Wednesday, November 30, 2011

ESFRI, the European Strategy Forum on Research Infrastructures; an example: euro-bioImaging

ESFRI, the European Strategy Forum on Research Infrastructures, is a strategic instrument to develop the scientific integration of Europe and to strengthen its international outreach. The competitive and open access to high quality Research Infrastructures supports and benchmarks the quality of the activities of European scientists, and attracts the best researchers from around the world.

The mission of ESFRI is to support a coherent and strategy-led approach to policy-making on research infrastructures in Europe, and to facilitate multilateral initiatives leading to the better use and development of research infrastructures, at EU and international level.

ESFRI’s delegates are nominated by the Research Ministers of the Member and Associate Countries, and include a representative of the Commission, working together to develop a joint vision and a common strategy. This strategy aims at overcoming the limits due to fragmentation of individual policies and provides Europe with the most up-to-date Research Infrastructures, responding to the rapidly evolving Science frontiers, advancing also the knowledge-based technologies and their extended use.

Since it was formed in 2002 at the behest of the European Council, ESFRI has witnessed significant advances towards unity and international impact in the field of research infrastructures. The publication of the first Roadmap for pan-European research infrastructures in 2006, and its update in 2008 was a key contributing factor, and several projects are now entering the realization phase. The Forum is determined to sustain the momentum in the implementation of the projects on the Roadmap, to expand the outreach to those scientific fields which are still evolving their conceptual approach in this direction, and to increase the involvement of all Countries by developing ad-hoc Regional policies. A further update of the ESFRI Roadmap, focusing on Energy, Food and Biology, will be published at the end of 2010, to coincide with a Conference to be held under the Belgian Presidency of the EU.

To keep Europe at the rapidly evolving forefront of science and technology, and to increase the capacity to meet the needs of the EU and World scientific community, much remains to be done: ESFRI looks forward to the challenging times ahead.
Ref: http://ec.europa.eu/research/infrastructures/index_en.cfm?pg=esfri

---------------an example:
http://www.eurobioimaging.eu/
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exaptation

Dans la théorie de l'évolution, l'exaptation (ou préadaptation) est une adaptation "sélective" dans laquelle la fonction actuellement remplie n'était pas celle remplie initialement (avant que n'intervienne la pression de la sélection naturelle).
L'origine du terme exaptation est attribuée aux biologistes Stephen J. Gould et Elizabeth Vrba, dans un célèbre article de 1982 qui expliquait comment des caractéristiques physiques complexes peuvent apparaître et évoluer à partir de structures initiales simples.


On considère généralement deux grands types d'exaptations :

  • Dans le premier, un organe (non modifié) est réutilisé à l'identique pour une fonction manifestement non sélectionnée à l'origine. C'est ainsi le cas de certaines aires du cerveau humain ; utilisées initialement pour la reconnaissance des formes, le langage ou l'audition, elles sont aujourd'hui réutilisées pour la lecture y compris en braille (via les doigts et non la vue).
  • Dans le second type, l'exaptation est une forme particulière d'adaptation naturelle, c'est-à-dire un ensemble de mutations génétiques (sélectionnées par la sélection naturelle pour aboutir à une forme de "survivant" actuel). Mais cette adaptation se fait sur la base d'un organe qui s'est initialement développé pour un tout autre usage. Il en va ainsi du poumon des tétrapodes ; apparus chez des poissons comme une adaptation à des milieux aquatiques pauvres en oxygène, et secondairement modifiés pour fonctionner en milieu purement terrestre.


L'exaptation s'oppose à la pensée d'Aristote: la fonction crée l'organe, qui persiste encore aujourd'hui. L'exaptation montre ainsi que, en ce qui concerne l'évolution, il n'y a pas de plan pré-établi et que l'évolution à plutôt tendance à bricoler.
C'est une forme d'interoperabilité.

Ref. http://fr.wikipedia.org/wiki/Exaptation
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Sunday, November 27, 2011

L'appel ERC Advanced Grants 2012; ERC European Research Council;choix neuro/math: résultats de ERC 2008

ERC: Conseil européen de la recherche
http://fr.wikipedia.org/wiki/Conseil_europ%C3%A9en_de_la_recherche
http://en.wikipedia.org/wiki/European_Research_Council

  • ERC Starting Grant: de jeunes chercheurs en début de carrière (entre 3 et 8 ans après avoir obtenu leur doctorat) 
  • ERC Advanced Grant:  des chercheurs expérimentés.


Publié le 16 novembre 2011, l'appel ERC Advanced Grants 2012 (ERC-2012-AdG) s'adresse aux chercheurs confirmés désireux de mener un projet de recherche exploratoire dans tous les domaines de la science et de la technologie.
Ce cinquième appel du Conseil Européen de la Recherche dispose d'un budget de 679.95 milions d'euros.

Trois dates de clôture sont proposées en fonction des trois grands domaines suivants :
16 février 2012, à 17h00 (heure de Bruxelles) : Sciences physique et ingénierie (PE) ERC-2012-ADG 20120216
14 mars 2012, à 17h00 (heure de Bruxelles) : Sciences du vivant (LS) ERC-2012-ADG 20120314
11 avril 2012, à 17h00 (heure de Bruxelles) : Sciences humaines et sociales (SH) ERC-2012-ADG 20120411
La soumission se fera en une seule étape via l'EPSS - Cf : Portail du participant - et l'évaluation sera effectuée par vingt-cinq panels de haut niveau.

Le budget est divisé selon les trois domaines :

Sciences physique et ingénierie : 44%
Sciences du vivant : 39%
Sciences humaines et sociales : 17%

EUROPEAN RESEARCH COUNCIL WORK PROGRAMME 2012:
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ERC panels
There are currently thus about 900 ERC panel members; together with the 2000 external reviewers they constitute the backbone of the ERC evaluation structure.
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résultats de ERC 2008

The list below ("priority list" - 201 proposals in alphabetic order - and "reserve list" - 229 proposals in rank order) shows the results of the first ERC Starting Grant competition. 



France’s Centre National de la Recherche Scientifique CNRS placed first among European research institutions by having the largest number of finalists for the ERC grants: 24 finalists. 
Spain’s Consejo Superior de Investigaciones Cientificas came second with 12 finalists. 
The University of Cambridge tied for third place : 11 winners.
Germany’s Max Planck Society : 11 winners.

The list has many surprises. Two Israeli institutions, the Technion and Hebrew University of Jerusalem, placed in the top-ten list, with nine and seven winners, respectively. Within Britain the top four winners were Cambridge, Oxford (nine), Imperial College London (eight) and University College London (five), matching their rankings on university league tables. In Switzerland, ETH-Zurich had two winners while arch-rival EPF-Lausanne had three. In Sweden, Karolinska Institutet came first with five finalists, but the country’s other leading universities had uninspiring results, with at most two winners each.  In Belgium, the Flemish Katholieke Universiteit Leuven came first with six finalists, while Francophone rivals Université Catholique Louvain and Université Libre de Bruxelles had three each.

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-----------------------some winners
Mr. Bellaiche, Yohanns;  Curie Institute;

Unité Génétique Biologie du Développement

 Cell polarity in Drosophila, UMR 144
Panel: LS1

Benton, Richard  ; University of Lausanne ; http://www.unil.ch/cig/page44404.html
Center for Integrative Genomics; neuroscience, neuron, sensory, olfaction, chemosensation, pheromone, receptor, genetics, Drosophila, insects, evolution
panel : LS4
rem: many nature and science

Boneca, Ivo ; Institut Pasteur; http://www.pasteur.fr/ip/easysite/pasteur/fr/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-et-genetique-de-la-paroi-bacterienne
Notre groupe de recherche étudie le métabolisme du peptidoglycane (PGN) ayant pour but de mieux comprendre comment les bactéries assemblent un PGN mature et essentiel conférant rigidité et forme à la bactérie malgré un processus dynamique accompagnant la croissance et la division cellulaire. Nous utilisons Helicobacter pylori comme model bactérien alternatif puisque l’analyse de son génome montre qu’il y a un ensemble minimal de gènes impliqués dans l’assemblage du PGN suggérant que H. pylori pourrait un model d’étude plus simple. 
panel : LS3

Breuillard, Emmanuel ; Ecole Polytechnique; http://www.math.u-psud.fr/~breuilla/

Lie Groups and their discrete subgroups, Arithmetic Groups, Geometry and Harmonic Analysis on groups, Ergodic Theory, Probability Theory and Random Walks, Combinatorics.
panel: PE1 

Cantillon, Estelle ; Université Libre de Bruxelle; http://www.ulb.ac.be/rech/inventaire/chercheurs/3/CH8383.html
Her ERC research project is entitled 'Market Design and the Evolution of Markets'

The main interest of my group is to study the function of cellular microstructures in cellular biology and to develop the physical modeling and the mathematical analysis. Our goal is to identify principles underlying cellular and network function in normal and pathological conditions. For that purpose, in collaboration with experimental groups, we aim to answer basic questions in cellular biology such as what defines trafficking in cells, how cells respond to stimuli, what makes viral particles optimal in trafficking. We are currently working on the nucleus organization, cytoplasmic viral trafficking and synapses.
In the field of applied mathematics and probability, using asymptotic analysis and Brownian simulations, we recently estimated the synaptic current at excitatory synapses and study the effect of the cleft geometry, receptor trafficking and other factors.
Other projects concern sensor cells, such as photoreceptors, where we work on building a complete model to better understand noise in cones and simulate the effect of drugs such as viagra which affects the the PDE enzyme activity.
We dedicate a large effort to develop physical and mathematical models to study cellular properties from the molecular level. We mainly develop approaches inspired from statistical physics, partial differential equations, stochastic dynamical systems and simulations. In the past, by using asymptotic analysis, we computed the expansion of the mean time for a Brownian molecule to escape through a small hole located on a piece of a cell membrane (Narrow escape problem). This computation defined the forward binding rate of chemical reactions occurring in microdomains.
Panel: PE1

Jefferis, Gregory;University of Cambridge;
Our broad goal is to understand how smell turns into behaviour in the fruit fly brain. We use a combination of genetic labelling and manipulation, targeted in vivo whole cell patch clamp recording and high resolution neuroanatomy to study olfactory circuits

Lauder, Alan; University of Oxford;
Number Theory. 

Lenormand, Thomas; CNRS; 
My primary research interests are evolutionary and ecological genetics. I have been doing "theoretical" work on the evolution of sex, mating systems, dispersal, recombination. I am also interested in the effect of mutations, on the process of speciation, local adaptation and genetic conflicts. On a more empirical side, I have worked on a variety of systems (mice, mosquitoes, snails, artemia, bacteria, corn).
Panel: LS5

Leutgeb, Stefan; Norwegian University of Science and Technology; http://biology.ucsd.edu/faculty/sleutgeb.html
Life-long memories are formed at an instant, but considerably outlast the neuronal activity that instigated them or even the synaptic modifications that initially retained them. In addition to early processes at the cellular level, the long-term retention of memories therefore requires that entire populations of neurons in widely distributed neural systems are reorganized. Such reorganization at the systems level is not only needed to ensure that each distinct memory is retained for long time periods, but also to provide a framework that allows for the integration of individual learning events into an accumulating knowledge base.
The main objective of research in our laboratory is to describe neuronal mechanisms of long-term memory storage at the systems level and to investigate how coordinated neuronal activity and synaptic plasticity in distributed cell assemblies can result in the formation of new cell assemblies. In addition, we are interested in the translational implications of this basic research and in understanding whether the neurodegenerative processes underlying dementia can result from a failure to appropriately organize neuronal activity and synaptic plasticity during our adult lives.
This is addressed by recording from many single neurons (up to 100) in the brain simultaneously and by testing how their activity is coordinated before, during, and long after learning. The recording methods are complemented by computational and analytical approaches, and also by molecular techniques that allow us to manipulate the activity of neuronal networks and to test whether the identified mechanisms are necessary for memory formation. Using these methods, we previously discovered neuronal network mechanisms that combine spatial and nonspatial information in the mammalian hippocampus, and showed that orthogonal encoding of the two types of information is used to generate very different neuronal firing patterns for very similar sensory input. Such pattern separation is thought to be a prerequisite for storing a large number of separate memories. To test this hypothesis, we currently investigate how multiple memories are encoded in the hippocampus as well as in a more widely distributed cortical network.

If variations in memory capacities have been observed among closely-related species, the relationship between environmental conditions and evolution of these capacities have only been rarely studied despite the importance of this topic in the understanding of the evolution of behavior. Memory has long been considered as a unique and continuous process of information storage and degradation. However, recent studies have shown that this process could be divided in different distinct phases separated in time and in their functional mechanism. To have a better comprehension of the evolutionary biology of cognitive abilities, it is therefore important to understand the different natural selection pressures favoring one or another memory phase, the fitness related costs of these different memory phases and the constraints on their evolution. The approach I took is based on studying the direct and correlated responses in selection experiments, using fruit flies (Drosophila) as a model system. It allows one to observe the evolutionary process directly while controlling for confounding factors. 
Panel: LS5

Mendelson, Shahar; Israel; http://maths.anu.edu.au/~mendelso/
Ph.D. thesis: Mathematical aspects of learning in Neural Networks:
Calculus of Variations, Elliptic and Parabolic differential equations: regularity problems for solutions
PE1

Mizrahi, Adi ; israel; http://elsc.huji.ac.il/mizrahi/home
Our lab is interested in how the brain computes sensory information and how these computations change with the experience of the animal. We study both the structure and the function of neurons mainly in two sensory modalities – olfaction and audition. Our animal model is the mouse.
Population dynamics in the mouse primary auditory cortex
Sensory processing in the mammalian brain is carried out by large populations of neurons.  We use both single cell electrophysiology and in vivo two-photon calcium imaging in mice to study the functional organization, dynamical principles, and functional plasticity of neural population in the primary auditory cortex.

 Buffa Annalisa;  Consiglio Nazionale delle Ricerch
Thesis:  Some numerical and theoretical problems in computational electromagnetism.
ERC Starting Independent Research Grant, awarded by the European Research Council for the project GeoPDEs: Innovative compatible discretization techniques for Partial Differential Equations.
Partial Differential Equations (PDEs) are one of the most powerful mathematical modeling tools and their use spans from life science to engineering and physics. PDEs describe in an implicit way the distribution of a field on a physical domain. The Finite Element Method (FEM) is by large the most popular technique for the computer-based simulation of PDEs and hinges on the assumption that the discretized domain and field are represented both by means of piecewise polynomials. Such an isoparametric feature is at the very core of FEM. However, CAD software, used in industry for geometric modeling, typically describes physical domains by means of Non-Uniform Rational B-Splines (NURBS) and the interface of CAD output with FEM calls for expensive re-meshing methods that result in approximate representation of domains.
This project aims at developing isoparametric techniques based on NURBS for simulating PDEs arising in electromagnetics, fluid dynamics and elasticity. 
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