open source platform developed at the University of California, Berkeley and with support from the National Science Foundation.

Volunteers can support the OpenZika search for a cure by joining World Community Grid. IBM also invites researchers to submit research project proposals to receive this free resource. For more information about IBM’s philanthropic efforts, please visit www.citizenIBM.com or follow @CitizenIBM on Twitter.

Contact(s) information

Ari Fishkind

IBM Media Relations

1 (914) 499-6420

fishkind@us.ibm.com

 

Angie Hu

IBM Media Relations

914-499-6532

ahu@us.ibm.com

 

May
17

‘CDD Models’ Case Studies

I just posted some examples of how the Bayesian models and Fingerprints described previously here, here and here, can be used in CDD to build models (here, here and here), generate predictions and be used (or not) to export the models.

For the test cases I used a few examples of public datasets. But the same approach could be taken with data in a private Vault. Bottom line it pretty simple to take a dataset, build the model, access it and then use to make predictions.

The models can then be exported to a mobile app like MMDS for running there on a phone or ipad too.

All of the data sets represent some biological data but that does not need to be the case as long as there is a binary endpoint. Even that may change as we develop new approaches for Bayesian modeling.

 

 

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