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  • richardmitnick 4:26 pm on April 17, 2017 Permalink | Reply
    Tags: , NERSC Cori II supercomputer, Pattern Discovery over Pattern Recognition: A New Way for Computers to See, UC Davis   

    From UC Davis: “Pattern Discovery over Pattern Recognition: A New Way for Computers to See” 

    UC Davis bloc

    UC Davis

    April 17th, 2017
    Andy Fell

    Jim Crutchfield wants to teach a machine to “see” in a new way, discovering patterns that evolve over time instead of recognizing patterns based on a stored template.

    It sounds like an easy task – after all, any animal with basic vision can see a moving object, decide whether it is food or a threat and react accordingly, but what comes easily to a scallop is a challenge for the world’s biggest supercomputers.

    Crutchfield, along with physics graduate student Adam Rupe and postdoc Ryan James, is designing these new machine learning systems to allow supercomputers to spot large-scale atmospheric structures, such as hurricanes and atmospheric rivers, in climate data. The UC Davis Complexity Sciences Center, which Crutchfield leads, was recently named as an Intel Parallel Computing Center and is collaborating with Intel Research, the Department of Energy’s National Energy Research Scientific Computing Center (NERSC) at the Lawrence Berkeley Lab, Stanford University, and University of Montreal. The entire Big Data Center project is led by Prabhat, leader of the Data And Analytics Services Group at the Berkeley lab.

    The team works on NERSC’s CORI II supercomputer, in the top five of the world’s fastest machines with over 600,000 CPU cores.

    NERSC CRAY Cori II supercomputer

    Modern science is full of “big data.” For climate science, that includes both satellite- and ground-based measurements that span the planet, as well as “big” simulations.

    “We need new kind of machine learning to interpret very large data and planet-wide simulations,” Crutchfield said. Climate and weather systems evolve over time, so the machines need to be able to find patterns not only in space but over time.

    UC Davis researchers plan to develop new tools so supercomputers can detect patterns in global climate simulations (NERSC/LBNL)

    “Dynamics are key to this,” Crutchfield said. Humans (and other visual animals) recognize dynamic changes very quickly, but it’s much harder for machines.

    Pattern Discovery is more than Pattern Recognition

    With existing technology, computers recognize patterns based on an existing template. That’s how voice recognition systems work, by comparing your voice to an existing catalog of sounds. These pattern recognition systems can be very useful but they can’t identify anything truly new – that isn’t represented in their template.

    Crutchfield and his team are taking a different approach, based on pattern discovery. They are working on algorithms that allow computers to identify structures in data without knowing what they are in advance.

    “Learning novel patterns is what humans are uniquely good at, but machines can’t do it,” he said.

    Using pattern discovery, a supercomputer would learn how to identify hurricanes or other features in climate and weather data. It might also identify new kinds of structures that are too complex for humans to perceive at all.

    While this application is in global climate modeling, Crutchfield hopes to make it a new paradigm for analyzing very large datasets.

    “Usually, you apply known models to interpret the data. To say that you will extract your model directly from the data is a radical claim,” he said.

    The collaboration is part of the Intel Parallel Computing Centers program, which provides funding to universities, institutions, and research labs to modernize key community codes used across a wide range of disciplines to run on industry-standard parallel architectures.

    More information

    Video: Global simulation of atmospheric water vapor produced by CORI supercomputer at NERSC

    See the full article here .

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    UC Davis Campus

    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

  • richardmitnick 4:32 pm on April 10, 2017 Permalink | Reply
    Tags: , , , , MACS1423-z7p64, UC Davis   

    From UC Davis: “Long Ago and Far Away, an Average Galaxy” 

    UC Davis bloc

    UC Davis

    April 10, 2017
    Andy Fell

    Astronomers used the gravity of a massive galaxy cluster as a lens to spot an incredibly distant galaxy, about 13.1 billion years in the past. They used the Hubble Space Telescope to find the galaxy and confirmed its age and distance with instruments at the Keck Observatory in Hawaii. Image credit: NASA/Keck/Austin Hoag/Marusa Bradac

    NASA/ESA Hubble Telescope

    Keck Observatory, Mauna Kea, Hawaii, USA

    Astronomers led by a graduate student at the University of California, Davis, have discovered one of the most distant galaxies in the universe, and it’s nothing out of the ordinary.

    “Other most distant objects are extremely bright and probably rare compared to other galaxies,” said Austin Hoag, a UC Davis graduate student in physics who is lead author on the paper, published April 10 in Nature Astronomy. “We think this is much more representative of galaxies of the time.”

    These ultradistant galaxies, seen as they were close to the beginning of the universe, are interesting to Hoag, UC Davis physics professor Marusa Bradac, and collaborators in the U.S., Australia and Europe because they fall within the “Epoch of Reionization,” a period about a billion years after the Big Bang when the universe became transparent.

    Reionization era and first stars, Caltech

    After the Big Bang, the universe was a cloud of cold, atomic hydrogen, which blocks light. The first stars and galaxies condensed out of the cloud and started to emit light and ionizing radiation. This radiation melted away the atomic hydrogen like a hot sun clearing fog, and the first galaxies spread their light through the universe.

    Much remains lost in the fog of reionization.

    “We have a before and an after, but not exactly a when,” Hoag said. There are also questions about what radiating objects drove reionization: Was it mostly young galaxies, or did objects such as black holes and gamma ray bursts contribute as well?

    Galaxy cluster is a giant lens in the sky

    The new object, named MACS1423-z7p64, is at a redshift of 7.6, putting it about 13.1 billion years in the past. (The farther away an object is, the farther its light is shifted into the red end of the spectrum, due to the expansion of the universe.) To find such faint, distant objects, the astronomers took advantage of a giant lens in the sky.

    As light passes by a massive object such as a galaxy cluster, its path gets bent by gravity, just as light gets bent passing through a lens. When the object is big enough, it can act as a lens that magnifies the image of objects behind it.

    Gravitational Lensing NASA/ESA

    Gravitational microlensing, S. Liebes, Physical Review B, 133 (1964): 835

    Hoag and colleagues are surveying the sky around massive galaxy clusters that are the right size and distance away to focus light from very distant galaxies. While it is similar to millions of other galaxies of its time, z7p64 just happened to fall into the “sweet spot” behind a giant galaxy cluster that magnified its brightness tenfold and made it visible to the team, using the Hubble Space Telescope. They were then able to confirm its distance by analyzing its spectrum with the Keck Observatory telescopes in Hawaii.

    The team plans to continue their survey of candidate galaxies with the Hubble and Keck telescopes. The upcoming launch of the James Webb Space Telescope, set for 2018, opens up new possibilities, Hoag said. The team is currently planning observations for the Webb telescope, which is bigger than Hubble and will allow astronomers to look at even more distant parts of the universe.

    “We will truly witness the birth of the first galaxies which will allow us to answer the longstanding question, of where did we come from,” Bradac said.

    Other authors on the paper are: at UC Davis, Kuang-Han Huang, Brian Lemaux and Julie He; Michele Trenti and Stephanie Bernard, University of Melbourne, Australia; Tommaso Treu, Louis E. Abramson, Charlotte Mason and Takahiro Morishita, UCLA; Kasper Schmidt, Leibniz-Institut für Astrophysik, Potsdam, Germany; Laura Pentericci, NAF Osservatorio Astronomico di Roma, Italy; and Tim Schrabback, Argelander-Institut für Astronomie, Bonn, Germany. The work was supported by NASA. The W.M. Keck Observatory is operated as a scientific partnership among the California Institute of Technology, the University of California and NASA and is made possible by the generous financial support of the W.M. Keck Foundation.

    Media contact(s)

    Marusa Bradac, UC Davis Physics, 530-752-6762 , marusa@physics.ucdavis.edu

    Austin Hoag, UC Davis Physics, athoag@ucdavis.edu

    Andy Fell, UC Davis News and Media Relations, 530-752-4533, ahfell@ucdavis.edu

    See the full article here .

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    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

  • richardmitnick 4:52 pm on June 17, 2016 Permalink | Reply
    Tags: , , UC Davis, World’s First 1000-Processor Chip   

    From UC Davis: “World’s First 1,000-Processor Chip” 

    UC Davis bloc

    UC Davis

    June 17, 2016
    Andy Fell

    This microchip with 1,000 processor cores was designed by graduate students in the UC Davis Department of Electrical and Computer Engineering. The chip is thought to be fastest designed in a university lab. No image credit.

    A microchip containing 1,000 independent programmable processors has been designed by a team at the University of California, Davis, Department of Electrical and Computer Engineering. The energy-efficient “KiloCore” chip has a maximum computation rate of 1.78 trillion instructions per second and contains 621 million transistors. The KiloCore was presented at the 2016 Symposium on VLSI Technology and Circuits in Honolulu on June 16.

    “To the best of our knowledge, it is the world’s first 1,000-processor chip and it is the highest clock-rate processor ever designed in a university,” said Bevan Baas, professor of electrical and computer engineering, who led the team that designed the chip architecture. While other multiple-processor chips have been created, none exceed about 300 processors, according to an analysis by Baas’ team. Most were created for research purposes and few are sold commercially. The KiloCore chip was fabricated by IBM using their 32 nm CMOS technology.

    Each processor core can run its own small program independently of the others, which is a fundamentally more flexible approach than so-called Single-Instruction-Multiple-Data approaches utilized by processors such as GPUs; the idea is to break an application up into many small pieces, each of which can run in parallel on different processors, enabling high throughput with lower energy use, Baas said.

    Because each processor is independently clocked, it can shut itself down to further save energy when not needed, said graduate student Brent Bohnenstiehl, who developed the principal architecture. Cores operate at an average maximum clock frequency of 1.78 GHz, and they transfer data directly to each other rather than using a pooled memory area that can become a bottleneck for data.

    The chip is the most energy-efficient “many-core” processor ever reported, Baas said. For example, the 1,000 processors can execute 115 billion instructions per second while dissipating only 0.7 Watts, low enough to be powered by a single AA battery. The KiloCore chip executes instructions more than 100 times more efficiently than a modern laptop processor.

    Applications already developed for the chip include wireless coding/decoding, video processing, encryption, and others involving large amounts of parallel data such as scientific data applications and datacenter record processing.

    The team has completed a compiler and automatic program mapping tools for use in programming the chip.

    Additional team members are Aaron Stillmaker, Jon Pimentel, Timothy Andreas, Bin Liu, Anh Tran and Emmanuel Adeagbo, all graduate students at UC Davis. The fabrication was sponsored by the Department of Defense and ARL/ARO Grant W911NF-13-1-0090; with support from NSF Grants 0903549, 1018972, 1321163, and CAREER Award 0546907; and SRC GRC Grants 1971 and 2321.

    See the full article here .

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    UC Davis Campus

    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

  • richardmitnick 4:00 pm on June 15, 2016 Permalink | Reply
    Tags: , , , New Type of Meteorite Linked to Ancient Asteroid Collision, UC Davis   

    From UC Davis: “New Type of Meteorite Linked to Ancient Asteroid Collision” 

    UC Davis bloc

    UC Davis

    June 15, 2016
    Becky Oskin

    The black, grainy meteorite embedded in rock from a Swedish quarry fell to Earth 470 million years ago. Chemically distinct from any meteorite yet discovered, it is likely debris from a massive collision in the asteroid belt. (Qing-zhu Yin, UC Davis).

    An ancient space rock discovered in a Swedish quarry is a type of meteorite never before found on Earth, scientists reported June 14 in the journal Nature Communications.

    “In our entire civilization, we have collected over 50,000 meteorites, and no one has seen anything like this one before,” said study co-author Qing-zhu Yin, professor of geochemistry and planetary sciences at the University of California, Davis. “Discovering a new type of meteorite is very, very exciting.”

    The new meteorite, called Ost 65, appears to be from the missing partner in a massive asteroid collision 470 million years ago. The collision sent debris falling to Earth over about a million years and may have influenced a great diversification of life in the Ordovician Period. One of the objects involved in this collision is well-known: It was the source of L-chondrites, still the most common type of meteorite. But the identity of the object that hit it has been a mystery.

    Ost 65 was discovered in Sweden’s Thorsberg quarry, source of more than 100 fossil meteorites. Measuring just under 4 inches wide, it looks like a gray cow patty plopped into a pristine layer of fossil-rich pink limestone. The Ost 65 rock is called a fossil meteorite because the original rock is almost completely altered except for a few hardy minerals — spinels and chromite. Analyses of chromium and oxygen isotopes in the surviving minerals allowed the researchers to conclude the Ost 65 meteorite is chemically distinct from all known meteorite types.

    By measuring how long Ost 65 was exposed to cosmic rays, the team established that it traveled in space for about a million years before it fell to Earth 470 million years ago. This timeline matches up with L-chondrite meteorites found in the quarry, leading the study authors to suggest the rock is a fragment of the other object from the Ordovician collision. The original object may have been destroyed during the collision, but it’s also possible that the remains are still out in space.

    Meteorites may have influenced evolution

    Researchers think that about 100 times as many meteorites slammed into Earth during the Ordovician compared with today, thanks to the massive collision in the asteroid belt. This rain of meteorites may have opened new environmental niches for organisms, thus boosting both the diversity and complexity of life on Earth.

    “I think this shows the interconnectedness of the entire solar system in space and time, that a random collision 470 million years ago in the asteroid belt could dictate the evolutionary path of species here on Earth,” Yin said.

    The study was led by Birger Schmitz, of Lund University in Sweden. Yin, of UC Davis, together with his postdoctoral fellow Matthew Sanborn, made the very precise measurement of chromium in tiny mineral grains within the meteorite. Researchers from the University of Hawaii at Manoa analyzed its oxygen isotopes.

    The new findings strengthen suspicions that more recent meteorite falls on Earth do not represent the full range of rocks drifting through the solar system. Yin said there is potential to better understand the history of our solar system by collecting meteorite fragments preserved in Earth’s ancient rocks. “If we can go back even further in time, we may eventually be able to find some of the true building blocks of Earth,” Yin said.

    The research was funded by NASA, the UC Office of the President and a European Research Council Advanced Grant.

    See the full article here .

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    UC Davis Campus

    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

  • richardmitnick 9:43 pm on December 28, 2015 Permalink | Reply
    Tags: , , UC Davis   

    From UC Davis: “Turning the Tables on Hidden HIV” 

    Temp 1

    Thirty years ago, contracting HIV was a death sentence.

    The virus attacks the immune system, specifically T-cells, until immunity breaks down completely. Patients would eventually develop AIDS, and ultimately succumb to opportunistic infections.

    The development of highly active antiretroviral therapies or HAART changed all that, converting a deadly disease into a chronic one. As long as patients stayed on the drug regimen, they could live normal lifespans. Their immune systems would recover and viral levels would decline to nearly zero.

    But there’s a catch. Nearly zero is not the same as zero. HIV has a latency mode, during which the virus is dormant – evading both HAART and the body’s immune system. Remove HAART treatment, and the virus comes roaring back.

    That means a lifetime consuming powerful and expensive treatments – if one’s body and health status can tolerate them in the first place. And no one knows how the drugs will affect patients after 20, 30 or 40 years.

    “We’ve made great progress, but at the end of the day you still have more than 30 million people living with HIV,” says Satya Dandekar, professor and chair of the UC Davis Department of Medical Microbiology and Immunology. “Without drugs, the virus can come back at the same threat level for patients.

    “Actually eradicating HIV is extremely critical.”

    For decades, UC Davis researchers have worked with that ultimate goal in mind. Scientists have learned important details about how HIV operates along the way; for example, that it first attacks immune cells in the gut.

    But now we’ve reached a new stage in the battle against HIV. The goal is no longer to control the disease, but to cure it. Two UC Davis groups are beginning clinical trials in hopes of doing just that.

    Shock and kill

    It would be hard to overstate the significance of HIV latency. The virus’s ability to evade treatment has made it difficult, if not impossible, to cure. The challenge for clinicians is to identify a two-pronged strategy: shock the latent virus out of hibernation, and hit it with immune treatments to kill it.

    No image credit found

    Dandekar, along with dermatologist Emanual Maverakis, are about to test the first part of that strategy. Just a few months ago, the Dandekar lab identified several agents that “wake up” HIV. One in particular, PEP005, has shown striking results. Even better, the drug is already approved by the U.S. Food and Drug Administration.

    “We found this was really effective at reactivating HIV and works beautifully with other latency reactivating agents,” says Dandekar. “The thing that’s really exciting is that the molecule is in the drug PICATO, which treats skin cancer. It’s already approved and being used by patients.”

    Now the UC Davis group hopes to extend PICATO’s uses to attacking HIV latency as well, and is launching a small clinical trial to test the drug’s safety in HIV patients. If the trial is successful, the team hopes to combine PICATO, and other drugs that reactivate HIV, with immunotherapies that would destroy the virus as it comes out of hiding.

    “It will have to be a combination,” says Dandekar. “Just reactivating HIV from latency won’t be enough. We need to position the patient so those reactivated cells can be cleared.”

    Reboot the system

    UC Davis researchers are moving another promising approach into clinical trials as well. It involves taking blood stem cells from patients, genetically engineering them with anti-HIV genes, and returning them to the patients – essentially “rebooting” their immune systems and empowering them to eradicate or adequately suppress remaining HIV on their own over the long term.

    “We are using our understanding of basic HIV biology to engineer each patient’s own stem cells to fight the virus,” says Joseph Anderson, an assistant adjunct professor who researches infectious diseases at the UC Davis Institute for Regenerative Cures, the university’s main stem cell research center. “We’re hoping that by reintroducing these cells in a bone marrow transplant, we can rebuild the immune system to resist HIV.”

    Temp 3

    Anderson and Mehrdad Abedi, a hematology professor and stem cell transplant specialist, are trying to replicate the treatment that cured Timothy Brown, also known as the “Berlin Patient.” Brown received a stem cell transplant from a donor whose genome contained an HIV-resistant mutation. That was seven years ago – and Brown remains HIV-free.

    Anderson, who has been investigating anti-HIV genes since he was a Ph.D. student, is using three different genes to attack the virus, each one hitting a different mechanism associated with HIV infection. Like the drug cocktails used for HAART, multiple attack vectors may reduce the virus’s ability to evade treatment.

    But a new key to the UC Davis team’s gene therapy strategy is also an improved viral vector that Anderson developed to help boost the treatment’s potency. The vector contains a gene that “tags” the surface of the stem cells that are HIV-resistant, allowing researchers to maximize their volume and potential power by culling out non-resistant cells before transplantation.

    Anderson and Abedi have received an $8.5 million grant from the state’s stem cell agency, the California Institute for Regenerative Medicine or CIRM, to conduct the trial. The study will test the engineered stem cells in patients with HIV-related lymphoma, since they already require bone marrow transplants to treat their cancer. This trial will also test the therapy’s safety.

    The team hopes the treatment will be a complete cure, but even a partial response would be great news for HIV patients.

    “Maybe we won’t be able to eradicate it in some patients,” said Anderson, “but hopefully we are giving them enough of an HIV-resistant immune system that they can live the rest of their lives without having to take the antiretroviral drugs.”

    See the full article here .

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    UC Davis Campus

    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

  • richardmitnick 10:48 am on October 11, 2015 Permalink | Reply
    Tags: , , UC Davis   

    From UC Davis: “New treatments a big step for patients with advanced kidney cancer” 

    UC Davis bloc

    UC Davis

    September 29, 2015
    Dorsey Griffith
    Phone: 916-734-9118

    In an editorial published in the New England Journal of Medicine, Primo Lara, associate director for Translational Research at the UC Davis Comprehensive Cancer Center and David Quinn, medical director, USC Norris Cancer Hospital, highlight two new drugs that have shown great efficacy against kidney cancer. In two studies, also published in the Sept. 25 edition of the journal, researchers showed that nivolumab, an immunotherapeutic drug, and cabozantinib, a multikinase inhibitor, are more effective against advanced kidney cancer than a current standard of care. In the accompanying editorial, Lara and Quinn note that the positive results are “unequivocal.”

    Primo Lara

    “These new drugs are clearly better than the older drug everolimus; they will soon find their place in the kidney cancer arsenal,” notes Lara. “Since these new agents are already approved for other indications, it is likely that their manufacturers will be applying to get FDA approval for kidney cancer soon.”

    Currently, kidney cancer patients are first treated with an angiogenesis inhibitor, which restricts or reduces blood vessel growth into tumors. When that that therapy ceases to be effective patients are sometimes switched to everolimus, which inhibits mTOR, a master protein that controls a number of important cell growth pathways.

    In the nivolumab study, called Checkmate, the median overall survival for patients treated with nivolumab was 25 months, compared to 19.6 months for those on everolimus. In addition, nivolumab reduced the risk of death by 27 percent and had far fewer side effects. Nivolumab is a checkpoint inhibitor, which takes the brakes off T-cells to help the immune system attack cancer. The drug is currently approved to treat advanced squamous cell lung cancer and metastatic melanoma.

    In the cabozantinib study, called METEOR, the drug improved progression-free survival by nearly four months and showed a strong trend to improving overall survival. Cabozantinib is a multi-kinase inhibitor that affects several proteins associated with cancer progression and is currently approved to treat medullary thyroid cancer.

    While these results are encouraging, the editorial noted some important caveats. Both trials failed to produce a significant number of complete responses, in which the cancer disappeared completely. There are also no good biomarkers that predict benefit from these agents.

    “We need to expand the spectrum benefit by finding a biomarker that predicts which patient will preferentially benefit,” said Lara. “There seems to be a fixed number of patients who respond to immunotherapy – about 20 to 30 percent. We need to find markers that identify these patients. We also need to develop new combinations that broaden the group that benefits.”

    The editorial also highlights another issue – value. These drugs are quite expensive, and the authors express their concerns that some patients will not have access due to inability to afford these pricey medicines.

    “No treatment will work if patients do not get it,” said Lara. “And no patient will get it if it’s not affordable.”

    Lara was a compensated member of the Independent Data Monitoring Committee for the METEOR trial.

    See the full article here .

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    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

  • richardmitnick 3:47 pm on August 19, 2015 Permalink | Reply
    Tags: , , , UC Davis   

    From UC Davis- “Investigating Immunotherapy: Cancer Breakthrough Leads to Startup 

    UC Davis bloc

    UC Davis

    August 18. 2015
    Jocelyn Anderson

    Chiao-Jung Kao

    UC Davis researchers are exploring novel immunotherapy strategies with the goal of developing targeted treatment for cancer patients.

    Cancer immunotherapy — harnessing the innate powers of the patient’s own immune system to fight the disease — dates back to as early as the 1890s, when one doctor discovered that bacterial infections could stimulate an immune system response that could also trigger cancer remission. More recently, the field has expanded, with new research supporting treatments that either stimulate or restore the immune system. For example, cancer vaccines are designed to make the person’s immune system more effectively attack cancer cells. Advantages include high specificity and relatively low toxicity.

    Results from a new study, published in July in Cancer Immunology Research, suggest that monitoring immune status may be necessary to optimize treatment regimens combining immunotherapy with chemo-radiotherapy.

    “Immunotherapy is poised to become the standard of care for many cancers,” said Chiao-Jung Kao, assistant adjunct professor in the Department of Obstetrics and Gynecology and lead author of the paper. “In the past, cancer immunotherapies such as cancer vaccines have been combined with chemotherapy with limited success.”

    Kao is part of a research team led by Michael DeGregorio, professor of medicine, in the Division of Hematology and Oncology Research within the Department of Internal Medicine at UC Davis.

    The team describes key differences in the effects of chemo-radiotherapy on biomarkers of immune response following two commonly employed treatment regimens in a lung cancer mouse model. While the paper focuses on lung cancer, the findings may be applied to other cancer types.

    “To our knowledge, this is the first clear demonstration in a preclinical mouse model that serial monitoring of a patient’s immune status can be critical when using cancer immunotherapy,” said Kao.

    Additionally, the researchers are testing several small molecule drug candidates for their ability to boost the immune system. Such drug modulators could potentially enhance the effectiveness of cancer immunotherapy. The lead proprietary compound, with the code name IMT-325, has shown promising activity in both in vitro and in vivo preclinical studies.

    “Our approach is to monitor immune status of cancer patients and fortify the immune system with an immune modulator for the purpose of optimizing personalized cancer immunotherapies,” said DeGregorio.

    A modulator would help regulate the immune system. Though the precise mechanism of action is still not widely understood, immune modulators currently are used to control some ailments like Crohn’s disease. Researchers also are investigating a connection to cancer.

    The same team made news a year ago with a potential lung cancer vaccine that shows promise for boosting immune response and reducing the number of tumors in mice with lung cancer. They now believe a drug modulator they are developing could improve the vaccine’s effect.

    Both projects have been supported by Germany-based pharmaceutical company Merck KGaA.

    With the discovery of this new therapeutic approach, DeGregorio and his team formed a startup focused on commercializing the therapy. (DeGregorio and Kao are scientific advisors to the new venture.) The company, called ImmunoTess, was founded in May and has already raised more than $1 million and filed two provisional patent applications.

    The UC Davis Office of Research helps university scientists like DeGregorio and Kao, turn their breakthroughs into commercial products, either through established corporate partners or the formation of startup companies. Such new ventures are facilitated by the Office of Corporate Relations and InnovationAccess, units within the Technology Management & Corporate Relations division. University startup formation is facilitated by Venture Catalyst, also within TMCR. Venture Catalyst and InnovationAccess worked closely with the founders of ImmunoTess throughout the entire process, from offering expertise on forming the new venture to filing provisional patents and licensing the technology to the company. Venture Catalyst’s START program also provided a suite of services designed specifically to help grow technology startups. UC Davis has an equity stake in ImmunoTess.

    “InnovationAccess and Venture Catalyst are immensely helpful resources for faculty members like myself who are motivated to move our research beyond the laboratory into clinical benefit for patients,” said DeGregorio. “The success of ImmunoTess in delivering treatments to patients suffering from cancer will benefit from this continued collaboration.”

    DeGregorio has more than 30 years of experience in drug development research, and is one of the inventors of two drugs approved by the U.S. Food and Drug Administration. Most notably, he developed Osphena, which was approved for women by the FDA in 2013 to treat dyspareunia, pain during sexual intercourse most often associated with menopause. It was approved by the European Medicines Agency in 2015 for the treatment of vulvar and vaginal atrophy in postmenopausal women. The drug also has potential use in breast cancer for preventing bone loss and treating quality-of-life issues in breast cancer survivors.

    With this newest venture, DeGregorio plans to assemble a regulatory and clinical research team and potentially partner with one or more pharmaceutical companies to allow for further development of immunotherapies.

    “As a serial innovator, Dr. DeGregorio has a strong track record of transforming his research into positive quality of life impact through its commercialization,” said Dushyant Pathak, associate vice chancellor for Technology Management and Corporate Relations. “Partnering with him in the success of ImmunoTess is an example of how UC Davis supports the formation of companies and facilitates their success in commercializing university technologies for societal benefit and economic impact.”

    See the full article here.

    Please help promote STEM in your local schools.

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    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

  • richardmitnick 7:54 pm on August 17, 2015 Permalink | Reply
    Tags: , , UC Davis   

    From UC Davis: “Finding biomarkers for early lung cancer diagnosis” 

    UC Davis bloc

    UC Davis


    August 17th, 2015
    Andy Fell

    Oliver Fiehn’s metabolomics lab uses high-tech equipment to capture metabolism in progress.

    Despite decades of warnings about smoking, lung cancer is still the second-most common cancer and the leading cause of death from cancer in the U.S. Patients are often diagnosed only when their disease is already at an advanced stage and hard to treat. Researchers at the West Coast Metabolomics Center at UC Davis are trying to change that, by identifying biomarkers that could be the basis of early tests for lung cancer.

    “Early diagnosis is the key to fighting lung cancer,” said Oliver Fiehn, director of the metabolomics center and a professor of molecular and cellular biology at UC Davis.

    Lung cancer can be diagnosed early with regular low-dose CT (computed tomography) scans of people at risk. But these tests are very expensive, and also involve exposing patients to X-ray radiation. Instead, Fiehn, project scientist William Wikoff and colleagues set out to look for biomarkers of developing lung cancer in blood from patients.

    Fiehn’s lab specializes in “metabolomics,” an approach that involves analyzing all the biochemical products of metabolism in cells and tissues at the same time. Like other “-omics” approaches, it’s made possible by new technology and computing power, and it’s opening up new ways to understand living processes.

    To find early biomarkers for lung cancer, the team needed to look at blood samples collected from people who developed the disease, months or years before they were diagnosed. Fortunately, they were able to access samples stored from the CARET clinical trial. The CARET study, which ran from 1985 until it was halted in 1996, attempted to test whether doses of antioxidant vitamins could prevent cancer in heavy smokers and other people at high risk. The trial failed, but the collection of blood, serum, and tissues and related data are maintained as the CARET Biorepository.

    Applying metabolomics, Wikoff and Fiehn found that one molecule, diacetylspermine, was almost doubled in serum collected from patients up to six months before they were diagnosed with lung cancer, compared to healthy controls.

    They then combined diacetylspermine with another previously identified biomarker, a protein called pro-surfactant protein B (pro-SFTPB), and tested for both markers in another set of sera collected from CARET patients months before they developed lung cancer.

    “Individually, the markers were about 70 percent predictive but in combination, that rose to 80 percent,” Fiehn said. In other words, eight out of ten people with early-stage cancer would be correctly identified by the combined test.

    If the double biomarker were in use as a clinical test, those patients could then be referred for a low-dose CT scan to confirm the presence of cancer.

    The study is published August 17 in the Journal of Clinical Oncology. The next step, Fiehn said, is to work with bigger cohorts of cancer patients to validate the approach.

    Other partners on the work include Brian De Felice, West Coast Metabolomics Center; Suzanne Miyamoto and David Gandara, UC Davis Comprehensive Cancer Center; Samir Hanash, Yang Zhao, Ziding Feng, and Ayumu Taguchi, University of Texas MD Anderson Cancer Center, Houston; and Matt Barnett and Gary Goodman, Fred Hutchison Cancer Research Center, Seattle.

    The work was funded by the NIH and Department of Defense through the Congressionally Directed Medical Research Program; the Canary Foundation, the Rubenstein Family Foundation, and the Lyda Hill Foundation.
    Link to paper.

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

  • richardmitnick 11:32 am on July 29, 2015 Permalink | Reply
    Tags: , UC Davis   

    From UC Davis: “UC Davis Awards Proof-of-Concept Funding for Cutting-Edge Technologies with Commercial Potential” 

    UC Davis bloc

    UC Davis

    University of California, Davis, is helping researchers with innovative technologies bridge the gap between research and commercialization.

    Wenbin Deng’s lab at UC Davis

    The UC Davis Science Translation and Innovative Research grant program provides funding for proof-of-concept research and development work aimed at demonstrating commercial feasibility of university-generated technology. Now in its second year, the STAIR program is one way UC Davis supports its entrepreneurial researchers.

    The STAIR program is run and managed by Venture Catalyst, a unit within the university’s Technology Management and Corporate Relations division of the Office of Research.

    “STAIR grants provide funding not available through traditional sources,” said Dushyant Pathak, associate vice chancellor for Technology Management and Corporate Relations. “Despite our rebounding economy, there remains a substantial gap in funding for proof-of-concept work and our unique program is an example of how we are investing campus resources to fill this crucial gap between cutting-edge research and commercial translation.”

    Five winners were selected from a total of 35 applications. The final awardees were selected after a multistage review process for their commercial potential, technical merit, and ability to achieve identified commercialization milestones with the funding requested. The STAIR program also exemplifies the ways TMCR implements the chancellor’s vision for commercializing innovative research.

    This year’s STAIR awardees:

    Aijun Wang, assistant professor, Department of Surgery
    Title: A Sutureless Artificial Graft for Arterial Replacement
    Funding amount: $50,000
    Wang’s team has created VasoFlo, an artificial arterial graft designed to address the complications that plague existing artificial vascular grafts. The design allows attachment to the vessel walls without sutures, and protects against turbulent blood flow, thrombosis, and intimal hyperplasia. With STAIR funding, the team will construct a viable prototype using FDA-approved materials and test the efficacy in a large animal bypass model.

    Wenbin Deng, associate professor, Department of Biochemistry and Molecular Medicine
    Title: A Drug Candidate for the Treatment of Multiple Sclerosis
    Funding amount: $50,000
    This team’s invention identifies a small-molecule drug candidate with potential therapeutic properties for the treatment of multiple sclerosis. The drug targets a transcription factor called Zfp488 that promotes remyelination in the treatment of MS, attenuates experimental autoimmune encephalomyelitis in mice, and reduces neural inflammation and neuropathology. This drug candidate could prevent neurodegeneration in MS patients, whereas current therapeutics only work on the immune system.

    Richard Levenson, professor and vice chair, Department of Pathology and Laboratory Medicine
    Title: Deep UV Surface Excitation Microscopy (MUSE)
    Funding amount: $50,000
    Levenson’s team has proposed microscope instrumentation for the assessment of freshly excised tissue specimens using a fast, nondestructive and inexpensive method called Microscopy with Ultraviolet Surface Excitation, or MUSE. Diagnostic-quality images can be generated in minutes using LED lights, eliminating the need for glass slides.

    Tingrui Pan, assistant professor, Department of Biomedical Engineering
    Title: Wearable Pressure Sensor for the Management of Chronic Venous Disease
    Funding amount: $50,000
    This team aims to develop a wearable pressure sensor for management of chronic venous disorder, commonly manifested as varicose veins. The sensor utilizes allows for wireless data transmission for continuous pressure assessment under compression therapy. The device is ultra thin with skin-like flexibility and can be mass-produced at a low cost.

    John Voss, professor, Department of Biochemistry and Molecular Medicine
    Title: A Novel Approach for Early Detection of Alzheimer’s Disease
    Funding amount: $34,000
    Voss’s team is developing technology based on a small molecule believed to have potential for the early detection of Alzheimer’s disease. The compound is innovative for its paramagnetic properties, which affect MRI intensities. Unlike available imaging methods, this would enable greater patient access, is less expensive and does not require radiation exposure for the patient.

    In addition to funding, each STAIR recipient is assigned a volunteer mentor to add value through the engagement process. Mentors represent the business community, providing essential industry connection, networking opportunities and invaluable advice.

    Samuel Wu is the managing director of MedImmune Ventures, a wholly-owned venture capital fund within the AstraZeneca Group, and got involved for the first round of STAIR. He was paired with Jared Shaw, an associate professor of chemistry, who spearheaded a project aimed at developing a novel class of antibiotics to treat drug-resistant infections.

    In addition to acting as a trusted adviser, Wu points to concrete benefits of his mentorship.

    “We set up a weekly call, much as I might with a CEO of a portfolio company, for the purposes of checking in,” said Wu. “The advantage of this was that [he] did not feel like he needed to have a buttoned-up update each time we talked, and he could easily seek advice on simple things, as well as on topics that may have been deemed tangential to the core project but were still relevant to the success of the technology.”

    The STAIR program’s inaugural year involved four award recipients from diverse areas of campus research. Each has made significant progress in moving the projects forward and achieving important milestones along the path to commercialization of their proprietary technologies.

    Charles Hunt, professor of electrical and computer engineering, used the STAIR funding to develop a prototype for his proprietary light source. His novel field emission light source is environmentally friendly, energy efficient, long lasting and low cost. Prototyping should be finished by the end of the summer, when he will have his light sources independently tested with the objective of moving into the marketplace. Such progress could not have been accomplished without the STAIR program, he said.

    “This [program] is exactly to provide funding to accomplish what other research sponsors don’t,” said Hunt. “And in our case, [the award amount was] just enough to tip the scales.”

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    The University of California, Davis, is a major public research university located in Davis, California, just west of Sacramento. It encompasses 5,300 acres of land, making it the second largest UC campus in terms of land ownership, after UC Merced.

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