TAG: "Imaging"

NSF grant to improve visualization capabilities for biosciences, geosciences


UC San Diego partnering with National Center for Atmospheric Research.

By Ioana Patringenaru, UC San Diego

The National Center for Atmospheric Research (NCAR) is partnering with UC San Diego to expand and enhance visualization capabilities in the bio- and geosciences through a grant from the National Science Foundation.

The collaboration builds on existing software capabilities developed at NCAR and UC San Diego, and it will combine them to produce new open source tools for scientists to explore large data sets.

The project is known as WASP (Wavelet-enabled Progressive Data Access and Storage Protocol).

Current advances in digital imaging and numerical modeling technologies have enabled the creation of vast amounts of data. A challenge for many researchers is making sense out of these digital outputs. One way of dealing with extremely large data sets is known as progressive data access (PDA), which is the enabling technology behind consumer applications like Google Maps. In mapping applications, PDA reduces data volumes by only loading areas of interest, not the entirety of the map database, and allows the user to view these images in greater detail or lesser detail.

The problem is that similar tools are scarce in the biosciences, despite a need for analyzing data gathered from advanced imaging technologies such as MRI and CT scans. And as the size and complexity of the data increase, the computing resources commonly available for data analysis are over-subscribed. The geosciences encounter similar issues, with models for weather, climate, oceans and other Earth systems generating very large and complex data.

Given the similar nature of the challenge across various disciplines, researchers at NCAR and UC San Diego put their heads together to work on a solution, capitalizing on complementary work that was already ongoing at both institutions. Though the bio- and geosciences are very different scientific disciplines, with different data, the underlying forms of the data and structure of the data are very similar, allowing for shared methods of dealing with the data.

Two software approaches

An NCAR team has developed a software solution known as VAPOR, (Visualization and Analysis Platform for Ocean, Atmosphere and Solar Researchers). VAPOR provides an interactive 3-D visualization environment that runs on most UNIX and Windows systems. At the heart of VAPOR is a progressive data access scheme based on mathematical linear transforms using wavelets. An NSF grant launched the development of the technology in 2003, and VAPOR is currently on its third major release, with over 6,000 users worldwide.

“VAPOR is an application specifically designed to facilitate researchers’ interaction with very large data sets, but while using only relatively modest computing resources,” said John Clyne, a software engineer and computer scientist who is the principal investigator for VAPOR in NCAR’s Computational and Information Systems Laboratory (CISL). “It is already widely used in the geosciences community, and with this award we will not only be able to expand and improve it for its current users, but also make it usable for the biosciences and bioimaging communities.”

At UC San Diego, the Center for Scientific Computation in Imaging has been developing a general analysis and visualization software toolkit for the bioimaging community, known as the Shape Analysis for Phenomics from 3-D Imaging Data (SAPID) ToolKit (STK).

The goal of the SAPID project is to develop advanced computational methods for researchers in evolutionary biology to characterize subtle morphological variations from high-resolution 3-D voxel-based digital imaging modalities. A critical issue that arose in this project was the necessity of being able to handle very large datasets. This new NSF award will address this important issue and thus provide these innovative capabilities to the bio-imaging community.

“This award is exciting because it allows us to take our existing software, combine and reuse it in new ways, and expand its capabilities to serve more broadly across scientific disciplines,” said UC San Diego’s Lawrence Frank, the principal investigator for the WASP award and the SAPID Project, as well as a researcher at the Institute of Engineering in Medicine.

Both Frank and Clyne point out that the most important aspect of this collaboration is that it will reuse existing NSF-funded software to provide a common framework that benefits both biological digital imaging and geosciences numerical modeling communities, and will have a profound impact for scientists working with large data sets.

“We’ll be able to provide better tools to the climate and weather science communities, while providing the first such tools for the biosciences community,” said Clyne. “It’s especially gratifying that NSF’s initial investments in both VAPOR and STK can be augmented with this award to produce an impactful and interdisciplinary tool.”

The University Corporation for Atmospheric Research manages the National Center for Atmospheric Research under sponsorship by the National Science Foundation. Any opinions, findings and conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

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First real-time MRI-guided brain surgery for Parkinson’s in SoCal


Deep brain stimulator also can be used to treat other movement disorders.

By Jackie Carr, UC San Diego

Neurosurgeons at UC San Diego Health System are the first in Southern California to implant a deep brain stimulator (DBS) in a patient with Parkinson’s disease using real-time 3-D magnetic resonance image (MRI) guidance.

Parkinson’s disease is a progressive disorder of the nervous system that affects movement. Symptoms include shaking, slowness of movement and difficulty walking. These unpredictable movements are caused by abnormal nerve cell activity in the brain. DBS therapy, like a heart pacemaker, transmits electrical signals to help restore normal activity.

Traditionally, DBS surgery is conducted while the patient is awake, and under pain management. This approach allows surgeons to continuously monitor the patient’s brain function and to ensure accurate placement of the device.

“Now, for some patients, this surgery can be performed in the MRI suite under general anesthesia so that a patient can sleep during the placement of the DBS electrodes,” David Barba, M.D., director of functional neurosurgery, UC San Diego Health System. “Within a few days of DBS therapy, many patients can resume life’s everyday activities.”

“Placing a DBS device while a patient is awake can be exhausting for the patient due to the length of the procedure and the need to perform neurologic testing in the operating room,” added Clark Chen, M.D., Ph.D., director of stereotactic and radiosurgery, UC San Diego Health System. “Fortunately, with continuous real-time MRI monitoring, we can now place the electrode in a safe location that provides maximal neurological benefit while the patient is under the comfort of general anesthesia.”

Bob S. Carter, M.D., Ph.D., professor and chief of neurosurgery and co-director of the UC San Diego Neurological Institute, said the collaborative endeavor introduces a new technology strategy to improve the care of patients with Parkinson’s and other diseases.

“Our capacity to perform these procedures will be further enhanced in the new A. Vassiliadis Family Hospital for Advanced Surgery at Jacobs Medical Center, which opens in 2016,” said Carter.

DBS also can be used to treat other movement disorders, including dystonia, essential tremor and obsessive compulsive disorder. It is in clinical trial testing as treatment for depression.

UC San Diego Health System is an internationally recognized leader in functional neurosurgery. Barba is a pioneer in the neurosurgical treatment of patients affected with movement disorders. Chen is an expert in MRI guided neurosurgery.

To learn more about MRI-guided DBS placement, please visit: health.ucsd.edu.

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Finding a better way to track emerging cell therapies using MRIs


Technique might speed development of relevant therapies.

Cellular therapeutics – using intact cells to treat and cure disease – is a hugely promising new approach in medicine, but it is hindered by the inability of doctors and scientists to effectively track the movements, destination and persistence of these cells in patients without resorting to invasive procedures, like tissue sampling.

In a paper published Sept. 17 in the online journal Magnetic Resonance in Medicine, researchers at the UC San Diego School of Medicine, University of Pittsburgh and elsewhere describe the first human tests of using a perfluorocarbon (PFC) tracer in combination with non-invasive magnetic resonance imaging (MRI) to track therapeutic immune cells injected into patients with colorectal cancer.

“Initially, we see this technique used for clinical trials that involve tests of new cell therapies,” said first author Eric T. Ahrens, Ph.D., professor in the Department of Radiology at UC San Diego. “Clinical development of cell therapies can be accelerated by providing feedback regarding cell motility, optimal delivery routes, individual therapeutic doses and engraftment success.”

Currently, there is no accepted way to image cells in the human body that covers a broad range of cell types and diseases. Earlier techniques have used metal ion-based vascular MRI contrast agents and radioisotopes. The former have proven difficult to differentiate in vivo; the latter raise concerns about radiation toxicity and do not provide the anatomical detail available with MRIs.

“This is the first human PFC cell tracking agent, which is a new way to do MRI cell tracking,” said Ahrens. “It’s the first example of a clinical MRI agent designed specifically for cell tracking.”

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CT scan is no better than ultrasound to detect kidney stones


UCSF study leader recommends change in standard practice.

Rebecca Smith-Bindman, UC San Francisco

To diagnose painful kidney stones in hospital emergency rooms, CT scans are no better than less-often-used ultrasound exams, according to a clinical study conducted at 15 medical centers and published in the Sept. 18 issue of the New England Journal of Medicine.

Unlike ultrasound, CT exposes patients to significant amounts of radiation. Although CT scans are favored by emergency-room physicians for kidney stone diagnosis, ultrasound should be used as the first step, according to senior study author Rebecca Smith-Bindman, M.D., a professor in the departments of radiology; epidemiology and biostatistics; and obstetrics, gynecology and reproductive medicine at UC San Francisco.

“Ultrasound is the right place to start,” Smith-Bindman said. “Radiation exposure is avoided, without any increase in any category of adverse events, and with no increase in cost.” Patients in the study who were first examined with ultrasound sometimes received a follow-up CT exam at the physician’s discretion.

“Our results do not suggest that patients should undergo only ultrasound imaging, but rather that ultrasonography should be used as the initial diagnostic imaging test, with further imaging studies performed at the discretion of the physician on the basis of clinical judgment,” the study authors said.

Kidney stone rates are increasing, and in a 2010 National Health and Nutrition Examination Survey, one in 11 people reported having had at least one kidney stone. The use of CT to diagnose kidney stones has risen 10-fold in the last 15 years. CT exams generally are conducted by radiologists, while ultrasound exams may be conducted by emergency room physicians as well as radiologists.

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Related link:
Innovation Profile: Rebecca Smith-Bindman

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MRI is a ‘game-changer’ in diagnosing prostate cancer


UC San Diego Health System is first to use new tool in San Diego.

Oncologists at UC San Diego Moores Cancer Center are the first in San Diego to meld magnetic resonance imaging (MRI) technology with a traditional ultrasound prostate exam to create a three-dimensional map of the prostate that allows physicians to view growths that were previously undetectable.

An ultrasound machine provides an imperfect view of the prostate, resulting in an under-diagnosis of cancer, said J. Kellogg Parsons, M.D., M.H.S., the UC San Diego Health System urologic oncologist who, along with Christopher Kane, M.D., chair of the Department of Urology and Karim Kader, M.D., Ph.D., urologic oncologist, is pioneering the new technology at Moores Cancer Center.

“With an ultrasound exam, we are typically unable to see the most suspicious areas of the prostate so we end up sampling different parts of the prostate that statistically speaking are more likely to have cancer,” said Parsons, who is also an associate professor in the Department of Urology at UC San Diego School of Medicine. “The MRI is a game-changer. It allows us to target the biopsy needles exactly where we think the cancer is located. It’s more precise.”

Armondo Lopez, a patient at Moores Cancer Center, had been given a clean bill of health using the traditional ultrasound biopsy method, but when his prostate-specific antigen (PSA) levels, a protein that is often elevated in men with prostate cancer, started to rise he began to worry. Parsons recommended a MRI-guided prostate biopsy. The new technology led to the diagnosis of an aggressive prostate cancer located in an area normally not visible using the ultrasound machine alone. The tumor was still in its early stage and treatable, said Parsons.

An early diagnosis typically improves a patient’s prognosis. In the United States, prostate cancer is the second leading cause of cancer death in men with more than 29,000 estimated deaths expected this year. The average age at the time of diagnosis is about 66.

Lopez is thankful he will be able to celebrate his 58th wedding anniversary with his wife.

“Life is going on as normal,” said Lopez. “This is the wave of the future. I see this new technology as the way to save thousands of lives. I commend Dr. Parsons for taking the lead in San Diego in this area.”

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Mapping the infant brain


Findings may be key in identifying, treating earliest signs of neurodevelopmental disorders.

A recent study conducted by researchers at the UC San Diego School of Medicine and the University of Hawaii demonstrates a new approach to measuring early brain development of infants, resulting in more accurate whole brain growth charts and providing the first estimates for growth trajectories of subcortical areas during the first three months after birth. Assessing the size, asymmetry and rate of growth of different brain regions could be key in detecting and treating the earliest signs of neurodevelopmental disorders, such as autism or perinatal brain injury.

The study will be published in JAMA Neurology today (Aug. 11).

For the first time, researchers used magnetic resonance imaging (MRI) of the newborn brain to calculate the volume of multiple brain regions and to map out regional growth trajectories during the infant’s first 90 days of life. The study followed the brain growth of full term and premature babies with no neurological or major health issues.

“A better understanding of when and how neurodevelopmental disorders arise in the postnatal period may help assist in therapeutic development, while being able to quantify related changes in structure size would likely facilitate monitoring response to therapeutic intervention. Early intervention during a period of high neuroplasticity could mitigate the severity of the disorders in later years,” said Dominic Holland, Ph.D., first author of the study and researcher in the Department of Neurosciences at UC San Diego School of Medicine.

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New terahertz modulator could lead to more advanced medical, security imaging


Could be used to examine human tissue for signs for disease without damaging cells.

Electron microscope image showing the metasurface for a terahertz modulator developed by a group led by UCLA professor Mona Jarrahi.

A UCLA Henry Samueli School of Engineering and Applied Science research team has developed a breakthrough broadband modulator that could eventually lead to more advanced medical and security imaging systems.

Modulators manipulate the intensity of electromagnetic waves. For example, modulators in cell phones convert radio waves into digital signals that the devices can use and understand. In terahertz-based communication and imaging systems, they modify the intensity of terahertz waves.

Today’s technologies take advantage of many parts of the electromagnetic spectrum — notably light waves and radio waves — but they rarely operate in the terahertz band, which lies between infrared and microwave on the spectrum.

Led by Mona Jarrahi, UCLA associate professor of electrical engineering, the group developed a terahertz modulator that performs across a wide range of the terahertz band with very high efficiency and signal clarity. Among the device’s advantages are that it could easily be incorporated into existing integrated circuit manufacturing processes, can operate at room temperature and does not require an external light source to operate.

The terahertz band has been the subject of extensive research, in large part because of its potential for medical imaging and chemical sensing technologies. For example, terahertz waves could be used to examine human tissue for signs for disease without damaging cells or the other health risks posed by X-rays. They also could be used in security screenings to penetrate fabric or plastics that conceal weapons.

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Minor head injury not reason enough for CT scan in children


Study helps emergency physicians avoid CT scans that carry cancer risks for young patients.

Nathan Kuppermann, UC Davis

A nationwide study of more than 40,000 children evaluated in hospital emergency departments for head trauma found that if children had only loss of consciousness, and no other signs or symptoms related to the head trauma, they are very unlikely to have sustained serious brain injuries. Children who have only isolated loss of consciousness after head trauma do not routinely require computed tomography (CT) scans of the head, reported researchers from UC Davis Health System and Boston Children’s Hospital.

Although CT scans are the standard way to determine if a child has life-threatening bleeding in the brain that may necessitate surgical intervention, the radiation involved carries a small but quantifiable long-term risk of cancer. As such, the data indicates CT evaluation for children with head trauma should not be routinely used if they are at low risk for clinically significant traumatic brain injuries.

The findings were published today in the journal JAMA Pediatrics in an article titled “Isolated loss of consciousness in children with minor blunt head trauma.”

“Fear of missing a clinically significant head injury, and the wide availability of CT scanners, have been the main factors driving an increase in the use of CT imaging over the past two decades,” said Nathan Kuppermann, professor and chair of the UC Davis Department of Emergency Medicine, and principal investigator of the original study from which the data and current analysis of head injuries were derived. “Our findings can help doctors confidently make a decision to forego CT testing when their patients are unlikely to benefit from it, enabling physicians to first observe their patients for a period of time before deciding on CT use.”

Whether the presence of a single factor suggestive of brain injury is reason enough to justify obtaining a CT scan has been a question Kuppermann and colleagues with the Pediatric Emergency Care Applied Research Network (PECARN) have been actively exploring through a series of studies over the past few years. The current study found that children who lost consciousness after head trauma, but then were awake and alert in the emergency department, and had none of the other five factors determined important by PECARN guidelines for identifying children at low risk for clinically significant brain injuries after head trauma (called the PECARN traumatic brain injury prediction rules), had a very low rate of clinically important brain injuries – only 0.5 percent, or 1 in 200 children.

If a child had isolated loss of consciousness without any other signs or symptoms of head trauma (i.e., including factors outside of the PECARN traumatic brain injury prediction rules), the incidence of an important brain injury dropped to only 0.2 percent, or 1 in 500 children. Furthermore, the duration of the loss of consciousness did not significantly affect risk.

“Children with clinically important brain injuries rarely have loss of consciousness alone, and almost always present other symptoms, such as vomiting or showing signs of neurological problems,” said Lois K. Lee, lead author of the current study and director of trauma research at Boston Children’s Hospital. “Being able to make treatment decisions backed by strong data helps doctors and parents feel better about deciding whether further testing is really needed.”

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Dr. Michael Buonocore, UC Davis professor of radiology, dies


Dedicated scientist was 59.

Michael Buonocore

Michael H. Buonocore, a professor in the UC Davis Department of Radiology for 27 years, died of cancer on June 21. He was 59.

“Dr. Buonocore was a brilliant scientist who preferred to stay out of the limelight, often performing his clinical physics evaluation of the MR scanners late in the evening,” said Raymond Dougherty, professor and chair of the Department of Radiology. “He dedicated himself to team science and collaborated with many faculty at UC Davis, nationally and internationally. His loss to our department as a scientist and esteemed colleague is enormous.”

Dr. Buonocore was born on Oct. 24, 1954, in Rochester, N.Y. He received his bachelor’s degree in chemistry and physics from Syracuse University in 1977. He then enrolled at Stanford University, where he received his master’s degree in electrical engineering in 1979, his Ph.D. in electrical engineering in 1982, and his medical degree in 1983.

From 1983-86, Dr. Buonocore served as chief scientist of Resonex, a magnetic resonance company, where one of his chief contributions was the invention of a widely used technique in modern magnetic resonance imaging (MRI) systems. He left Resonex in 1986 to work as a research scientist at the UC Berkeley Pure and Applied Mathematics Department.

In July 1987, Dr. Buonocore joined the UC Davis Department of Radiology and quickly developed clinical and research MRI opportunities for the UC Davis School of Medicine and UC Davis Medical Center. He developed many courses in advanced MRI for the biomedical engineering program at UC Davis, and was an advisor and mentor for many students.

Dr. Buonocore specialized in functional MRI and was a brain mapping expert. He implemented many novel and advanced MRI programs for the non-invasive measurement of physiological processes, working in consultation with fellow faculty members in the radiology department, as well as faculty in other departments, including psychiatry, neurology, cognitive neuroscience and anesthesiology.

His most successful projects included measurement and visualization of blood flow in the heart and major vessels; measurement of neural activation in the cerebral cortex during cognitive and sensorimotor tasks; measurement of kidney filtration parameters; and measurement of tissue perfusion in breast tumors.

Dr. Buonocore served as MRI technical director for the radiology department, and as technical director of the UC Davis Imaging Research center.

Dr. Buonocore is survived by his wife, Kim, and his son, Christopher.

In lieu of flowers, gifts may be made to the Dr. Michael Buonocore Memorial Fund by contacting Jennifer Marsteen of UC Davis Health System Health Sciences Development at (916) 734-9448. The fund will be used to advance research and teaching in magnetic resonance imaging in medicine at UC Davis, a cause to which Dr. Buonocore devoted much of his professional career.

Planning for a memorial service is under way.

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Using bubbles to reveal fertility problems


New ultrasound procedure can identify blockages in fallopian tubes.

Sanjay Agarwal, UC San Diego

Many women struggling to become pregnant may suffer from some degree of tubal blockage. Traditionally, an X-ray hysterosalpingogram (HSG) that uses dye is the most common procedure to determine whether a blockage exists, but it can cause extreme discomfort to the patient. UC San Diego Health System’s doctors are the first fertility specialists in the county to use a new ultrasound technique to assess fallopian tubes by employing a mixture of saline and air bubbles that is less painful, avoids X-ray exposure and is more convenient to patients during an already vulnerable time.

Using the FemVue Sono HSG, the physician delivers the mixture of saline and air bubbles into the uterus through a small catheter, which then flows into the fallopian tubes. Under ultrasound, the air bubbles are highly visible as they travel through the tubes, allowing the physician to determine if a blockage exists.

“The traditional X-ray approach involves higher pressure and usually causes significant cramping as the dye is administered. The anticipated pain prevents some women from even attempting the test. Others cannot do the test because they are allergic to the dye. Assessing the tubes for a blockage is a key component of the diagnostic workup in fertile couples, and not doing so because of pain or allergy is a real concern,” said Sanjay Agarwal, M.D., director of fertility services in the Department of Reproductive Medicine at UC San Diego Health System. “The new approach is not only much more comfortable for patients, it also uses saline, so the issue of an allergy does not arise. We are also able to assess the cavity of the uterus at the same time – all without X-rays.”

Kristina, a mother who has been trying to conceive a second child for almost a year, agreed: “I was willing to do whatever it took to address the fertility issues we were facing, but after everything we had been through emotionally, it was a relief to undergo a procedure that wasn’t physically painful.”

The ultrasound is performed in the clinic, and at present, ideal candidates include those with a prior pregnancy and those at low risk for tubal disease.

“Like the traditional X-ray HSG, the new test should be performed after the period has ended but before ovulation. The fact that the patient can schedule this ultrasound-based test in the clinic and not in radiology prevents a delay in care and allows the patient’s physician to be more involved in the process,” said Agarwal, also director of the UC San Diego Center for Endometriosis Research and Treatment (CERT).

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UCSF Mission Bay hospitals to introduce patient-friendly scan suites


Design intended to help put patients at ease.

A model of a cable car-themed scan suite planned for the new UCSF Benioff Children's Hospital San Francisco.

Patients undergoing imaging at the new UCSF Medical Center at Mission Bay will be transported to the tranquility of Muir Woods, or take in the sights of San Francisco from a cable car or boat, thanks to images projected on the suites’ walls and ceiling. They can admire lush visuals, such as a sunset over Golden Gate Bridge, and listen to the sounds of nature or soothing music that they select themselves.

Younger patients at the new UCSF Benioff Children’s Hospital San Francisco may prefer a more active role. Instead of a stark room with a table and scanning equipment, they may opt for the driver’s seat of a trolley car, where they can trundle around the city, take in local landmarks and participate in hands-on activities working with a cast of animated critters. Or perhaps they prefer to captain a boat for a nautical expedition.

These suites will be available when UCSF Medical Center at Mission Bay opens on Feb. 1, 2015, for patients undergoing MRI or SPECT and CT, two imaging techniques that look inside the body and help doctors pinpoint any areas of disease. The procedures can take from 30 minutes to an hour and are used to diagnose a variety of conditions from tumors and congenital abnormalities, to skeletal trauma such as ACL injury.

Among cancer patients, scanning may be especially stressful because it determines the success or failure of treatment.

The design of the rooms was the result of collaboration between GE Healthcare and a UCSF team comprising faculty, staff, patients and their families participating in workshops and “visioning sessions” in which optimal features of the suites were identified and the feasibility of implementing them were discussed. Opinions were also sought from pediatric patients who viewed suite mock-ups.

Making the scan suites child-friendly was the primary focus, said John MacKenzie, M.D., chief of radiology at UCSF Benioff Children’s Hospital San Francisco, who provided a physician’s perspective and worked with the team from UCSF and GE Healthcare.

“Most children have never encountered an MRI machine before – it’s not something they see in a playground. Typically they enter an MRI room and hesitate when they’re told to hop on the table. But if instead they’re told, ‘Let’s go take a ride on the boat,’ they’re more likely to be intrigued than anxious,” said MacKenzie.

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New test makes Parkinson’s-like disorder detectable in young adults


Brain abnormalities may begin to develop two decades before symptoms might occur.

UC Davis MIND Institute

The very earliest signs of a debilitating neurodegenerative disorder, in which physical symptoms are not apparent until the fifth decade of life, are detectable in individuals as young as 30 years old using a new, sophisticated type of neuroimaging, researchers at UC Davis, the University of Illinois and UCLA have found.

People with the condition — fragile X-associated tremor/ataxia syndrome (FXTAS) — experience tremors, poor balance, cognitive impairments and Parkinsonism. The genetic condition results from a mutation in the fragile X mental retardation gene (FMR1). FXTAS develops in about 40 percent of male and 15 percent of female carriers of the mutated FMR1 gene.

“Our findings suggest that the brain abnormalities of FXTAS may begin to develop about two decades before symptoms might occur,” said Tony J. Simon, study senior author and professor, Department of Psychiatry and Behavioral Sciences.

“Altered Structural Brain Connectome in Young Adult Fragile X Premutation Carriers,” is published in Human Brain Mapping.

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