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The hidden map of science: analyzing the flows of research manuscripts 


Vincent  Calcagno

  Researcher, French Institute for Agricultural Research (INRA)

Vincent Calcagno is an evolutionary biologist and ecologist. He obtained his PhD in 2007 at the University of Montpellier, France, and then spent 3 years at McGill as a postdoc, before getting a permanent position at the INRA. His research is about the theory and modelling of how natural selection causes changes in traits within communities and foodwebs, and the consequences this has. He also tests theory on real-life ecological systems, mostly insects in agricultural ecosystems. Incidentally, he has studied a non-natural ecosystem: the “foodweb” of scientific journals competing for research manuscripts (http://vcalcagnoresearch.wordpress.com)

Wednesday, 5 December 2012 at 16H00

McINTYRE Medical Building, Room #1101


I'll present recently-published results from the fist large-scale survey of manuscript submission, covering more than 950 journals in 16 biological disciplines. From the 80,000 manuscript submission histories we retrieved, I'll construct the network of manuscript flows connecting scientific journals. Analysis of this network reveals interesting aspects of the structure of biological sciences, journal perceived importances, and the submission strategies of authors. In particular, it shows that most published articles (about 75% overall) were submitted on first intention to the journal that would publish them but, surprisingly, this value  declines with journal impact factor. Impact factor also has a strong influence in shaping resubmission strategies.

Interestingly, I'll show that submission history may affect the post-publication impact of articles. Articles previously rejected from another journal attracted more citations on average, but resubmissions between journals from different fields were significantly less cited than resubmissions within one field.


Inferring the past for traits that alter speciation and extinction

Sarah P. OTTO

Evolutionary geneticist and mathematical modeler
Winner of a MacArthur "genius grant" in 2011


Dr. Otto is a professor at the University of British Columbia in the Department of Zoology (http://www.zoology.ubc.ca/~otto/).  She works on questions in population genetics and evolutionary biology, using mathematical models to answer questions about how populations change over time.  Particular research interests include the evolution of ploidy level, mating systems, and genomic architecture.  She is a co-author, with Troy Day, of a comprehensive textbook in her field, A Biologist's Guide to Mathematical Modeling in Ecology and Evolution, and has published more than 125 papers. She was a recipient of the MacArthur Foundation's "genius grant" in 2011, (http://www.macfound.org/fellows/12/).  She is also the Director of the Biodiversity Research Centre at UBC (http://www.biodiversity.ubc.ca), an institute with a mission "to understand and conserve the diversity of life on earth through research, education, and outreach", with more than fifty faculty members, plus postdocs and graduate students, pursuing a wide variety of research questions related to biodiversity.

Tuesday, 4 December 2012 at 16H00 

McINTYRE Medical Building, Room # 1034


I will describe BiSSE, a likelihood-based approach to infer how speciation and extinction rates depend on the state of a particular character.  The phylogenetic tree of a group of species contains information about character transitions and about diversification: higher speciation rates, for example, give rise to shorter branch lengths.  The likelihood method that we have developed uses the information contained in a phylogeny and integrates over all possible evolutionary histories to infer the speciation and extinction rates for species with different character states.  Our method can be used to provide more detailed information than previous methods, allowing us to disentangle whether a particular character state is rare because species in that state are prone to extinction, are unlikely to speciate, or tend to move out of that state faster than they move in.

External Artificial Pancreas for Type 1 Diabetes: Modelling and Control

Wednesday, 21 November 2012 at 16H00

McINTYRE Medical Building, Room # 1034

Speaker:  Ahmad HaidarMcGill University


Type 1 diabetes is a chronic disease caused by an autoimmune destruction of pancreatic beta cells and is currently treated with life-long insulin-replacement therapy. Current treatment strategies do not achieve glycemic targets in most patients and glucose control remains problematic. An artificial pancreas is a long-awaited goal for diabetes and its development was recently triggered by advances in continuous glucose monitoring and insulin infusion pumps.

In this talk, I will present a novel bi-hormonal artificial pancreas system that delivers insulin and glucagon subcutaneously based on real-time glucose sensor readings as guided by a mathematical dosing algorithm. The algorithm is based on fuzzy-supervised model predictive controller combined with extended Kalman filtering and a set of heuristic rules. The artificial pancreas system was compared with conventional pump therapy in 15 adult patients utilizing a 15hrs randomized crossover trial. The artificial pancreas system significantly improved glucose control and reduced the risk of hypoglycemia.

Clinical trials are an integral part of the development process but are time-consuming, resource demanding, and costly. Pre clinical testing in a computer-simulation environment accelerates development and facilitates optimization of dosing algorithms.  In this talk, I will present a novel fully probabilistic method to generate stochastic virtual patients for the assessment of control algorithms. The method adopts a non-linear physiologically-motivated time-varying model of glucose regulation and uses Bayesian inference and Markov chain Monte Carlo methods to estimate individual parameters. The method performs one to one mapping of individual experimental data into stochastic virtual patients in a process termed “stochastic e-cloning”. I will conclude with an overview of future work in the field of artificial pancreas systems.



A Systems Approach to the Deregulation of Metabolic Pathways in Disease

Thursday, 8 November 2012 at 16H00

McINTYRE Medical Building, Room #1101

Speaker: Dr. Mathieu Cloutier, Researcher, GERAD-Chemical Engineering, Ecole Polytechnique de Montreal, Montréal, QC, Canada


Systems Biology (SB) appeared about a decade ago as a new approach in biological sciences. A central challenge in SB is to understand how simple feedback interactions can induce complex, dynamic biological behavior. In that context, engineers and mathematician can and should contribute to the life sciences and this will constitute the next paradigm shift in biology and medicine[1].

In this talk, I will present a few research challenges in biology where modeling and control theory were used to provide original insights on the importance of metabolic regulation in disease. I will emphasize two major themes: (1) How control theory can be used as a framework to analyze complex behavior in metabolic pathways.; (2) Applications in Parkinson's disease and cancer, more specifically on the modeling of metabolic pathways deregulation during pathogenesis.  

[1] The 3rd Revolution: The Convergence of Life Sciences, Physical Sciences and Engineering. MIT White Paper on Convergence.  http://web.mit.edu/dc/Policy/MIT%20White%20Paper%20on%20Convergence.pdf



Optical imaging of local signaling and remodeling in dendrites: CaMKII points the way

Friday, 26 October 2012 at 11H00  

McINTYRE Medical Building, Room #1034

Speaker: Prof. Paul De Koninck, Deputy Director Bordeaux Polytechnic Institute, University of Bordeaux

For more information, please visit Department of Physiology/Seminars  


Smart stimulators for Parkinson's disease

Thursday, 25 October 2012 at 12H00 (Brown Bag Research Discussions)

McINTYRE Medical Building, Room #1101

Speaker: Prof. Anne Beuter, Deputy Director Bordeaux Polytechnic Institute, University of Bordeaux

Let's imagine the cruise control of your car locked at 120 km/hour on any road in any condition (city, country, highway, sunny or rainy weather), or your car air conditioner set on maximum cold in any temperature condition (even during a snowy winter): would you find it efficient? That would probably not be the most optimal strategy for a proper and comfortable driving experience. As surprising as this may seem, this is a pretty accurate illustration of how deep brain stimulation (DBS), is used today to treat Parkinson's disease motor symptoms, and other neurological disorders such as essential tremor, obsessive-compulsive disorder, or epilepsy.
Journal Name: Frontiers in Computational Neuroscience



New pacing protocols and analyses to evaluate cardiac restitution and alternans

Friday 19 Oct. 2012 at 12H00

Auditorium Jean-Parisien (salle C-1890), Institut de Cardiologie de Montréal, 5000, rue Bélanger (coin Viau), Montreal, Qc, H1T 1C8


Thursday, October 18  at 16H00

Room 1120, Pavillon Paul-G.-Desmarais Campus de l'Université de Montréal 2960 Chemin de la tour, Montréal (Québec) H3T 1J4


Speaker: Prof. Jan P Kucera,  Dept. of Physiology, University of Bern

Cardiac function relies on the coordinated propagation of the action potential (AP), the rhythmic electrical signal that triggers the contraction of every cardiac cell.  Arrhythmias are frequent complications of heart disease and can potentiate heart failure, lead to stroke and cause sudden death. The AP is an intricate dynamic phenomenon, which relies on the function of ion channels. The complexity of the AP and of cardiac conduction explains why the prevention and treatment of arrhythmias still remains a great challenge. Our research addresses cardiac conduction with an interdisciplinary approach unifying in vitro experiments and computer simulations. In vitro, we use a custom developed system to stimulate and record the electrical activity of cardiac cell cultures with microelectrode arrays. This approach is combined with techniques to pattern the cultures to predefined geometries. In computer simulations, we reconstruct conduction using mathematical models of the cardiac cell. These simulations provide insights into aspects not accessible experimentally.

For more information, please contact : Dr. Philippe Comtois, Université de Montréal



What does that mean to be a Pharmacometrician in the pharmaceutical industry?

Thursday, October 18, 2012 at 12H00

S1-111, Pavillon Jean-Coutu, Université de Montréal, Faculté de pharmacie, 2940 Chemin de la polytechnique,   Métro Université de Montréal

Speaker: Dr. Nicolas Frey, Global head of Modeling and Simulation, Hoffmann-La Roche,Basel Area, Switzerland

For more information, please contact : Université de Montréal , Faculté de pharmacie



The Structural Basis for Microtuble Nucleationby γ-tubulin complexes

Friday, October 12, 2012 at 11H00  

Room 1034, 10th floor, McIntyre Medical Sciences Building,  3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6

Speaker: Dr. Justin Kollman, Ph.D., Department of Anatomy & Cell Biology, McGill University

For more information, please contact Dr. Pejmun Haghighi 514-398-8985 or pejmun [dot] haghighi [at] mcgill [dot] ca, Anna Maria Rossi 514-398-4318, anna [dot] m [dot] rossi [at] mcgill [dot] ca (anna [dot] m [dot] rossi [at] mcgill [dot] ca )or visit the Seminar and Events, Department of Physiology



Building a mitotic spindle one microtubule at a time

Monday, October 1st, 2012 at 16H00

Stewart Auditorium, Room #: N2/2

Speaker: Prof. Jackie Vogel, McGill-Canadian Pacific Professor, Member, School of Computer Science, Associate Member, Goodman Cancer Cenre, Department of Biology, McGill University

For more information, please visit http://aguada.biol.mcgill.ca/



Cardiovascular studies at multiple length scales

Wednesday, 19 September 2012 at 16H00

McINTYRE Medical Building, Room #1101

Speaker: Prof. Elena Di Martino, Department of Civil Engineering, Centre for Bioengineering Research and Education, University of Calgary

Biological tissue remodelling is a process of both volumetric growth and structural modification that happens as a result of stimuli of different origin. Remodelling aims at restoring the preferred form and function in the organ (homeostatic conditions). The clinical relevance of remodeling studies stems from the interpretation of many diseases as the result of an adverse remodelling process.

Our laboratory studies the remodelling process that occurs in the cardiovascular system at three levels of magnification: organ, tissue and micro structural components.  We studied the effect of atrial fibrillation on left atrium mechanics by generating a computational model of the left atrium that includes structural and electrical phenomena as well as the anatomical features that guide and constraint the atrium movement during the cardiac cycle. Computational results suggest that stress-mediated mechanisms contribute to the onset and progression of atrial fibrillation.  The second study that I will present concerns the contribution of micro structural constituents (collagen fibbers, elastic material and smooth muscle cells) in supporting the mechanical loads applied to large conduit arteries. A mixture theory model was used to predict the redistribution of stresses among the components of the arterial tissue in response to a perturbation of the external loads. The proposed model can be used to assess the contribution of the different micro structural components to the progression of specific diseases.



Structure of the Normal and Epileptic EEG: A Phenomenological View

Thursday, 20 September 2012 at 16H00

McINTYRE Medical Building, Room  # 1101

Speaker: Prof. Giri Kalamangalam, University of Texas Health Science Center

The mammalian electroencephalogram (EEG) represents summated electrotonic cortical potentials on time and space scales spanning several orders of magnitude. Investigator bias and methodological constraints largely determine the resolution at which research questions regarding normal brain function or neurological disease are probed. In this talk we discuss insights provided at the mesoscopic scale – the level of clinical recordings of ECoG (electrocorticogram). We review mechanisms proposed to explain the broadband nature of the EEG and offer an alternative viewpoint based on interacting multi-oscillator systems. Next, we show examples of hitherto unexplained clinical EEG phenomena that nevertheless recall features typical of systems driven by nonlinear dynamics. We finally discuss in some depth clinical observations on cortical after-discharge (epileptic paroxysms following electrical stimulation of the brain) and illustrate a novel modeling approach inspired by the classic theory of nonlinear oscillators.