Communications of the ACM
Free, Open Virtual Laboratory For Infectious Diseases
Credit: Hoboken Women's Association
Doctors around the world will soon have a powerful new tool at their disposal in the fight against infectious diseases: a virtual laboratory that will help them match drugs to patients and make treatments more effective. The ViroLab Virtual Laboratory, the core components of which are scheduled to be available online in 2010, uses the latest advances in machine learning, data mining, grid computing, modeling and simulation to turn the content of millions of scientific journal articles, disparate databases and patients' own medical histories into knowledge that can effectively be used to treat disease.
Developed by a multidisciplinary team of European researchers working in the EU-funded ViroLab project, the virtual laboratory is already being used in seven hospitals to provide personalized treatment to HIV patients and is eliciting widespread interest as a potent decision-support tool for doctors.
"ViroLab finds new pathways for treatment by integrating different kinds of data, from genetic information and molecular interactions within the body, measured in nanoseconds, up to sociological interactions on the epidemiological level spanning years of disease progression," says Peter Sloot, a computational scientist at the University of Amsterdam and the coordinator of ViroLab.
Sloot came up with the idea for ViroLab a decade ago when he met a virologist at a scientific conference who told him about the problems doctors face when trying to find the right cocktail of antiretroviral drugs to treat people infected with HIV, the virus that causes AIDS. Because HIV frequently mutates and can quickly become resistant to drugs, doctors need to know which medications are likely to be effective in slowing the progression of the disease. For that, they must take into account not only the strain of the virus the person is infected with but also the patient's own medical history, genetic information and even sociological factors.
"It's like a lock and key. Drugs are keys made to fit certain locks, which are part of the viruses. If the locks change then the key no longer fits—and each lock is different for each patient. That is why we need personalized medicine," Sloot says.
Drawing Meaning From Data
The ViroLab Virtual Laboratory uses a combination of technologies and methods to help doctors make decisions about the best medication to give each individual patient, accessed through a simple-to-use Web interface.
The system continuously crawls grid-connected databases of virological, immunological, clinical, genetic and experimental data, extracts information from scientific journal articles (such as the results of drug resistance experiments) and draws on other sources of information. This data is then processed to give it machine-readable semantic meaning and analyzed to produce models of the likely effects of different drugs on a given patient. Each medication is ranked according to its predicted effectiveness in light of the patient's personal medical history.
Crucially, the system incorporates the concept of provenance, ensuring that every step a doctor takes in creating a workflow to find the right drug for a patient and every step the system takes to provide a recommendation is recorded. Because of the distributed nature of the virtual laboratory, cases can be compared to those of other patients living a few streets or thousands of kilometers away. And the system can even generate models simulating the likely spread and progression of different mutations of viruses based not only on medical data but also on sociological information.
"Say a government has 500 million euros to spend on HIV research and wants to know whether they should focus on funding the development of new drugs or on preventive measures such as encouraging people to change their sexual behavior. We can give them an answer as to what would be more effective," Sloot says.
The ViroLab coordinator says the project's focus on HIV was driven not only by the scale and importance of the epidemic but also by the wealth of information about it. "I make mathematical models and for models you need data," Sloot says.
The ViroLab Virtual Laboratory could be equally effectively used to create personalized drug rankings to aid in the treatment of people suffering from other diseases. It is something Sloot and other members of the ViroLab consortium are exploring in DynaNets, a follow-on EU-funded project that will look at drug dynamics in groups people infected with the H1N1 flu virus and co-infections, in addition to drug-resistant HIV.
Sloot, who "went back to school" during the project to study virology and epidemiology, puts the success of ViroLab, which received funding from the EU's Sixth Framework Program, down to the multidisciplinary nature of the team involved. It has proven to be a productive collaboration that is set to continue.
"We are committed to continuing our work with whatever funding we can get. We are not at present interested in commercializing this technology," Sloot says. "We want it to be open and free. The goal is not to make money from it but to contribute something to the world."
ViroLab was funded under the ICT strand of the EU's Seventh Framework Program for research.
From ICT Results
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Anonymous
After 6 months of offering stem cell therapy in combination with the venous angioplasty liberation procedure, patients of CCSVI Clinic have reported excellent health outcomes. Ms. Kasma Gianopoulos of Athens Greece, who was diagnosed with the Relapsing/Remitting form of MS in 1997 called the combination of treatments a cure. I feel I am completely cured says Ms. Gianopoulos, my symptoms have disappeared and I have a recovery of many functions, notably my balance and my muscle strength is all coming (back). Even after six months, I feel like there are good changes happening almost every day. Before, my biggest fear was that the changes wouldnt (hold). I dont even worry about having a relapse anymore. Im looking forward to a normal life with my family. I think I would call that a miracle.
Other recent MS patients who have had Autologous Stem Cell Transplantation (ASCT), or stem cell therapy have posted videos and comments on YouTube. www.youtube.com/watch?v=jFQr2eqm3Cg.
Dr. Avneesh Gupte, the Neurosurgeon at Noble Hospital performing the procedure has been encouraged by results in Cerebral Palsy patients as well. We are fortunate to be able to offer the treatment because not every hospital is able to perform these types of transplants. You must have the specialized medical equipment and specially trained doctors and nurses. With regard to MS patients, We are cautious, but nevertheless excited by what patients are telling us. Suffice to say that the few patients who have had the therapy through us are noticing recovery of neuro deficits beyond what the venous angioplasty only should account for.
Dr. Unmesh of Noble continues: These are early days and certainly all evidence that the combination of liberation and stem cell therapies working together at this point is anecdotal. However I am not aware of other medical facilities in the world that offer the synthesis of both to MS patients on an approved basis and it is indeed a rare opportunity for MS patients to take advantage of a treatment that is quite possibly unique in the world.
Autologous stem cell transplantation is a procedure by which blood-forming stem cells are removed, and later injected back into the patient. All stem cells are taken from the patient themselves and cultured for later injection. In the case of a bone marrow transplant, the HSC are typically removed from the Pelvis through a large needle that can reach into the bone. The technique is referred to as a bone marrow harvest and is performed under a general anesthesia. The incidence of patients experiencing rejection is rare due to the donor and recipient being the same individual.This remains the only approved method of the SCT therapy.
Anonymous
Unnecessary risks are being taken by patients seeking the liberation treatment. says Dr. Avneesh Gupte of the CCSVI Clinic. It has been our contention since we started doing minimally invasive venous angioplasties nearly 6 years ago that discharging patients who have had neck vein surgery on an outpatient basis is contra-indicated. We have been keeping patients hospitalized for a week to 10 days as a matter of safety and monitoring them for symptoms. Nobody who has the liberation therapy gets discharged earlier than that. During that time we do daily Doppler Ultrasounds, blood work and blood pressure monitoring among other testing. This has been the safe practice standard that we have adopted and this post-procedure monitoring over 10 days is the subject of our recent study as it relates to CCSVI for MS patients.
Although the venous angioplasty therapy on neck veins has been done for MS patients at CCSVI Clinic only for the last 18 months it has been performed on narrow or occluded neck veins for other reasons for many years. Where we encounter blocked neck veins resulting in a reflux of blood to the brain, we treat it as a disease, says Gupte. Its not normal pathologyand we have seen improved health outcomes for patients where we have relieved the condition with minimal occurrences of re-stenosis long-term. We believe that our record of safety and success is due to our post-procedure protocol because we have had to take patients back to the OR to re-treat them in that 10-day period. Otherwise some people could have run into trouble, no question.
Calgary MS patient Maralyn Clarke died recently after being treated for CCSVI at Synergy Health Concepts of Newport Beach, California on an outpatient basis. Synergy Health Concepts discharges patients as a rule without in-clinic provisions for follow up and aftercare. Post-procedure, Mrs. Clarke was discharged, checked into a hotel, and suffered a massive bleed in the brain only hours after the procedure. Dr. Joseph Hewett of Synergy Health recently made a cross-Canada tour promoting his clinic for safe, effective treatment of CCSVI for MS patients at public forums in major Canadian cities including Calgary.
That just couldnt happen here, but the sooner we develop written standards and best practices for the liberation procedure and observe them in practice, the safer the MS community will be, says Dr. Gupte. The way it is now is just madness. Everyone seems to be taking shortcuts.We know that it is expensive to keep patients in a clinical setting over a single night much less 10 days, but its quite absurd to release them the same day they have the procedure. We have always believed it to be unsafe and now it has proven to be unsafe. The thing is, are Synergy Health Concepts and other clinics doing the Liberation Treatment going to be changing their aftercare methods even though they know it is unsafe to release a patient on the same day? The answer is no, even after Mrs. Clarkes unfortunate and unnecessary death. Therefore, they are not focused on patient safetyits become about money only and lives are being put at risk as a result.
Joanne Warkentin of Morden Manitoba, an MS patient who recently had both the liberation therapy and stem cell therapy at CCSVI Clinic agrees with Dr. Gupte. Discharging patients on the same day as the procedure is ridiculous. I was in the hospital being monitored for 12 days before we flew back. People looking for a place to have the therapy must do their homework to find better options. We found CCSVI Clinic and theres no place on earth thats better to go for Liberation Therapy at the moment. I have given my complete medical file from CCSVI Clinic over to my Canadian physician for review. For more information Log on to http://ccsviclinic.ca/?p=866 OR Call on toll free: 888-419-6855.
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