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Microsoft Research Connections Blog

The Microsoft Research Connections blog shares stories of collaborations with computer scientists at academic and scientific institutions to advance technical innovations in computing, as well as related events, scholarships, and fellowships.

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    Preserving Latin America’s Wildlife

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    Watch the video with Spanish subtitles

    In the late 1800s, the guanaco, a close relative of the llama, was hunted to near extinction. As we mark this year’s Earth Day (April 22), I want to share my excitement about a new tool that looks to make the future a little brighter for the guanaco and other threatened species in Latin America. That new tool is LiveANDES (Advanced Network for the Distribution of Endangered Species).

    Developed by a partnership among researchers at the Pontifical Catholic University of Chile, the LACCIR (Latin American and Caribbean Collaborative ICT Research) Virtual Institute, and Microsoft Research, LiveANDES is designed to collect, house, and analyze data about Latin America’s wildlife—data that could prove vital to the preservation of the region’s rich but increasingly threatened biodiversity, which has suffered grievously from loss of habitat and climate change.

    Mariano de la Maza, a wildlife officer in Chile’s Parks and Protected Areas Service, sees this decline on a daily basis. “The main problems of the Chilean forest are habitat loss and the fragmentation and degradation of native forests,” he says.

    LiveANDES begins with field observations, made not just by wildlife biologists and park rangers but by “citizen scientists,” including hikers, eco-tourists, and other nature enthusiasts. As Cristian Bonacic, director of the wildlife laboratory at Pontifical Catholic University, notes, “When people go to the wild, they can encounter an endangered animal by chance.” These chance encounters can provide extremely valuable information about the location and status of threatened and endangered wildlife.

    LiveANDES mobile phone appAll that’s needed is a smartphone equipped with the LiveANDES app. Imagine you’re hiking in the Chilean countryside, and you think you’ve spotted a rare species. You simply take its picture with your smartphone and upload the picture and any sighting comments into LiveANDES. Your photo and annotations, along with the phone’s recognition of your geographical location and a time stamp, are then logged into the LiveANDES database, ready for parsing by the university team.

    Once processed, the data becomes available to scientists locally and around the world, as well as to the public, in both Spanish and English. Bonacic praises LiveANDES for the way it helps researchers “share that information with the scientific community, park rangers, and people at large.”

    Knowing where and under what circumstances a threatened species is living can help biologists devise strategies to stabilize and, one hopes, restore these vulnerable populations. Moreover, the information gathered in LiveANDES also will help keep the International Union for Conservation of Nature (IUCN) red list of endangered and threatened species accurate, complete, and up-to-date.

    The LiveANDES platform was built by using Microsoft technologies, including Windows Phone, Microsoft SQL Server data management software, and Bing Maps for locating and visualizing the animals, and the Microsoft .NET Framework for programming. It not only houses data about Latin America’s wildlife, including photographs, audio and video recordings, and location and sighting data, but it also makes parsing huge volumes of data manageable for researchers.
     
    According to Ignacio Casas, the executive director of LACCIR, LiveANDES integrates with the fourth paradigm, a foundational concept of eScience, in which data-intensive computing facilitates scientific discovery. LiveANDES is designed to make parsing the huge volumes of data recorded manageable for researchers.

    Bonacic and his colleagues look forward to receiving a barrage of wildlife data from rangers, biologists, and, of course, citizen scientists. Thanks to LiveANDES, this data deluge will be manageable and actionable.

    The "culpeo zorro" or Andean fox is most common on the western slopes of the Andes.I am inspired by this project, as it tackles an extremely challenging environmental problem, which is the rapid decline of important elements of our natural heritage. Each animal species is an important piece of a puzzle, and each citizen scientist and researcher can play a crucial role in the preservation of endangered species for the next generation. I’m hopeful that LiveANDES will help the guanaco and other vulnerable species survive to see Earth Day 2113!

    Jaime Puente, Director, Latin America and the Caribbean, Microsoft Research Connections

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    Machine Learning Summit Goes Virtual

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    This April, Paris will be even more exciting than usual, as the Microsoft Research Machine Learning Summit takes place on the company’s “Le Campus.” This year, we will be streaming the keynotes and interviews live from the summit on April 23, from 13:30 to 17:00 GMT (9:30 A.M. to 1:00 P.M. Eastern Time and 6:30 A.M. to 10:00 A.M. Pacific Time). 

    The future of machine learning: interviews and talks: streamed live from Paris, April 23, 2013, 13:30-17:00 GMT

    This free online event will kick off at 13:30 GMT with the opening keynote (recorded earlier in the day) from Andrew Blake, director of Microsoft Research Cambridge. Professor Blake will describe advances in computer vision, with machines that learn to see. Then at 15:00 GMT, you can watch the live stream of Judea Pearl, director of the Cognitive Systems Laboratory at the University of California, Los Angeles. Professor Pearl will speak about the development and application of mathematical tools to study cause-and-effect relationships. What’s more, following their keynotes, these renowned experts will conduct an online Q&A—giving you the opportunity to engage directly with these eminent researchers.
     
    In addition, there will be “Research in Focus” interview segments that describe cutting-edge work in machine learning. Fei-Fei Li of the Stanford Vision Lab and Sebastian Nowozin of Microsoft Research will discuss developments in teaching machines to see, and Zoubin Ghahramani of the University of Cambridge will describe his work on building an “automated statistician.”

    Don’t miss these informative and lively discussions of the challenges posed by this new machine-learning era. Watch the Machine Learning Summit live on April 23 (http://microsoftmls.com).

    Chris Bishop, Distinguished Scientist at Microsoft Research Cambridge
    Evelyne Viegas, Director of Semantic Computing at Microsoft Research Redmond

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    HLA-C: An Underappreciated Force in HIV Control

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    HLA-C: An Underappreciated Force in HIV ControlAlthough medical science has made great progress in managing HIV infection through modern drugs, 1.7 million people die of AIDS each year, with a disproportionate number of deaths in developing countries. Even access to life saving drugs cannot cure the disease: patients require lifelong drug maintenance and face the never-ending danger of developing resistance or adverse side effects to the medications.

    An HIV vaccine thus remains an utmost public health priority. To this end, studying the mechanisms by which some people are able to naturally control infection offers hope for researchers seeking insights into what constitutes an effective immune response—and how we might design a vaccine to illicit such a response. In the April 5 issue of Science, an investigative team, led by Richard Apps and Mary Carrington of the National Cancer Institute and aided by researchers in the eScience group at Microsoft Research, reported a new finding that sheds light on the protective potential of the human gene HLA-C, an often overlooked player in the adaptive immune response.

    Left untreated, the vast majority of HIV-infected individuals will progress to AIDS, marked by the loss of important cells of the immune system and the resulting onset of opportunistic infections. However, the rate of progression varies widely: the virus progresses within weeks in some individuals, while others control the virus and remain AIDS-free for decades.

    Epidemiologic studies of HIV control have repeatedly pointed to the importance of the MHC locus, a cluster of genes that encode proteins that the immune system uses to identify cells that have become virally infected. Of these genes, HLA-B has emerged as a dominant player. Its neighbor, HLA-C, has been largely ignored. The reasons for this are varied, including the relatively low cell-surface expression of HLA-C proteins compared to HLA-A and HLA-B, the observation that HIV actively down regulates surface expression of HLA-A and HLA-B but appears to ignore HLA-C, and the problem that HLA-B and HLA-C genes tend to be inherited together, so any positive effects that could be attributed to HLA-C are often assumed to be the result of neighboring HLA-B. The result is a relative dearth of scientific knowledge regarding the role HLA-C plays in controlling HIV.

    Recently, several genome wide association studies have been published that report common genetic variants that correlate with natural HIV control. One of the largest such studies, published in Science in 2010 and coauthored by many of the same investigators as the current study, found a number of important variations in MHC, but the most significant signal was immediately adjacent to the HLA-C gene. Several follow-up studies from Dr. Carrington’s group and others have provided circumstantial evidence that this genetic variant is an imperfect marker for variations in the level of HLA-C cell surface expression—that is, the number of HLA-C proteins present on the cell surface. Now, Dr. Carrington has provided epidemiological evidence that HLA-C expression directly correlates with control, while Microsoft Research Distinguished Scientist David Heckerman and I used models of sequence evolution combined with functional immune response data to provide a proposed mechanism and corroborating evidence that HLA-C expression modulates immune and viral responses. Thus, in contrast to HLA-A and HLA-B, it isn’t that individual variants of HLA-C proteins contribute to varying degrees of control (although that could also be the case), but that overall cell-surface quantities of the protein, regardless of variant, are directly correlated with control, rates of immune targeting, and magnitude of evolutionary pressure exerted upon the virus. These findings suggest a broader role for variations in HLA surface expression across a range of diseases. Indeed, in addition to the protective effect of HLA-C expression on HIV, we observed a correlation between HLA-C expression and increased susceptibility to Crohn’s disease, a complex inflammatory bowel disease that may be related to an overly active adaptive immune response.

    Although the finding that increased HLA-C expression levels can contribute to both pathogen control and disease susceptibility complicates our understanding of the immune system, it highlights the importance of this long-overlooked protein and may unlock new research into the mechanisms of natural control, providing potential new targets for vaccine design.

    Microsoft Research’s involvement in this study is the result of more than seven years of ongoing research in the HIV community. We have forged ongoing collaborations with more than a dozen labs and have developed statistical models of HIV evolution that have:

    Our ongoing research develops and uses tools derived from machine learning and applied statistics to move toward the development of an effective HIV vaccine.

    Jonathan Carlson, Researcher, eScience Research Group, Microsoft Research Connections

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