UTHealth is located in the Texas Medical Center, considered the largest medical center in the world. It is composed of six schools: UTHealth Medical School, The University of Texas Graduate School of Biomedical Sciences, UTHealth School of Dentistry, UTHealth School of Nursing, UTHealth School of Biomedical Informatics, and UTHealth School of Public Health.
UTHealth faculty have been instrumental in pioneering the use of Tissue plasminogen activator and the development of Life Flight.
UTHealth research articles from Innovation Toronto
Researchers develop a pipeline to enable fast, accurate image processing for precision medicine
One of the main tools doctors use to detect diseases and injuries in cases ranging from multiple sclerosis to broken bones is magnetic resonance imaging (MRI). However, the results of an MRI scan take hours or days to interpret and analyze. This means that if a more detailed investigation is needed, or there is a problem with the scan, the patient needs to return for a follow-up.
A new, supercomputing-powered, real-time analysis system may change that.
Researchers from the Texas Advanced Computing Center (TACC), The University of Texas Health Science Center (UTHSC) and Philips Healthcare, have developed a new, automated platform capable of returning in-depth analyses of MRI scans in minutes, thereby minimizing patient callbacks, saving millions of dollars annually, and advancing precision medicine.
The team presented a proof-of-concept demonstration of the platform at the International Conference on Biomedical and Health Informatics this week in Orlando, Florida.
The platform they developed combines the imaging capabilities of the Philips MRI scanner with the processing power of the Stampede supercomputer – one of the fastest in the world – using the TACC-developed Agave API Platform infrastructure to facilitate communication, data transfer, and job control between the two.
An API, or Application Program Interface, is a set of protocols and tools that specify how software components should interact. Agave manages the execution of the computing jobs and handles the flow of data from site to site. It has been used for a range of problems, from plant genomics to molecular simulations, and allows researchers to access cyberinfrastructure resources like Stampede via the web.
“The Agave Platform brings the power of high-performance computing into the clinic,” said William (Joe) Allen, a life science researcher for TACC and lead author on the paper. “This gives radiologists and other clinical staff the means to provide real-time quality control, precision medicine, and overall better care to the patient.”
For their demonstration project, staff at UTHSC performed MRI scans on a patient with a cartilage disorder to assess the state of the disease. Data from the MRI was passed through a proxy server to Stampede where it ran the GRAPE (GRAphical Pipelines Environment) analysis tool. Created by researchers at UTHSC, GRAPE characterizes the scanned tissue and returns pertinent information that can be used to do adaptive scanning – essentially telling a clinician to look more closely at a region of interest, thus accelerating the discovery of pathologies.
The researchers demonstrated the system’s effectiveness using a T1 mapping process, which converts raw data to useful imagery. The transformation involves computationally-intensive data analyses and is therefore a reasonable demonstration of a typical workflow for real-time, quantitative MRI.
A full circuit, from MRI scan to supercomputer and back, took approximately five minutes to complete and was accomplished without any additional inputs or interventions. The system is designed to alert the scanner operator to redo a corrupted scan if the patient moves, or initiate additional scans as needed, while adding only minimal time to the overall scanning process.
“We are very excited by this fruitful collaboration with TACC,” said Refaat Gabr, an assistant professor of Diagnostic and Interventional Imaging at UTHSC and the lead researcher on the project. “By integrating the computational power of TACC, we plan to build a completely adaptive scan environment to study multiple sclerosis and other diseases.”
Ponnada Narayana, Gabr’s co-principal investigator and the director of Magnetic Resonance Research at The University of Texas Medical School at Houston, elaborated.
“Another potential of this technology is the extraction of quantitative, information-based texture analysis of MRI,” he said. “There are a few thousand textures that can be quantified on MRI. These textures can be combined using appropriate mathematical models for radiomics. Combining radiomics with genetic profiles, referred to as radiogenomics, has the potential to predict outcomes in a number diseases, including cancer, and is a cornerstone of precision medicine.”
According to Allen, “science as a service” platforms like Agave will enable doctors to capture many kinds of biomedical data in real time and turn them into actionable insights.
“Here, we demonstrated this is possible for MRI. But this same idea could be extended to virtually any medical device that gathers patient data,” he said. “In a world of big health data and an almost limitless capacity to compute, there is little reason not to leverage high-performance computing resources in the clinic.”
Learn more: REAL-TIME MRI ANALYSIS POWERED BY SUPERCOMPUTERS
Rice-led study shows how particles quench damaging superoxides
Injectable nanoparticles that could protect an injured person from further damage due to oxidative stress have proven to be astoundingly effective in tests to study their mechanism.
Scientists at Rice University, Baylor College of Medicine and the University of Texas Health Science Center at Houston (UTHealth) Medical School designed methods to validate their 2012 discovery that combined polyethylene glycol-hydrophilic carbon clusters — known as PEG-HCCs — could quickly stem the process of overoxidation that can cause damage in the minutes and hours after an injury.
The tests revealed a single nanoparticle can quickly catalyze the neutralization of thousands of damaging reactive oxygen species molecules that are overexpressed by the body’s cells in response to an injury and turn the molecules into oxygen. These reactive species can damage cells and cause mutations, but PEG-HCCs appear to have an enormous capacity to turn them into less-reactive substances.
The researchers hope an injection of PEG-HCCs as soon as possible after an injury, such as traumatic brain injury or stroke, can mitigate further brain damage by restoring normal oxygen levels to the brain’s sensitive circulatory system.
The results were reported today in the Proceedings of the National Academy of Sciences.
“Effectively, they bring the level of reactive oxygen species back to normal almost instantly,” said Rice chemist James Tour. “This could be a useful tool for emergency responders who need to quickly stabilize an accident or heart attack victim or to treat soldiers in the field of battle.” Tour led the new study with neurologist Thomas Kent of Baylor College of Medicine and biochemist Ah-Lim Tsai of UTHealth.
PEG-HCCs are about 3 nanometers wide and 30 to 40 nanometers long and contain from 2,000 to 5,000 carbon atoms. In tests, an individual PEG-HCC nanoparticle can catalyze the conversion of 20,000 to a million reactive oxygen species molecules per second into molecular oxygen, which damaged tissues need, and hydrogen peroxide while quenching reactive intermediates.
Tour and Kent led the earlier research that determined an infusion of nontoxic PEG-HCCs may quickly stabilize blood flow in the brain and protect against reactive oxygen species molecules overexpressed by cells during a medical trauma, especially when accompanied by massive blood loss.
Their research targeted traumatic brain injuries, after which cells release an excessive amount of the reactive oxygen species known as a superoxide into the blood. These toxic free radicals are molecules with one unpaired electron that the immune system uses to kill invading microorganisms. In small concentrations, they contribute to a cell’s normal energy regulation. Generally, they are kept in check by superoxide dismutase, an enzyme that neutralizes superoxides.
But even mild traumas can release enough superoxides to overwhelm the brain’s natural defenses. In turn, superoxides can form such other reactive oxygen species as peroxynitrite that cause further damage.
“The current research shows PEG-HCCs work catalytically, extremely rapidly and with an enormous capacity to neutralize thousands upon thousands of the deleterious molecules, particularly superoxide and hydroxyl radicals that destroy normal tissue when left unregulated,” Tour said.
“This will be important not only in traumatic brain injury and stroke treatment, but for many acute injuries of any organ or tissue and in medical procedures such as organ transplantation,” he said. “Anytime tissue is stressed and thereby oxygen-starved, superoxide can form to further attack the surrounding good tissue.”
Read more: Nano-antioxidants prove their potential