Fifth AUB Biomedical Engineering Winter School
March 07-08, 2019, College Hall, Auditorium B1

The Joint MSFEA/FM Biomedical Engineering Program and the Center for Advanced Mathematical Sciences (CAMS) at AUB cordially invite you to the Fifth AUB Biomedical Engineering Winter School. The event will take place over two days and will feature four international distinguished speakers giving lectures on emerging topics in Biomedical Engineering and Mathematical Biology. The lectures will highlight the importance of mathematical and computational modeling in biomedical research at the molecular and physiological levels. Each lecture will be divided into two parts: the first part will cover basics and fundamentals, whereas the second part will cover state-of-the-art research findings and open research directions. The School is technically endorsed by the IEEE EMBS Lebanon Chapter and supported by the AUB Biomedical Engineering Student Society (AUB BMESS).

Dr. Bard Ermentrout

Distinguished Professor of Computational Biology, Department of Mathematics, University of Pittsburgh - USA

If space turned out to be time: Resonances in the visual cortex

When subjects are exposed to full field flicker in certain frequencies, they perceive a variety of complex geometric patterns that are often called flicker hallucinations. On the other had, when looking at high contrast geometric patterns like op art, shimmering and flickering is observed. In some people, flicker or such op art can induce seizures. In this talk, I describe a simple network model of excitatory and inhibitory neurons that comprise the visual area of the brain. I show that these phenomena are reproduced and then give an explanation based on symmetry breaking bifurcations and Floquet theory. Symmetric bifurcation theory also shows why one expects a different class of patterns at high frequencies from those at low frequencies. Next, I will describe the flip side of this coin and discuss a theory of uncomfortable images. Many people exhibit visual discomfort when looking at high contrast geometric patters such as seen in op art. I'll discuss some recent results where we show that such patterns can induce global oscillations in a network similar to the one used in the flicker study.

Bard Ermentrout is a Distinguished University Professor of Computational Biology and Professor of Mathematics at Pittsburgh where he has been since 1982. Dr. Ermentrout received his PhD in Theoretical Biology at the University of Chicago, a Sloan Fellow and a SIAM Fellow. He've had more than 30 PhD students and authored over 200 papers in the area of mathematics applied to biology. He is an avid, if feckless gardener, collect old fountain pens, and have an encyclopedic knowledge of Popeye.

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Dr. Christian Hansel

Professor of Neuroscience, Department of Neurobiology, University of Chicago - USA

Intrinsic plasticity and engram formation in neural circuits: neuro-computational principles

One of the hallmark features of our brains is their enormous capacity to learn and to adapt to changing environments. Theories of memory storage in neural circuits largely focus on activity dependent changes in synaptic weights – e.g. long-term potentiation (LTP) – as plausible learning correlates. But does our synapto-centric view of the cellular events underlying learning really capture the essence of memory engrams? Recent studies on the formation of engrams, or ‘mnemic traces’ (a concept introduced by Richard Semon in 1904), suggest that the ultimate step in memory engram participation is the suprathreshold activation of neurons. I will here lay out the theoretical basis of a complementary, neurocentric view, in which the participants in a functionally active engram are at least partly determined by cell-autonomous regulation of the intrinsic excitability of individual neurons. In this view, synaptic plasticity controls the formation of reciprocal connectivity patterns within and between engrams, and thus remains an important factor in circuit plasticity and learning. Recent reports indicate that a substantial percentage of pyramidal cells do not engage (remain silent) or are extremely unreliable when these neural circuits are activated, even in primary sensory cortices upon presentation of appropriate stimuli. My laboratory makes use of this phenomenon to provide a proof-of-principle demonstration of a role of changes in membrane excitability (‘intrinsic plasticity’) in engram formation. We will test the hypothesis that intrinsic plasticity activates previously silent (‘dormant’) or unreliable neurons and integrates them into reliable engrams, thus providing a mechanism to dynamically regulate engram composition. We propose that activation of dormant or unreliable neurons constitutes a memory trace in cortical circuits (‘intrinsic theory’ of memory), by enhancing the capacity for input pattern representation, by increasing the engram activation probability, or by promoting engram stability. In my presentation, the computational advantages of such network presentation/encoding will be discussed. In addition to presenting this new intrinsic memory concept, I will also show data from the cerebellum (the brain structure most often studied to describe supervised learning concepts), in which we currently try to delineate step-by-step how nonsynaptic plasticity components contribute to a memory engram.

Dr. Christian Hansel received a diploma in Zoology from the University of Zurich (Switzerland) in 1992, and performed his Ph.D. work at the Max-Planck-Institute for Brain Research in Frankfurt (Germany) under the supervision of Prof. Wolf Singer (1996). He then joined the laboratory of Prof. David Linden at Johns Hopkins University as a postdoctoral fellow. In 2000, Dr. Hansel became Professor at Erasmus University in Rotterdam (The Netherlands), where he established the first research laboratory on his own, and became ‘Academy Researcher’ of the Royal Netherlands Academy of Arts and Sciences. In 2008, he became Professor at the University of Chicago (Department of Neurobiology), where he is also a member of the graduate programs in neurobiology and computational neuroscience. Dr. Hansel studies cellular learning processes and has focused much of his career on the study of supervised learning in cerebellar motor circuits using patch-clamp electrophysiology as well as confocal microscopy. More recently, Dr. Hansel has presented the hypothesis that non-synaptic plasticity, i.e. changes in membrane excitability, provide an important second component of learning, which regulates neuronal participation in memory engrams and is computationally crucial for ensemble dynamics. He will present this novel hypothesis during the Winter School at AUB.

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Dr. Rutger Hermsen

Assistant Professor of Theoretical Biology and Biophysics, Department of Biology, Utrecht University - Netherlands

Mathematical models of the growth and evolution of bacterial cells challenged by antibiotics

The rapid emergence of bacterial strains resistant to multiple antibiotics is posing a growing public health risk. The response of bacterial cells to antibiotics and the mechanisms underlying their rapid evolution of drug resistance, however, are poorly understood. In this talk, we will discuss two interconnected lines of research. First, we will discuss recent coarse-grained mathematical models of the physiology of bacterial cells that can help elucidate their (often unintuitive) growth behavior under various conditions. In particular, we will explain how these models explain their complex response to antibiotics. Second, we study how the heterogeneity of the environments in which bacteria encounter antibiotic drugs could play an important role in their rapid evolution. To explore this, we present quantitative models describing an environment in which a gradient of antibiotic is present, in which bacteria evolve under the stochastic processes of proliferation, migration, mutation and death. Analytical and numerical results demonstrate that concentration gradients can foster a mode of adaptation that is impossible in uniform environments. It allows resistant mutants to evade competition and circumvent the slow process of fixation by invading compartments with higher drug concentrations, where less resistant strains cannot subsist. We argue that these models may also be applicable to other adaptive processes involving environmental heterogeneity and range expansion.

Dr. Rutger Hermsen is an Assistant Professor at Utrecht University, in the field of Theoretical Biology. He obtained Masters degrees in Theoretical Physics and Philosophy of the Exact Sciences from Utrecht University, and a PhD from the Free University (VU) in Amsterdam based on his work in Prof. ten Wolde’s Biochemical Network Group at FOM Institute AMOLF. Subsequently, he held a postdoctoral position with Prof. Terence Hwa at UC San Diego. In 2012, a NWO “Veni” grant allowed him to continue his research as an independent postdoc in the Bionanoscience Department at the TU Delft, supported by Prof. Cees Dekker. In September 2013, he started his current position as Assistant Professor at Utrecht University. The focus of his current work is on mathematical models of the growth of bacterial cells and the role of spatio-temporal heterogenetity in evolutionary processes.

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Dr. Abdul Jarrah

Professor of Mathematics, Biosciences and Bioengineering Research Institute, American University of Sharjah - UAE

Discrete mathematical modeling in systems biology: Theory and Applications

Over the last two decades, biology has rapidly been shifting from being a descriptive science to a quantitative one. Observations and data can now be collected at several levels for the whole biological system. Translating the collected information into knowledge is a challenge, however. Mathematical modeling emerged as an essential ingredient, providing indispensable tools to formalize and analyze models that capture the structure and dynamics of the system and hence insights at the system level. In this talk, I will focus on discrete models, which are generalizations of Boolean networks. I will provide examples of such models, methods to construct them including forward modeling (bottom-up) and reverse engineering (top-down), and software to analyze their structure and dynamics.

Dr. Abdul Jarrah is a professor of mathematics and a member of the Biosciences and Bioengineering Research Institute (BBRI) at the American University of Sharjah (AUS), UAE. His research is at the intersection of discrete dynamical systems, computational systems biology and computational commutative algebra. In particular, he is interested in developing, implementing, and using mathematical methods for the modeling and simulation of biological systems, focusing mainly on applications the immune system. Dr. Jarrah obtained his Ph.D. in Mathematics from New Mexico State University, USA. Before joining AUS in 2009, he worked at Virginia Tech and East Tennessee State University, USA.

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Day 1 – Thursday March 07, 2019

8:30 - 9:00: Registration & Morning Coffee

9:00 - 9:15: Opening Remarks - Dr. Arij Daou

9:15 - 10:30: Lecture 1 - Dr. Rutger Hermsen (Utrecht University)

Mathematical models of the growth and evolution of bacterial cells challenged by antibiotics

10:30 - 11:45: Lecture 2 - Dr. Christian Hansel (University of Chicago)

Intrinsic plasticity and engram formation in neural circuits: Neuro-computational principles

11:45 - 12:00: Coffee Break

12:00 - 12:15: BME Program at AUB - Dr. Massoud Khraiche

12:15 - 13:30: Lecture 3 - Dr. Abdul Jarrah (American University of Sharjah)

Discrete mathematical modeling in systems biology: Theory and applications

13:30 - 14:30: Lunch Break

14:30 - 16:00: CAMS Talks Mathematical Biology: A Panel Discussion

16:00 - 17:00: Lecture 4 - Dr. Bard Ermentrout (University of Pittsburgh)

If space turned out to be time: Resonances in the visual cortex

17:00 - 18:00: Student Advising and Networking Session

Day 2 – Friday March 08, 2019

8:30 - 9:00: Morning Coffee

9:00 - 11:00: Graduate Research Presentations Session


For more information, please contact Dr. Arij Daou (