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    Computer Science Faculty, Students Awarded Best Poster at ITiCSE


    Department of Computer Science faculty and students presented two posters, a paper, and chaired a session at the 26th Annual Conference on Innovation and Technology in Computer Science Education (ITiCSE), conducted online June 26 to July 1, 2021.

    “A Visualization for Teaching Integer Coercion,” a poster presented by James Walker with Steven Carr, Ahmed Radwan, Yu-Hsiang Hu, Yu Chin Cheng, Jean Mayo, and Ching-Kuang Shene, was one of three posters that received the conference’s Best Poster Award.

    The poster describes the Expression Evaluation (EE) visualization tool. The tool is designed to aid students in understanding type conversions that take place implicitly in C. Understanding type conversions is essential to avoid Integer errors in C which continue to be a source of security vulnerabilities.

    An additional paper and poster were presented at the conference, below. Dr. Linda Ott chaired a conference session on Students: Diversity.


    Poster: Modeling the Growth and Spread of Infectious Diseases to Teach Computational Thinking by Meara Pellar-Kosbar, Dylan Gaines, Lauren Monroe, Alec Rospierski, Alexander Martin, Ben Vigna, Devin Stewart, Jared Perttunen, Calvin Voss, Robert Pastel and Leo Ureel II

    The poster discusses a simulation model developed to teach middle school students about the spread of infectious diseases augmented with affordances to help students develop computational thinking skills. The simulation was partially developed as a Citizen Science project in the courses CS4760 and CS5760, User Interface Design and Human Computer Interaction.

    Presentation: Frozen in the Past: When it Comes to Analogy Fears, It’s Time For Us to “Let it Go” by Briana Bettin and Linda Ott

    This position paper describes a fundamental difference in attitudes toward the use of analogy in the computer science education community versus other STEM education communities. Additionally, it provides suggestions for how to address concerns in the CS education research community in order to advance research into the use of analogy in computing education

    The 26th annual conference on Innovation and Technology in Computer Science Education (ITiCSE) was sponsored by ACM, the ACM Special Interest Group on Computing Education (SIGCSE), the ACM Europe Council, and Informatics Europe.


    Jingfeng Jiang Awarded $347K NIH R-D Grant

    Jingfeng Jiang (BioMed/HRI) is the principal investigator on a project that has a received a $346,966 research and development grant from the National Institutes of Health.

    The project is titled “Personalized Management of Intracranial Aneurysms Using Computer-aided Analytics.”

    Jinshan Tang (AC/HRI) is a co-PI on this potential four-year project, which could total $1,349,106.


    Get to Know Dr. Sangyoon Han, Biomedical Engineering


    Dr. Sangyoon Han is an assistant professor in Michigan Tech’s Biomedical Engineering department, and an affiliated assistant professor in the Mechanical Engineering-Engineering Mechanics department. He is also advisor to the Korean Students Association. He has been with Michigan Tech since 2017.

    Han recently joined the Institute of Computing and Cybersystems and its Data Sciences research group. His primary research interests are in mechanobiology, cell migration, and image data modeling. His research goals include applying computer vision to microscopic images to capture meaningful information, and he’s looking for collaborators.

    “Anyone with a good machine learning background is encouraged to contact me to discuss potential research,” he says. “Also, students who learned assignment problems or particle tracking are encouraged to contact me to discuss potential tracking-related projects.”

    Teaching and Mentoring

    Han’s teaching interests include computer vision for microscopic images, fluid mechanics, cell biomechanics and mechanobiology, and soft tissue mechanics. This academic year, he instructed Computer Vision for Microscopic Images in the Fall semester, and Fluid Mechanics this Spring.

    Han enjoys teaching and interacting with students, “and feel their energy, too.” He says he makes a deliberate effort in his classes to pause from time to time so that his students can ask questions.

    Han advises two Biomedical Engineering Ph.D. students, Nikhil Mittal and Mohanish Chandurkar.

    “Nik is working on finding myosin-independent mechanosensitivity mechanism for stiffness sensing, and Mohanish works on the project finding mechano-transmission for fluid shear stress sensing by endothelial cells,” he says.

    Research Aspirations

    Han’s Mechanobiology Lab is interested in finding fundamental mechanisms governing mechanotransduction, and how cells sense mechanical forces and convert them into biochemical signals.

    “We image cells and associated forces using high-resolution live imaging, which we analyze to obtain statistically meaningful quantity of data,” Han explains. “We apply force-measuring and molecular-imaging/analysis technologies for stiffness sensing, shear flow sensing, adhesion assembly, and cancer mechanobiology.”

    Han is working to gain a thorough understanding of the mechano-chemical interaction between cancer cells and their microenvironment, and develop a an effective mechano-therapeutic strategy to stop the progression of cancer, and breast cancer in particular. Ultimately, he wants to apply that knowledge to cancer mechanobiology

    Han is principal investigator of a three-year NIH/NIGMS research project, “Nascent Adhesion-Based Mechano-transmission for Extracellular Matrix Stiffness Sensing.” The research aims to determine whether newly-born adhesions can sense tissue stiffness through the accurate measurement of the mechanical force and molecular recruitment of early adhesion proteins.

    Some Background

    In 2012, Han received his Ph.D. in Mechanical Engineering from the University of Washington in the areas of cell mechanics, multiphysics modeling, and bioMEMS.

    For his postdoctoral training, he joined the Computational Cell Biology lab led by Dr. Gaudenz Danuser in the Cell Biology department of Harvard Medical School. In 2014, he joined the UT Southwestern (University of Texas) Department of Cell Biology and Bioinformatics. Han received his B.S and M.S. degrees in mechanical engineering at Seoul National University, Korea, in 2002 and 2004, respectively.

    Han holds several patents and in 2015, he developed an open-source TFM (Traction Force Microscopy) Package, which is shared via his lab’s website: hanlab.biomed.mtu.edu/software.

    Beyond Research and Teaching

    Han loves science and discovering something new in his research investigations. Beyond his work as a professor and scientist, he describes himself as a husband to Sunny, and a dad to his son, Caleb.

    “I am just a normal Korean who likes singing and dancing,” he says. “Unfortunately, my voice is still recovering from surgery, but I hope to get back to it soon. I also like to listen to all kinds of music, including hip-hop, classics, and pop.”

    He appreciates a good sense of humor, but he says that being humorous in American English is something he continues to learn.

    Han says he tries to be “normal” and not too nerd-like when he’s not pursuing his research, but “there are times when I am making my own hypothesis about some phenomena I observe in my daily life.”

    Han enjoys life at Michigan Tech and in the Cooper Country. He likes getting to know his energetic students and he finds Michigan Tech faculty members very strong and collegial. He also enjoys the snow, hockey, and the mountains.

    “I really like the snow here. I am already sad that the weather is becoming too mild!” he confirms. “It’s also a safe environment to raise kids, which is a big plus.”

    And he likes his academic department. “Everyone is so nice in the Biomedical Engineering program, they have been so welcoming and appreciative my research,” Han says. “It’s a family-like environment.”


    Active Research

    1R15GM135806-01 (09/16/2019 – 08/31/2022)

    Funding Agency: NIH/NIGMS

    Nascent Adhesion-Based Mechano-transmission for Extracellular Matrix Stiffness Sensing

    Project Goals: To determine whether newly-born adhesions can sense tissue stiffness by accurate measurement of mechanical force and of molecular recruitment of early adhesion proteins using traction force microscopy and computer vision techniques.
    Role: Principal Investigator


    Additional Information

    The Mechanobiology Lab studies mechanobiology, particularly how adherent cells can sense and respond to mechanical stiffness of the extracellular matrix. To investigate this, the lab has established experimental and computational frameworks for force measurement and adhesion dynamics quantification. Researchers apply these frameworks, with cutting edge computer vision technique, on live-cell microscope images to investigate the fundamental mechanism underlying mechanosensation in normal cells, and the biomechanical signature of the diseased cells whose signaling has gone awry.

    The Institute of Computing and Cybersystems (ICC) creates and supports an arena in which faculty and students work collaboratively across organizational boundaries in an environment that mirrors contemporary technological innovation. The ICC’s 60+ members, in six research centers, represent more than 20 academic disciplines at Michigan Tech. https://www.mtu.edu/icc/

    The ICC Center for Data Sciences (DataS) focuses on the research of data sciences education, algorithms, mathematics, and applications. https://www.mtu.edu/icc/centers/data-sciences/

    The National Institutes of Health (NIH), a part of the U.S. Department of Health and Human Services, is the nation’s medical research agency — making important discoveries that improve health and save lives. https://www.nih.gov/

    The National Institute of General Medical Sciences (NIGMS) supports basic research that increases understanding of biological processes and lays the foundation for advances in disease diagnosis, treatment, and prevention. https://www.nigms.nih.gov/


    Recent Publications

    • Han, S. J.; Azarova, E. V.; Whitewood, A. J.; Bachir, A.; Guttierrez, E.; Groisman, A.; Horwitz, A. R.; Goult, B. T.; Dean, K. M.; Danuser, G. Pre-Complexation of Talin and Vinculin without Tension Is Required for Efficient Nascent Adhesion Maturation. eLife 2021, 10, e66151. https://doi.org/10.7554/eLife.66151.
    • Schäfer, C., Ju, Y., Tak, Y., Han, S.J., Tan, E., Shay, J.W., Danuser, G., Holmqvist, M., Bubley, G. (2020) TRA-1-60-positive cells found in the peripheral blood of prostate cancer patients correlate with metastatic disease. Heliyon 6(1), e03263.
    • Isogai, T., Dean, K.M., Roudot, P., Shao, Q., Cillay, J.D., Welf, E.S., Driscoll, M.K., Royer, S.P., Mittal, N., Chang, B., Han, S.J., Fiolka, R., Danuser, G., Direct Arp2/3-vinculin binding is essential for cell spreading, but only on compliant substrates and in 3D, BioRxiv, 2019
    • Mohan, A.S., Dean, K.M., Isogai, T., Kasitinon, S.Y., Murali, V.S., Roudot, P., Groisman, A., Reed, D.K., Welf, E.S., Han, S.J., Noh, J., and Danuser, G. (2019). Enhanced Dendritic Actin Network Formation in Extended Lamellipodia Drives Proliferation in Growth-Challenged Rac1P29S Melanoma Cells. Developmental Cell, 49(3), pp.444-460.
    • Manifacier I., Milan, J., Beussman, K., Han, S.J., Sniadecki, N.J., About, I (2019) The consequence of large-scale rigidity on actin network tension. In press. Comp Meth Biomech Biomed Eng, 2019 Oct;22(13):1073-1082.
    • Costigliola, N., Ding, L., Burckhardt, C.J., Han, S.J., Gutierrez, E., Mota, A., Groisman, A., Mitchison, T.J., and Danuser, G. (2017) Vimentin directs traction stress. PNAS2017 114 (20) 5195-5200.
    • Han, S.J., Rodriguez M.L., Al-Rekabi, Z., Sniadecki, N.J. (2016) Spatial and Temporal Coordination of Traction Forces in One-Dimensional Cell Migration, Cell Adhesion & Migration. 10(5): 529-539.
    • Oudin, M.J., Barbier, L., Schäfer, C, Kosciuk, T., Miller, M.A., Han, S.J., Jonas, O., Lauffenburger, D.A., Gertler, F.B. (2016) Mena confers resistance to Paclitaxel in triple-negative breast cancer. Mol Cancer Ther.DOI: 10.1158/1535-7163. MCT-16-0413. 
    • Milan,J., Manifacier, I., Beussman, K.M., Han, S.J., Sniadecki, N.J., About, I., Chabrand, P. (2016) In silico CDM model sheds light on force transmission in cell from focal adhesions to nucleus. J Biomechanics. 49(13):2625-2634. 
    • Lomakin. A.J., Lee, K.C., Han, S.J., Bui, A., Davidson, M., Mogilner, A., Danuser G. (2015) Competition for molecular resources among two structurally distinct actin networks defines a bistable switch for cell polarization, Nature Cell Biology. 17, 1435–1445
    • Han, S.J., Oak, Y., Groisman, A., Danuser, G. (2015) Traction Microscopy to Identify Force Modulation in Sub-resolution Adhesions, Nature Methods. 12(7): 653–656


    Sangyoon Han Publishes Paper in eLife

    eLife, a prestigious journal in cell biology, has published a paper co-written by Sangyoon Han, “Pre-complexation of talin and vinculin without tension is required for efficient nascent adhesion maturation.”

    Dr. Han is an assistant professor in the Biomedical Engineering department, and a member of the Data Sciences research group of the Institute of Computing and Cybersystems (ICC).

    View the paper here.

    eLife is a non-profit organization created by funders and led by researchers. Their mission is to accelerate discovery by operating a platform for research communication that encourages and recognizes the most responsible behaviors.


    Biocomputing, Digital Health Focus of New Research Center


    The Institute of Computing and Cybersystems (ICC) and the Health Research Institute (HRI) have established the Joint Center of Biocomputing and Digital Health (BDH).

    The new research institute was co-founded by HRI member Jingfeng Jiang (BME) and ICC member Jinshan Tang (CC).

    The mission of Joint Center of Biocomputing and Digital Health (BDH) is to conduct research, develop innovative solutions, and provide educational opportunities in the area of biocomputing and digital health, thereby enhancing Michigan Tech’s ability to recruit and retain high-quality researchers and students, elevating Michigan Tech’s presence in developing technologies for healthcare delivery, and increasing knowledge sharing in the global community.

    Jingfeng Jiang is a professor with the Department of Biomedical Engineering. His research interests are in biomechanics, automated control of ultrasound scanning including the use of 3D printing technology, image and signal processing, non-invasive assessment of biomechanical properties of soft tissues, and computer aided analyses of cardiovascular flow.

    Jinshan Tang is a professor in the Department of Applied Computing. His research interests are in image processing and pattern recognition, biomedical imaging and medical image analysis, and medical informatics and intelligent medical diagnosis systems. Tang is a member of the ICC’s Center for Cyber-Physical Systems.

    The Institute of Computing and Cybersystems (ICC) creates and supports an arena in which faculty and students work collaboratively across organizational boundaries in an environment that mirrors contemporary technological innovation.

    The Health Research Institute (HRI) aims to establish and maintain a thriving environment that promotes translational, interdisciplinary, and increasingly convergent health-related research and inspires education and outreach activities.

    Please contact Jingfeng Jiang (jjiang1@mtu.edu) with questions.


    Sangyoon Han to Present Chemistry Seminar this Friday, Nov. 13, at 3 pm

    A Chemistry Seminar will be presented Friday, September 13, 2020, at 3:00 p.m., via online meeting.

    Dr. Sangyoon Han will present his lecture, “Toward Discovery of the Initial Stiffness-Sensing Mechanism by Adherent Cells.” Han is an Assistant Professor in Biomedical Engineering, an Affiliate Assistant Professor in Mechanical Engineering-Engineering Mechanics, and advisor for the Korean Student Association. Han is a member of the ICC’s Center for Data Science.

    Lecture Abstract

    The stiffness of the extracellular matrix (ECM) determines nearly every aspect of cellular/tissue development and contributes to metastasis of cancer. Adherent cells’ stiffness-sensing of the ECM triggers intracellular signaling that can affect proliferation, differentiation, and migration of the cells. However, biomechanical and molecular mechanisms behind this stiffness sensing have been largely unclear. One critical early event during the stiff-sensing is believed to be a force transmission through integrin-based adhesions, changing the molecular conformation of the molecules comprising the adhesions that link the ECM to the cytoskeleton. To understand this force transmission, my lab develops experimental and computational techniques, which include soft-gel-based substrates, live-cell imaging, computer-vision-based analysis, and inverse mechanics, etc. In this talk, I will talk about how we use soft-gel to quantify the spatial distribution of mechanical force transmitted by a cell, how we use light microscopy and computer vision to analyze the focal adhesions, and how these techniques are related to stiffness sensing. In particular, I will show you new data where cells can transmit different levels of traction forces in response to varying stiffness, even when the activity of the major motor protein, myosin, is inhibited. At the end of the talk, potential molecules responsible for the differential transmission will be discussed. 

    Researcher Bio

    Sangyoon Han received his Ph.D. in Mechanical Engineering at the University of Washington (UW) in 2012 and did postdoctoral training with Dr. Gaudenz Danuser in the Department of Cell Biology at Harvard Medical School and the University of Texas Southwestern Medical Center for five years until 2017. Before the Ph.D., he received B.S and M.S. degree from Mechanical Engineering at Seoul National University, Seoul, Korea in 2002 and 2004.

    He joined Michigan Tech, Biomedical Engineering from fall 2017, and started Mechanobiology Laboratory. His lab’s interests are in understanding the dynamic nature of force modulation occurring across cell adhesions and cytoskeleton that regulate cells’ environmental sensing. His lab develops a minimally-perturbing experimental approach and computational techniques, including soft-gel fabrication, nano-mechanical tools, live-cell microscopy, and image data modeling, to capture the coupling between force modulation and cellular molecular dynamics.


    Faculty / Researcher Profile: Weihua Zhou

    Faculty/Researcher Profile: Weihua Zhou, Multi-Disciplinary Digital Healthcare Solutions

    By Karen Johnson, Communications Director, College of Computing and Institute of Computing and Cybersystems

    How can the cost-effectiveness of healthcare be improved, especially for complicated chronic diseases? This is the overarching question Dr. Weihua Zhou is seeking to answer with his research. The multi-disciplinary solutions he is investigating merge the fields of medical imaging and informatics, computer vision, and machine learning. 

    An assistant professor in Michigan Tech’s Health Informatics program, and an affiliated associate professor in the Biomedical Engineering department, Zhou is working with students on a number of research projects in Michigan Tech’s Medical Imaging and Informatics Lab, which he directs. He is a member of the Institute of Computing and Cybersystems’s Center for Data Science.

    Zhou says his research is driven by clinical significance, and he is especially interested in developing practical solutions to improve the cost-effectiveness of treating complicated chronic diseases, such as coronary artery disease, heart failure and senile dementia. 

    He is excited about his career, his international research, and his work at Michigan Tech. “We have a very productive team, including dedicated Ph.D. students, self-motivated graduate and undergraduate students, and a lot of experienced clinical and technical collaborators,” he says of his colleagues and collaborators at Michigan Tech and around the world.

    Zhou feels that he can be dedicated to both his research and teaching at Michigan Tech. “I joined the Health Informatics program at Michigan Tech, both because health informatics is my research focus, and because Michigan Tech’s leading reputation among engineering schools opens opportunities to find new and respected technical collaborators. 

    Zhou often calls himself a salesman. “I sell techniques to our clinical collaborators and ask them to design the projects with me, provide the patient data, and test our tools,” he explains. “I also sell my ideas about clinical problems to technical collaborators and ask them to work with us to solve the important clinical problems.”

    And when he communicates with his Ph.D. students, “sometimes I also consider them as my buyers and let them appreciate my ideas so that they can be really inspired.”

    Primary Research

    Zhou identifies two of his research projects of as primary. 

    “This first is exploring image-guided approaches to improving the treatment of heart failure, which has been supported by AHA grants, and is now being supported by a new faculty startup grant,” Zhou says. “The second main project is seeking to employ machine learning to improve the risk stratification for osteoporosis, which is supported by a National Institutes of Health (NIH) subcontract award from Tulane University.”

    On the NIH grant, awarded in December 2019, Zhou is working with internationally renowned researcher and educator Dr. Hong-Wen Deng, an endowed chair and professor in the School of Public Health and Tropical Diseases at Tulane University, New Orleans, La. Zhou and Deng are studying trans-omics integration of multi-omics studies for male osteoporosis.

    Zhou is also co-PI with Jinshan Tang, professor of Applied Computing at Michigan Tech, on a Portage Health Foundation Infrastructure Enhancement Grants titled, “High Performance Graphics Processing Units.” The project is focused on building big data computing capabilities toward advancing research and education. Several additional proposals are under review and revision. Zhou’s past research support includes an American Heart Association award, which studied a new image-guided approach for cardiac resynchronization therapy.

    Teaching and Mentoring

    Zhou, who started at Michigan Tech in fall 2019, instructed Introduction to Health Informatics in the fall semester, and Applied Artificial Intelligence in Health this spring.  He says that in the Medical Informatics program, the subjects he teaches are very practical.

    “I believe the following strategies are very important and I practice them in my classes every day: 1) Make the class interactive; 2) Make the assignments and projects practical; 3) Emphasize the learning process; and 4) Keep the teaching materials up to date,” Zhou says.

    Zhou supervises two Ph.D. candidates in the Department of Applied Computing, and a Health Informatics master’s student.

    Applied Computing Ph.D. candidate Zhuo He’s primary research project concerns information fusion between electrical signal propagation and mechanical motion to improve the treatment of heart failure. Ph.D. candidate Chen Zhao’s primary research concerns using image fusion and computer vision to improve interventional cardiology. And Zhou’s Health Informatics master’s student, Rukayat Adeosun, is studying nuclear image-guided approaches to improving cardiac resynchronization therapy.

    Education and Post-Doc

    Zhou was awarded his Ph.D. in computer engineering by the Department of Electrical and Computer Engineering at Southern Illinois University Carbondale in 2012; his dissertation is titled, “Image reconstruction and imaging configuration optimization with a novel nanotechnology enabled breast tomosynthesis multi-beam X-ray system.”

    Following, Zhou was a post-doctoral researcher in the Department of Radiology and Imaging Sciences at Emory University, Atlanta, Georgia, then he was appointed a Nina Bell Suggs Endowed Professor at University of Southern Mississippi, where he was a tenure-track assistant professor. Zhou also completed an MSc.-Ph.D. in computer science (2007) and a B.E. in computer science and technology (2003), both at Wuhan University, China.

    Achievement

    Zhou received the USM College of Arts and Sciences Scholarly Research Award in March 2019, participated in the AHA Research Leaders Academy of the American Heart Association in September 2017 and August 2018, and received the USM Butch Oustalet Distinguished Professorship Research Award in April 2018.

    University and Professional Service

    Zhou serves on Michigan Tech’s Review Committee for Graduate Dean’s Awards Advisory Committee, and in October 2019 he served on the Review Committee for Research Excellence Fund (REF) – Research Seed Grants (RS).

    He was an invited speaker at the Machine Learning in SPECT MPI Applications session at the Annual Scientific Session of the American Society of Nuclear Cardiology in Washington, D.C., in 2009.

    Zhou is a member of the American Heart Association (AHA) and the American Society of Nuclear Cardiology (ASNC).

    Peer-Review

    Since Zhou joined Michigan Tech in August 2019, he has published five scholarly papers, in Journal of Nuclear Cardiology and the IEEE Journal of Translational Engineering in Health and Medicine. Two additional articles are under revision with Journal of Nuclear Cardiology and the journal Medical Physics, and one is under review by the Medical Image Computing and Computer Assisted Intervention (MICCAI) Conference 2020.

    Since 2007, he has published more than 80 peer-reviewed journal and conference papers and book chapters in publications including JACC: Journal of The American College of Cardiology: Cardiovascular Imaging, Journal of Nuclear Cardiology, and IEEE Journal of Translational Engineering in Health and Medicine.

    Zhou is a translator of featured papers and abstracts for the Journal of Nuclear Cardiology, and a paper reviewer for the Journal of Nuclear Cardiology, JACC: Journal of The American College of Cardiology, and JACC: Cardiovascular Imaging. He is a reviewer for American Heart Association data science grants. 

    Commercial Success

    Zhou holds a number of patents and invention disclosures, including new methods to 1) diagnose apical hypertrophic cardiomyopathy from gated single-photon emission computed tomography (SPECT), and 2) measure right-ventricular and interventricular mechanical dyssynchrony from gated single-photon emission computed tomography (SPECT) myocardial perfusion imaging (MPI); and 3) the integration of fluoroscopy venogram and myocardial perfusion SPECT image with left-ventricular contraction sequence and scar distribution to guide the real-time surgery of cardiac resynchronization therapy. 

    He and his colleagues have developed a number of software tools, some of which are being used in hospitals for research purposes, and he believes that the tools can be successfully validated and become commercially available. For example, Zhou’s nuclear image-guided software toolkit to improve cardiac resynchronization therapy is being validated by a large clinical trial. 

    A personal note.

    Zhou loves independent thinking, facts and exact numbers, and he values persistence, all of which express themselves in his teaching and research, and his life.

    Follow Weihua Zhou on Twitter: @LabMiil

    The College of Computing’s Department of Applied Computing officially starts on July 1, 2020. The new department will replace the CMH Division.