Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Policing mammalian transcriptomes: regulation of long ncRNA synthesis by transcriptional termination, gene loops and R-loops. (POLYLOOP)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Advanced grants
Action type: Support for frontier research (ERC)
Panel: Molecular and Structural Biology and Biochemistry
Countries involved: United Kingdom
Call:  (ERC-2013-ADG, 2013)
Start date: 2014-02-01
End date: 2019-05-31
Duration (months): 64.0
Total project cost (EUR): 2499464.0
EU funding (EUR): 2499464.0
Participants: 1
Project status: CLOSED

.Mammalian transcriptome analysis reveals that while most of the genome is transcribed, only a minority fraction produces protein coding, messenger RNA or functional, structural RNA. Instead a substantial fraction is transcribed, often tissue specifically, into long non coding (lnc)RNA of mostly unknown function. Many lncRNA are rapidly degraded and may reflect promiscuous, non-functional transcription. However some lncRNA have important cellular functions. I reason that defining promoters and terminators of lncRNA genes will provide valuable information on which lncRNA are likely to be functional. LncRNA gene promoters often correspond to nucleosome depleted regions of protein coding gene promoters and enhancers, which generate bidirectional transcription. Regions of single-strand DNA, exposed by R-loop formation can also initiate transcription and so act as a potential source of lncRNA, as will be investigated here. Since transcription initiation of lncRNA genes appears relatively promiscuous, terminating lncRNA transcription may be of critical importance. This will prevent read-through transcription with consequent negative affects on downstream genes by transcriptional interference or the formation of overlapping transcripts leading to RNA interference effects. Consequently I will focus on transcription termination mechanisms of lncRNA genes. I will determine if known protein coding gene terminators also operate for lncRNA genes or whether many lncRNA use alternative termination mechanisms. In particular I will investigate the role of G-rich pausing elements that promote Pol II termination by forming R-loop structures on lncRNA genes. I will also investigate which classes of lncRNA genes form gene loop conformations when transcribed, as a likely identifier of more highly expressed, functional lncRNA. Overall I predict that understanding how lncRNA are synthesised will provide critical information on which lncRNA warrant scrutiny as likely functional transcripts

Keywords: mammalian transcriptome,long non coding rna,rna polymerase ii,terminator,promoter,r-loop,gene loop.
PHYSICIAN AIDED RECONSTITUTION OF THE IMMUNE SYSTEM (PARIS)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Advanced grants
Action type: Support for frontier research (ERC)
Panel: Immunity and infection
Countries involved: United Kingdom
Call:  (ERC-2013-ADG, 2013)
Start date: 2013-10-01
End date: 2018-07-31
Duration (months): 58.0
Total project cost (EUR): 1999905.0
EU funding (EUR): 1999905.0
Participants: 1
Project status: CLOSED

Unwanted immune responses to self-tissues and transplants have a major impact on human health and wealth. Their management has required long-term immunosuppressive drugs which penalise the whole immune system. The big challenge has been to understand how the individual is naturally tolerant to self, and to exploit this knowledge for treatments better targeted to the relevant antigens. Since 1980 the applicant’s laboratory have, in rodent models, defined mechanisms of acquired tolerance, and used monoclonal antibodies to transiently block lymphocyte function, or deplete lymphocytes with the goal of establishing tolerance therapeutically. This led to the discovery of ”infectious tolerance” where tolerance was shown to require regulatory CD4+FoxP3+ T cells. Although efficacious in rodent models, equivalent blockading antibodies for man, although available, have not been commercialised by the pharmaceutical industry. To deplete lymphocytes in man, our laboratory has also developed the anti-CD52 monoclonal antibody, CAMPATH-1H. This was the first humanised therapeutic antibody (Alemtuzumab/Lemtrada) and is being actively pursued for multiple sclerosis and stem cell and organ transplantation. Although lymphocyte depletion has clearly proven to be clinically useful, it has not, when used alone, permitted tolerance to transplanted organs or allowed for durable immune reprogramming in autoimmune disease. This proposal seeks to understand how to build on the benefits of lymphocyte depletion with CAMPATH-1H, and promote tolerance by exploiting tolerance–promoting mechanisms learned from our studies of co-receptor/co-stimulation blockade. The novel approach taken by this project is to investigate and manipulate the reconstitution phase of lymphocyte recovery through Physician Aided Reconstitution of the Immune System (PARIS), by aiming to contain those T-cells that mediate damage whilst empowering competing regulatory T-cells.

Keywords: regulation of the immune system transplantation autoimmune disease immunosuppression
Trans-Atlantic Imaging of Lithosphere Asthenosphere Boundary (TRANSATLANTICILAB)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Advanced grants
Action type: Support for frontier research (ERC)
Panel: Earth system science
Countries involved: France
Call:  (ERC-2013-ADG, 2013)
Start date: 2014-11-01
End date: 2020-06-30
Duration (months): 68.0
Total project cost (EUR): 3499900.0
EU funding (EUR): 3499900.0
Participants: 1
Project status: CLOSED

The Plate Tectonics Theory is the most important discovery in all of earth sciences. It is based on the concept of plates (lithosphere) that float over the asthenosphere. Although the lithosphere is a basic building block of the plate tectonics theory, its nature, its thickness, its boundary with the asthenosphere (LAB) are still matter of heated debates. Here we propose to image the LAB and internal structure of the lithosphere at a very high-resolution using a combination of different geophysical methods in a systematic manner across the Atlantic Ocean (Trans-Atlantic) for a lithosphere of 0-100 Ma age. Along with using seismological and magnetotelluric methods, we propose to use a technology newly developed for the oil and gas exploration that is capable of providing a seismic reflection image down to 120 km depth with a few hundred metres resolution, resolving the controversy on the formation and evolution of the oceanic lithosphere once and for all, filling the gap between seismological and seismic reflection methods, opening up a new frontier of research, and creating synergy between academic and industrial research to address fundamental scientific problems. These new seismic data should also provide images of melt lenses in the mantle beneath the spreading centre axis, if present, which will help us to build a new model of melt generation and migration from the mantle. We should also be able to image deep penetrating faults that might have been generated due to the cooling of the lithosphere as it moved away from the spreading centre, allowing the development of a new model of hydration of the oceanic lithosphere, which would be extremely valuable for the understanding of the earthquake process at subduction zones. The imaging of the structure down to 120 km in an oceanic environment would be a major breakthrough, and likely to open up new horizons for deep seismic imaging.
Cortical algorithms for perceptual grouping (CORTIC_AL_GORITHMS)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Advanced grants
Action type: Support for frontier research (ERC)
Panel: The Human Mind and its complexity
Countries involved: Netherlands
Call:  (ERC-2013-ADG, 2013)
Start date: 2014-05-01
End date: 2019-04-30
Duration (months): 60.0
Total project cost (EUR): 2500000.0
EU funding (EUR): 2500000.0
Participants: 1
Project status: CLOSED

Why do we perceive objects? Visual perception starts with localized filters that subdivide the image into fragments that undergo separate analyses. Our visual system has to reconstruct the objects that surround us. It has to bind image fragments of the same object and to segregate them from other objects and the background. The standard view in psychology is that perceptual grouping is achieved by a parallel, pre-attentive process that relies on Gestalt grouping cues. My work has started to challenge this view by demonstrating that the visual cortex also implements a serial, attention-demanding algorithm for perceptual grouping. This grouping process may represent the first serial brain algorithm that can be understood at the psychological, neurophysiological and computational level. The present proposal therefore has the potential to revolutionize our view of visual cognition. Understanding feature binding would represent a breakthrough in cognitive neuroscience. Different brain areas represent distinct visual features. How is activity in these areas integrated? We propose that perceptual grouping relies on two complementary processes, “base-grouping” and “incremental grouping”. We hypothesize that base-grouping is pre-attentive and relies on feed-forward connections from lower to higher areas that activate neurons and determine their stimulus selectivity. In contrast, we propose that incremental grouping relies on feedback and horizontal connections, which propagate enhanced neuronal activity to highlight all the features that belong to the same perceptual object. The present proposal will determine the role of attention in feature binding, the interactions between brain areas for grouping with fMRI in humans and with electrophysiology in non-human primates to reveal the algorithms for perceptual grouping as they are implemented in our brains.

Keywords: binding problem,perceptual organization,gestalt grouping rules,decision making,object-based attention
The other side of optogenetics: multicolored genetically encoded hybrid voltage sensors (GEVOS) for ultrafast membrane potential measurements in cortical microcircuits (MULTIGEVOS)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Advanced grants
Action type: Support for frontier research (ERC)
Panel: Neurosciences and neural disorders
Countries involved: Germany
Call:  (ERC-2013-ADG, 2013)
Start date: 2014-02-01
End date: 2019-01-31
Duration (months): 60.0
Total project cost (EUR): 3437138.0
EU funding (EUR): 3437138.0
Participants: 1
Project status: CLOSED

Optogenetics are used to activate or silence specific sets of neurons, intracellular signaling pathways, or to examine brain structure at an unprecedented detail. The only optogenetic approach lagging behind all others is the genetically encoded optical monitoring of multi-neuronal activity at a time resolution of single action potentials. Such ultrafast (<1 ms) resolution is important to understand network function in healthy and diseased nervous systems because timing of neuronal firing and synchrony are the foremost determinants of brain function. Techniques exist to measure membrane voltage and/or cellular activity using optical probes, but all have drawbacks either in their genetic targeting, optical sensitivity and/or temporal resolution. Recent developments using genetically encoded hybrid voltage sensor (GEVOS) methodology showed that this approach has an excellent potential to become an ultrafast voltage sensing system. The GEVOS technique can easily be adapted to work with multiple colors simultaneously, thus recording the activities of genetically distinct cell types in the same preparation. The overall objective of this proposal is to advance the GEVOS method so that it can be used with multiple colors simultaneously in at least two different genetically targetable cell types. Two major advances are sought after in this proposal: a technical/ methodological innovation (improve upon the GEVOS technique and extend it to two fluorescent proteins) and a scientific vision. The latter relates to gaining insights into the parallel functioning of local microcircuits and the optical recording of the concurrent behavior of pre- and postsynaptic elements during GABAergic inhibition. These studies will advance high temporal resolution optical voltage sensing (the other side of optogenetics) and will provide an unprecedented look at the functioning of cortical microcircuits with their specific components monitored at the same time..

Keywords: optical membrane voltage imaging,cellular and synaptic physiology,optogenetics,neuronal microcircuits,gaba,neurotransmitter uncaging,adult neurogenesis,dentate gyrus,entorhinal cortex
Philosophy on the Border of Civilizations and Intellectual Endeavours: Towards a Critical Edition of the Metaphysics (Ilahiyyat of Kitab al-Shifa’) of Avicenna (Ibn Sina) (PHIBOR)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Advanced grants
Action type: Support for frontier research (ERC)
Panel: Cultures and cultural production
Countries involved: Italy
Call:  (ERC-2013-ADG, 2013)
Start date: 2014-02-01
End date: 2019-01-31
Duration (months): 60.0
Total project cost (EUR): 1140800.0
EU funding (EUR): 1140800.0
Participants: 2
Project status: CLOSED

For its tremendous impact on subsequent philosophers and theologians, not only in the Islamic, but also in the Christian and Jewish worlds, Avicenna’s metaphysics represents a turning-point in the history of philosophy until modern times. A reliable edition of his most important metaphysical work, the Ilahiyyat (Divine Things) of the Shifa’ (The Cure), is therefore a major desideratum. Avicenna (Ibn Sina, d. 1037CE), the greatest philosopher in Islamic civilization and an influential physician, intended the Shifa’ as a detailed summa of all parts of philosophy, updating and completing Aristotle’s corpus. The Ilahiyyat (the metaphysical section of this summa) is an enlarged version of Aristotle’s natural theology, incremented with materials taken from Neoplatonic works, and argues for metaphysics as a science that provides a rational interpretation of all monotheistic religions, including Islam. The project aims at replacing the existing faulty printed versions of this work with a reliable edition, established critically along the standards of classical philology, with facing translation, running commentary, and comprehensive lexica. As a first step, the numerous manuscripts of the work will be systematically investigated, and their census and description, as well as images of their relevant parts, will be published on a web-site. Secondly, editorial technologies designed by computer science for works with a massive manuscript tradition will be applied. Finally, the on-line publication of the results will ensure their wide diffusion and the possibility of a constant updating on the basis of the progress of research. Scholars will thus have a solid – but, at the same time, flexible and adaptable – access to one of the most significant philosophical works that not only realized, but also fostered fruitful dialogue among different cultures (Greek, Arabic, Latin, Hebrew), religions (Islamic, Christian, Jewish), and intellectual endeavours (philosophy, theology, science).

Keywords: metaphysics,arabic medieval philosophy,manuscripts,critical edition,computer science
Finite Element Exterior Calculus and Applications (FEEC-A)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Advanced grants
Action type: Support for frontier research (ERC)
Panel: Mathematical foundations
Countries involved: Norway
Call:  (ERC-2013-ADG, 2013)
Start date: 2014-02-01
End date: 2019-01-31
Duration (months): 60.0
Total project cost (EUR): 2059687.0
EU funding (EUR): 2059687.0
Participants: 1
Project status: CLOSED

The finite element method is one of the most successful techniques for designing numerical methods for systems of partial differential equations (PDEs). It is not only a methodology for developing numerical algorithms, but also a mathematical framework in which to explore their behavior. The finite element exterior calculus (FEEC) provides a new structure that produces a deeper understanding of the finite element method and its connections to the partial differential equation being approximated. The goal is to develop discretizations which are compatible with the geometric, topological, and algebraic structures which underlie well-posedness of the partial differential equation. The phrase FEEC was first used in a paper the PI wrote for Acta Numerica in 2006, together with his coworkers, D.N. Arnold and R.S. Falk. The general philosophy of FEEC has led to the design of new algorithms and software developments, also in areas beyond the direct application of the theory. The present project will be devoted to further development of the foundations of FEEC, and to direct or indirect use of FEEC in specific applications. The ambition is to set the scene for a nubmer of new research directions based on FEEC by giving ground-braking contributions to its foundation. The aim is also to use FEEC as a tool, or a guideline, to extend the foundation of numerical PDEs to a variety of problems for which this foundation does not exist. The more application oriented parts of the project includes topics like numerical methods for elasticity, its generalizations to more general models in materials science such as viscoelasticity, poroelasticity, and liquid crystals, and the applications of these models to CO2 storage and deformations of the spinal cord.

Keywords: numerical pdes,finite elements,exterior calculus,compatible discretizations,applications
MUSE Imaging of the Cosmic Web – Ultra-Deep Observations of Intergalactic and Circumgalactic Gas (MUSICOS)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Advanced grants
Action type: Support for frontier research (ERC)
Panel: Universe sciences
Countries involved: France
Call:  (ERC-2013-ADG, 2013)
Start date: 2014-03-01
End date: 2019-02-28
Duration (months): 60.0
Total project cost (EUR): 2498400.0
EU funding (EUR): 2498400.0
Participants: 1
Project status: CLOSED

This project aims at making major advances in our understanding of galaxy formation through the direct detection and spectroscopic mapping of gas outside of galaxies at high redshifts. This experiment will employ the 2nd generation ESO-VLT instrument MUSE, currently being finalised under my leadership. MUSE is a highly innovative integral field spectrograph featuring an unparalleled combination of large field of view, excellent angular resolution, and sensitivity to faint signals. The instrument will arrive at the observatory in mid 2013 and soon after begin with the buildup of a revolutionary set of “spectroscopic deep fields”, which will constitute a significant fraction of the 255 nights of observing time granted to the MUSE consortium in return for their investment. The focus of this ERC proposal is the study of the gaseous environments of galaxies, and their links to the general inter¬galactic medium. Observationally it is extremely difficult to trace the inferred gas flows, because of their low predicted surface brightnesses and filamentary geometry. Only MUSE will have the sensitivity to detect and map them directly, through the Lyα emission line of recombining hydrogen. MUSE will also provide spectroscopic (kinematic) constraints on these gas flows, which will be essential for quantitative comparisons with numerical simulations. A dedicated team will address the many challenges of this scientific endeavor in a comprehensive way. It will involve the characterization of the instrument and its systematics; the development of advanced data reduction and data analysis tools in a coordinated multidisciplinary approach, involving astronomers as well as experts in image and signal processing; and the interpretation of the results in conjunction with the latest high-resolution cosmological simulations. Upon completion, MUSICOS will deliver an entirely new view at the early stages of galaxy formation and the growth of baryonic mass in the young universe.
Colloids with complex interactions: from model atoms to colloidal recognition and bio-inspired self assembly (COMPASS)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Advanced grants
Action type: Support for frontier research (ERC)
Panel: Condensed matter physics
Countries involved: Sweden
Call:  (ERC-2013-ADG, 2013)
Start date: 2014-02-01
End date: 2019-01-31
Duration (months): 60.0
Total project cost (EUR): 2498040.0
EU funding (EUR): 2498040.0
Participants: 1
Project status: CLOSED

Self-assembly is the key construction principle that nature uses so successfully to fabricate its molecular machinery and highly elaborate structures. In this project we will follow nature’s strategies and make a concerted experimental and theoretical effort to study, understand and control self-assembly for a new generation of colloidal building blocks. Starting point will be recent advances in colloid synthesis strategies that have led to a spectacular array of colloids of different shapes, compositions, patterns and functionalities. These allow us to investigate the influence of anisotropy in shape and interactions on aggregation and self-assembly in colloidal suspensions and mixtures. Using responsive particles we will implement colloidal lock-and-key mechanisms and then assemble a library of “colloidal molecules” with well-defined and externally tunable binding sites using microfluidics-based and externally controlled fabrication and sorting principles. We will use them to explore the equilibrium phase behavior of particle systems interacting through a finite number of binding sites. In parallel, we will exploit them and investigate colloid self-assembly into well-defined nanostructures. Here we aim at achieving much more refined control than currently possible by implementing a protein-inspired approach to controlled self-assembly. We combine molecule-like colloidal building blocks that possess directional interactions and externally triggerable specific recognition sites with directed self-assembly where external fields not only facilitate assembly, but also allow fabricating novel structures. We will use the tunable combination of different contributions to the interaction potential between the colloidal building blocks and the ability to create chirality in the assembly to establish the requirements for the controlled formation of tubular shells and thus create a colloid-based minimal model of synthetic virus capsid proteins.