In the news / Bioinformatics

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Since the beginning of the COVID-19 pandemic, dozens of countries have deployed digital apps attempting to identify people exposed to the SARS-CoV-2 coronavirus and stop onward transmission. Evidence that these ‘contact tracing’ apps work has been hard to come by. Now, studies from a handful of nations show mounting evidence that apps can help prevent infections and are a valuable public-health tool. One way apps could improve is in how they measure exposure risk, says Dr. Joanna Masel, an evolutionary biologist at the University of Arizona, who is leading a pilot study of the COVID Watch app at the university.
 
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A UArizona Health Sciences research project called Saguaro Study, is designed to identify issues unique to University employees who are at least 50 years old and then test ways to help address or mitigate those concerns among the 5,700 employees in that age group. The team led by BIO5 member and chair of the Department Epidemiology and Biostatistics in the College of Public Health Dr. Zhao Chen, are examining the balance of keep stress in check during the pandemic, while also maintaining physical activity and retaining social connections.
 
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The idea behind these rapid tests is to detect symptomatic, pre-symptomatic and asymptomatic infectious people before they can spread the coronavirus. But despite massive distribution of these tests by federal officials – including to date over 40 million of 150 million rapid tests ordered from the medical company Abbott – COVID-19 transmission has been surging in every state since early November. For rapid tests to effectively limit spread of the coronavirus, experts suggest that they must be conducted with high frequency.
 
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Dr. Brian Enquist teamed up with Nirav Merchant, CyVerse co-principal investigator and director of UArizona Data Science Institute, to lead an interdisciplinary collaboration of the nation's scientists aiming to harness the power of big data and cyberinfrastructure to predict global biodiversity changes under different climate outcome scenarios. The project was funded this year at $2.5 million under the National Science Foundation's Harnessing the Data Revolution program, with just over $966,000 awarded to UArizona. The grant stemmed from work done by the Bridging Biodiversity and Conservation Science group, a new interdisciplinary initiative at the University of Arizona.
 
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The NASA Astrobiology Program has selected eight new interdisciplinary research teams to inaugurate its Interdisciplinary Consortia for Astrobiology Research program, including two teams at the University of Arizona. One team led by Dr. Betül Kaçar, Molecular and Cellular Biology assistant professor and BIO5 member, was selected from a pool of more than 40 proposals. The breadth and depth of the research of these teams spans the spectrum of astrobiology research, from cosmic origins to planetary system formation, origins and evolution of life, and the search for life beyond Earth.
 
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The daily number of cases according to Arizona's COVID dashboard have nearly doubled in the past weeks. Dr. Michael Worobey, head of the the University of Arizona's Department of Ecology and Evolutionary Biology and associate director at the BIO5 Institute, has written and researched pandemics worldwide. He agrees Arizona is on the edge right now. "We need to be preparing for a potentially very tough winter," Dr. Worobey said. While he says we need to take the possibility of a wave seriously in the next weeks, it should be done within context.
 
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A new study authored by Dr. Michael Worobey, UArizona Department of Ecology and Evolutionary Biology head and BIO5 member, tracks the spread of coronavirus through North America and Europe. The study investigates when, where, and how COVID-19 established itself globally, using airline passenger flow data, disease incidence rates, and genomic sequence data.
 
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Since the University of Arizona opened its doors, more than 9,000 students, faculty and staff had been tested for COVID-19 and everyone on campus was wearing a mask. The school had even begun sampling its wastewater to quickly detect a potential hot spot. But the centerpiece in the school's preemptive battle against COVID-19 was the "Covid Watch" smartphone app, which uses Bluetooth technology to send an alert to someone's phone if they are exposed to the virus.
 
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Harnessing the power of technology, the BIO5 Institute will virtually connect University of Arizona faculty and researchers with representatives from biotech, biomedical, and life science companies at the FINE event on Thursday, August 13, 2020.
 
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A study by Dr. Ali Akoglu, electrical and computer engineering associate professor, and his graduate students Nirmal Kumbhare and Joshua Mack was selected as the Featured Paper in the August issue of IEEE Transactions on Computers due to its novelty and practicality. Their paper, "DS3: A System-Level Domain-Specific System-on-Chip Simulation Framework,” presents a system-level domain-specific systems-on-chip simulation (DS3) framework.
 
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To address the critical need of local COVID-19 data, a collaboration of researchers from UArizona Health Sciences & The Data Science Institute including BIO5’s Drs. Nirav Merchant and Sriram Iyengar, launched a 2-way texting system to gather valuable info to track the virus in Arizona. The application will assist with identifying areas where resources are needed.
 
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We all do better when we work together. Using cutting edge technology and big data analysis, the newly formed Arizona COVID-19 Genomics Union (ACGU) will track the virus’ evolution and transmission. Co-founded by UArizona Department of Ecology & Evolutionary Biology head and BIO5 associate director Dr. Michael Worobey, the cross-university collaboration between NAU, TGen and UArizona is another example of how our combined strength will provide solutions to better Arizona.
 
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A collaboration between the Information School, Computer Science, and Family Studies and Human Development has been awarded a $7.5M grant to develop a theory of mind-based cognitive architecture for teams (ToMCAT). The grant is part of the DARPA Artificial Social Intelligence for Successful Teams (ASIST) program. The collaborating team includes computer science professor Dr. Jacobus Barnard. The project aims to build artificially intelligent agents that understand both the social and goal-oriented aspects of teams in mission-like scenarios and are able to reason about possible interventions. 
 
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Directed by Dr. Hsinchun Chen, a UArizona cybersecurity program aims to train the next generation of cyberspace defenders. Thanks to a $3.6 million grant renewal from the NSF, the two-year program, the AZSecure Cybersecurity Fellowship, will continue to cover tuition and fees for graduate students and provides a stipend of $34,000 per academic year. About 30 students have already taken advantage of the program since 2013, and the renewal funding will allow the program to roughly 20 more students over the next five to seven years.
 
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The use of new technologies and automation raises questions about the impact on the job market and their respective hacking vulnerabilities. Dr. Larry Head, BIO5 faculty member and professor of Systems and Industrial Engineering at UA, discusses the importance of consumers doing research about the safety of autonomous vehicles before using them. 
 
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Science has the power to improve health, strengthen economies and shed light on the unknown throughout the universe, but a small and growing number of research papers are being retracted by journals for a myriad of reasons, including falsified evidence, conflicts of interest and plagiarism, speciali
 
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New DNA analysis conducted by BIO5 faculty member and University of Arizona Plant Sciences professor Dr. Judith Brown, along with researchers at the Los Alamos National Laboratory, has found genetic diversity in predatory pest, Vampirovibrio chlorellavorus. This discovery complicates efforts to protect algae ponds used in the biofuels industry from destructive algae strains and pests.
 
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Scientists lead by The BIO5 Institute's Dr. Michael Worobey at the University of Arizona were able to extract from the tissue a nearly complete genetic sequence of an HIV virus — the oldest nearly full-length genetic code for an HIV-1 virus recovered thus far, and one that supports the theory that the virus that causes AIDS began to transmit among people within the first decade or two of the 20th century.