Shape Analysis in Medical Imaging
By Tanya Schmah, Assistant Professor, Department of Mathematics and Statistics
Abstract: How can we detect and describe shape variations? This problem arises in many areas of computer vision and pattern recognition. In medical imaging (e.g. MRI, CT), it arises in the comparison of images from different patients, or from the same patient at different times. Some differences between images can be described as shape deformations, arising either from the imaging process or from anatomical changes due to natural aging or disease progression, or to differences between people. After shape deformations are accounted for, the remaining “non-shape” changes in appearance are also important as they may indicate disease, for example stroke lesions or tumours. To quantify both kinds of variation in a set of images, we often begin by “registering”, i.e. aligning, the images to a common template, which produces both a set of registered images and the set of spatial deformations used. Both can be analysed statistically: the deformations to quantify shape changes, and the registered images to quantify “non-shape” appearance changes. State-of-the-art methods combine these steps in a unified shape and appearance model. I will discuss some of the mathematical, statistical and data science aspects of this problem, and relationships with other problems in biology and engineering.
Biography: Tanya Schmah is an Assistant Professor at the University of Ottawa, in the Department of Mathematics and Statistics. After completing a Bachelor degree in Mathematics and Computer Science, she worked in industry for five years before beginning graduate studies in Mathematics. She earned her PhD in 2001 from the EPFL (Switzerland) with a thesis in geometric mechanics, a subject on which she later co-authored a graduate text. She worked as a Lecturer at the University of Warwick (U.K.) and Macquarie University (Australia). In 2007 she moved to the University of Toronto and into the fields of statistical machine learning and neuroinformatics. In 2013 she became the Program Manager of the Neuroinformatics Research Group at the Rotman Research Institute, Baycrest (Toronto), before joining the University of Ottawa in 2015. Her main current research interest is the application of geometry and statistical machine learning to neuroimage registration and analysis, with a particular focus on stroke lesion mapping.
Naked Inhibition: Metabolic Adaptations to Hypoxia in African Mole Rats
By Matthew Pamenter, Assistant Professor and Canada Research Chair in Comparative Neurophysiology, Department of Biology, uOttawa Brain and Mind Research Institute
Abstract: The Pamenter Lab is focused on the study and exploitation of naturally evolved mechanisms of hypoxia-tolerance. By examining both proactive and reactive responses to low oxygen stress in hypoxia-tolerant and –intolerant species (respectively), we seek to understand the biochemical, cellular, and systemic adaptations that allow some species to tolerate acute or prolonged low oxygen stress, whereas others suffer rapid cellular and whole organism death. Advancing our knowledge in this area will allow us to develop a deeper understanding of pure biological questions related to the control and evolution of systemic responses to hypoxia. In addition, it may also provide an applied translational benefit by informing the development of novel strategies and therapeutics to treat pathologies related to hypoxia, such as ischemic stroke and chronic pulmonary disorders
Biography: Matt obtained his PhD in Zoology in the Buck lab at the University of Toronto (2008), where he used electrophysiology and live cell imaging to study neuroprotective mechanisms against long-term anoxia in turtle and fish brain. He then undertook two postdoctoral appointments, first with Gabriel Haddad in the Department of Pediatrics at UCSD (2008-2012), studying cell death mechanisms in ischemic stroke models, and then with Bill Milsom in the Zoology Department at UBC (2012-2015), where he started his work with naked mole rats. Matt joined the Department of Biology at uOttawa in July of 2015 as the Canada Research Chair (Tier II) in Comparative Neurophysiology.
The Chemistry and Biology of Viral Infection and the Host Response
By John Pezacki, Full Professor, Department of Chemistry and Biomolecular Sciences
Abstract: Viruses alter host cellular metabolism in order to meet the material and energy demands of their life cycles. Several viruses induce specific lipid microenvironments to facilitate different stages of their life cycles, including entry, replication, and assembly. Metabolic pathways subverted by viruses for their propagation represent strategic targets for host innate defenses against viral infection, yet limited examples of such links have been reported. My research program aims to identify virus dependency factors, like host cell metabolic pathways, used by different viruses during infection and illuminate the host cells responses to infection. The program takes advantage of leading edge approaches such as activity-based protein profiling (ABPP), the functional proteomic technique that examines enzyme activity during infection and small molecule annotation of microRNA and long noncoding RNA function to identify molecules, enzyme activity, and regulators of the relevant pathways during infection. The overarching goal of this program is the identification of novel diagnostic and therapeutic strategies that may be used to combat viral infection.
Biography: Dr. John Pezacki is a Full Professor at the University of Ottawa in the Department of Chemistry and Biomolecular Sciences with several cross-appointments. He is an internationally recognized researcher whose work has had broad impact in the fields of chemical biology and molecular virology. His research program has led to the creation of new biomolecular sensing and imaging tools and the ground-breaking applications of these tools, yielding new insights into the molecular basis of complex biological processes such as host-pathogen interactions. These include the development of new approaches to visualize and understand how viruses infect their host and what changes are required for pathogenesis at the molecular level. Dr. Pezacki also develops innovative chemical tools and reactions that are incorporated into cutting edge methodologies for studying host-virus interactions and cellular metabolism. He also has had many interactions with industry including projects with Merck and Pfizer on both drug discovery and probe development, and also works with several government departments on projects related to security. Professor Pezacki is an associate editor with the journal ACS Infectious Diseases and an editorial board member for Scientific Reports. Dr. Pezacki has published over 100 papers in scientific journals and has won many awards for his work on the chemical biology of host-pathogen interactions including the Rutherford Memorial Medal from the Royal Society of Canada, Teva Lectureship from the Canadian Society for Chemistry, and the Queen Elizabeth II Diamond Jubilee Medal for outstanding contributions to Canada.