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I love my job, as I have the privilege of highlighting Microsoft Research Connections’ collaborations with some of the brightest minds at universities and research institutions around the world. And with so many inspiring projects, it’s difficult to pick my favorites—which is why I’m glad that your clicks can let us know which blogs most sparked your interest. So, here are the best of the best as selected by you: the 10 most widely read Microsoft Research Connections blogs of 2013.
Number 10: New cloud computing training for researchers worldwideToday’s data-intensive scientific research requires vast computing power—just what cloud computing provides. So no wonder a blog that announces free training on using Windows Azure, Microsoft’s cloud computing platform, got a lot of attention. Did you miss this one? Well, it not too late to take advantage of the two-day training programs we offer at sites around the world. Read more...Number 9: Preserving Latin America’s WildlifeThe future is a little brighter for species that are increasingly threatened by habitat destruction and climate change in Latin America. This blog highlights LiveANDES (Advanced Network for the Distribution of Endangered Species), a new tool that enables wildlife biologists, government officials, and citizen scientists to collect, house, and analyze data about Latin America’s wildlife. Read more... Number 8: Computerworld Honors Microsoft Research for Breakthroughs in Pneumonia and HIV Although it is gratifying to receive honors for using technology to promote positive social change, it’s not nearly as rewarding as knowing our research contributes to the fight against two scourges that affect millions around the world. This blog recounts our collaborative efforts towards improving the efficacy of pneumonia vaccinations and perfecting an effective vaccine against HIV infection. Read more...Number 7: Encouraging the next generation of women in computing It’s a sad fact that women students are woefully underrepresented among computer science majors, today comprising only 13 percent of those earning bachelor’s degrees in the field. While we recognize that no single person—or even single organization—can solve this problem, readers of this blog learned that programs like she++, a grassroots community that encourages women’s involvement in computing, just might. Read more... Number 6: Microsoft Research gives promising computer science faculty a boost This might strike a personal chord with many readers: how challenging it is for university faculty to get funding for innovative research—particularly in the early stages of their career. This blog describes how Microsoft Research Faculty Fellowships provide support that helps early-career academics in the field of computer science pursue their vision and make an impact. Read more... Number 5: Windows Azure for Research Remember the cloud computing training covered in our tenth most popular blog? Well, that training is just one part of an extensive initiative to empower researchers to use “cloud power” to tackle Big Data. This blog lays out the entire program, which includes grants, technical resources, and community engagements, as well as the aforementioned training events. Read more... Number 4: Confronting Global Grand Challenges Who can resist a blog whose title promises so much? Granted, it doesn’t promise to solve these challenges (now that would be a blog!), but this post frames the issues and highlights the efforts of a group of talented students to crack six of these grand trials. Plus, it offers wisdom from one of The Black Eyed Peas! Read more... Number 3: Join us in exploring the future of computing—virtually! Another intriguing title, underpinned by an irresistible invitation: to view and even engage in live online interviews with some the world’s foremost academic researchers during the Microsoft Research Faculty Summit. Add the appeal of hearing Bill Gates field questions from the audience about the role of computing in solving global problems, and you’ve got a must-view event promoted in a must-read blog. Read more... Number 2: Kinect Fusion Boosts Kinect for Windows SDK Update Ever since its release, the Kinect for Windows software development kit (SDK) has stimulated researchers’ imaginations and given rise to some outstanding advances in natural user interface (NUI) applications. So it’s no surprise that this blog, which provides information on the latest updates to the SDK, ranked number two on our top-10 list. Read more... Number 1: Try F#—Data Console to Big and Broad DataAnd here it is: the most widely read Microsoft Research Connections blog of 2013, a crowd pleaser that alerted readers to the latest release of resources that teach users to write F# code in their browser. The popularity of this blog implies that perhaps you should give Try F# a whirl if you haven’t already—and why not? It’s free. Read more...There you are—our top-10 list for 2013. I hope you’ve enjoyed our blogs over the past year, and I invite you to stay in touch in 2014 by following us on Twitter, Facebook, or Microsoft Research Connections, or by subscribing to our RSS feed.
Happy New Year from your friends at Microsoft Research Connections!—Lisa Clawson, Senior Manager, Microsoft Research ConnectionsLearn more
Researchers believe that pathogens are evolving to evade detection from the human immune system. I recently co-published a paper that discussed research into the ongoing evolutionary struggle between the immune system and pathogens. In this study, we sought to identify possible commonalities in HLA (human leukocyte antigen) binding preferences that would reveal patterns of optimization of this component of the immune system in response to the variation in pathogens.
I worked with post-doctoral student Tomer Hertz (now with Fred Hutchinson Cancer Research Lab) and a distinguished group of colleagues from the Institute for Immunology and Infectious Diseases, Royal Perth Hospital, and Murdoch University (Western Australia); the School of Anatomy and Human Biology, Centre for Forensic Science, University of Western Australia (Western Australia); and Fundacion Ciencia para la Vida (Chile).
Our paper, "Mapping the Landscape of Host-Pathogen Coevolution: HLA Class I Binding and Its Relationship with Evolutionary Conservation in Human and Viral Proteins," appeared in the American Society for Microbiology's Journal of Virology in February 2011. I'd like to share some highlights from the study with you.
Identifying Possible Commonalities in HLA Binding Preference
The majority of the cells in our bodies express something called HLA molecules, whose role is to sample cellular proteins and present them on the cellular surface for external surveillance by the specialized cells of our immune systems. This action forces all cells to reveal imprints of their inner workings.
When something out of the ordinary is detected—for example, the presence of an unusual mutation or a gene expression—the type and quality of the presented samples can spur the immune system's specialized killer cells into action. By sending kill signals to "odd" cells, the immune system can stop diseases such as cancer or viral infections. (Viruses bring their own genetic material to the cell and use the cellular resources to propagate.)
However, this scrutiny of the immune system creates evolutionary pressure on viruses, which often mutate to evade detection. Since the system of HLA molecules is highly selective in its sampling of protein segments, the mutational patterns in viruses are not entirely random: mutations tend to occur within the segments that HLA molecules are most likely to present.
On the other hand, over many generations, the distribution of thousands of HLA variants present in human populations may change. Additionally, in different geographic regions, we find significant variation in frequencies of different HLA molecules. This sets up an evolutionary game between the viruses on the one side and our immune systems on the other.
In order to analyze the results of the evolutionary processes that are driven by the interaction of HLA molecules with a wide diversity of viral intruders, we quantified the HLA binding preferences by using a novel measure called "targeting efficiency."
Targeting efficiency entails capturing the correlation between HLA-peptide binding affinities with the genetic conservation in the targeted proteomic regions. If HLA molecules possessed such targeting efficiency, this would (presumably) prove beneficial to humans. In theory, HLA molecules would draw attention to protein segments that are shared across related viral species as functionally important and thus immutable sections of their proteins. Individual invading viruses would find it more difficult to evade surveillance by mutating, because mutation within these segments would ruin the protein function. Targeting efficiency could even allow the immune system to generalize across related viral species.
Our analysis of targeting efficiencies for 95 HLA Class I alleles over thousands of human proteins and 52 human viruses indicate that HLA molecules do indeed prefer to target conserved regions in these proteomes! However, the arboviral Flaviviridae (for example, Dengue virus) proved a notable exception in which non-conserved regions were the preferred target of most alleles.
HLA molecules are encoded in three separate parts of the human genome: A, B, and C. During our study, we discovered that the oldest versions of our HLA molecules—namely the HLA-A alleles and several HLA-B alleles that had maintained a close sequence identity with chimpanzee homologues—were targeting conserved human proteins and DNA viruses (for example, Herpesviridae and Adenoviridae) most efficiently.
By contrast, the HLA-B alleles were targeting RNA viruses efficiently. This is reminiscent of predator-prey patterns that have been identified in evolutionary theory. For example, we know the following factors to be true:
Based on this information, we can extrapolate that evolution is going to drive their binding properties in different directions, thus splitting their targets, as in the established Lotka-Volterra (predator-prey) model of different types of foxes and rabbits inhabiting the same forest. In addition, we identified various patterns of host/pathogen specialization that are consistent with co-evolutionary selection and were also functionally relevant in specific cases. For example, preferential HLA targeting of conserved proteomic regions is associated with improved outcomes in HIV infections as well as protection against Dengue Hemorrhagic Fever.
I have just scratched the surface of the study in this blog. For complete study details, including a complete presentation of our methodology and findings, please follow the links below.
—Nebojsa Jojic, Principal Researcher, Microsoft Research eScience Group
As computer-science researchers, we at Microsoft Research are committed to strong computer-science education programs. With more than 800 researchers worldwide, we know firsthand the value of a solid computer-science education, which is why Microsoft Research is a proud supporter of the second annual Computer Science Education Week (CSEdWeek), celebrated this year from December 5-11 in the United States.
This week's focus on computer-science education couldn't be timelier. The recent report from the Association for Computing Machinery, Running on Empty, reveals that the state of computer-science education in the United States is alarming. Only nine states count computer-science courses as a core academic subject in high-school graduation requirements. Meanwhile, there will be a projected 1.4 million new computing jobs by 2018, so we need more states to see the light and join in producing qualified students.
Making matters worse, funding cuts in local school districts have hit computer-science programs heavily. Statistics show that in many school districts, teachers who can teach computer science are being reassigned to mathematics or science classes. How can we as a nation afford to cut corners on this vital component of a 21st-century education?
CSEdWeek is a call to action. It's a rallying point for teachers, parents, and schools at all levels—from K-12 through college—to focus attention on this problem and to build more robust computer-science education programs throughout the United States. Corporations, too, must make their voices heard in support of policies and programs that advance the state of computer-science education. I'm proud that Microsoft is a supporter of CSEdWeek and a strong advocate of computer-science education.
At Microsoft Research, we have a number of tools designed for high-school students, showing them how scientific computing can be part of their daily lives—and fun, as well. Two of these are showcased on our associated website:
I encourage you to give them a try!
Recently, Chris Stephenson, executive director of the Computer Science Teachers Association, made a telling statement: "Effective computer-science education means far more than learning how to use a computer. It is about computational thinking: problem decomposition, data analysis, and solution design, all of which can be incorporated across disciplines and benefit students with interests outside of computer science. But we know that until we eliminate the roadblocks to quality computer-science education, we are denying access to important skills and future opportunities."
Echoing the same sentiments, Rick Rashid, senior vice president of Microsoft Research, said: "Today, more than ever, we need to empower students with the enthusiasm and creative problem-solving skills needed to address some of the world's greatest challenges, from improving healthcare to reducing our impact on the environment."
Do you want to do more to advance computer-science education? You can explore CSEdWeek resources, including tools; suggestions for celebrations, reports, and statistics lesson plans; and event listings across the United States and Canada. You also can sign this pledge in support of CSEdWeek. And please don't confine your activism to this week. Boosting the state of computer-science education in the United States is a 24/7/52 matter!
—Judith Bishop, Director of Computer Science for the External Research division of Microsoft Research