Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
AUTOMATED NMR STRUCTURE-BASED ASSIGNMENTS (NMR-SBA)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Türkiye
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-10-01
End date: 2013-09-30
Duration (months): 36.0
Total project cost (EUR): 75000.0
EU funding (EUR): 75000.0
Participants: 1
Project status: CLOSED

While automation is revolutionizing many aspects of biology, the determination of three-dimensional protein structure remains a long, hard, and expensive task. Novel algorithms and computational methods in biomolecular NMR are necessary to apply modern techniques such as structure-based drug design on a much larger scale. The goal of this project is to address a key computational bottleneck in NMR structural biology, resonance assignments. We will accelerate protein NMR assignment by exploiting a priori structural information. By analogy, in X-ray crystallography, the molecular replacement (MR) technique allows solution of the crystallographic phase problem when a “close” or homologous structural model is known, thereby facilitating rapid structure determination. In contrast, a key bottleneck in NMR structural biology is the assignment problem. An automated procedure for rapidly determining NMR assignments given an homologous structure, will similarly accelerate structure determination. Moreover, even when the structure has already been determined by crystallography or computational homology modeling, NMR assignments are valuable because NMR can be used to probe protein-protein interactions and protein-ligand binding (e.g. via chemical shift mapping), and dynamics (via, e.g., nuclear spin relaxation). We will develop an MR-like approach for structure-based assignment of resonances and NOEs, to be applied when a homologous protein is known. The tool that we develop will accept both CH- and NH- RDCs, and 4-D NOESY data, and will implement a Bayesian scoring function for structure-based assignments. It will provide the user the option to use only NH RDCs or NH and CH RDCs and will be tested on real proteins. The source code will be released as open source with the user manual.

Keywords: structural bioinformatics,automated nmr assignments,protein structure determination,nmr structural biology
Stem cells specification and meristem maintenance at the shoot apical meristem of Arabidopsis thaliana (SHOOT APICAL MERISTEM)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Israel
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-01-01
End date: 2013-12-31
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

A central question in biology is how cell fates are established and maintained. In general, the cellular phenotype is determined by the transcriptional program, which is orchestrated by transcription factors (TFs) – proteins that bind specific DNA sequences to activate or repress transcription. Often, expression of a single transcription factor can lead to a radical alteration in cell fate. Although a number of such crucial TFs have been identified, we know relatively little about TF-regulated genes that determine the cellular phenotype. This is especially true in plants. The dome-shaped shoot apical meristem (SAM) of plant is a highly structured organ composed of multiple, functionally distinct zones. The SAM sustains plant growth by continuously producing new lateral organs throughout the life cycle. This unique capacity is achieved by a pool of self-renewing pluripotent stem cells reside at the tip of the SAM and by their daughter cells, which remain undifferentiated to proliferate before being incorporated into organs. Many of the TFs required to pattern the SAM are known, but their target genes, and thus their mechanisms of action, are almost completely unknown. Here I propose to use genomic and genetic tools to map in Arabidopsis thaliana the direct targets of two TF&apos;s crucial for proper meristem formation and maintenance. WUS which is required for stem cell specification and STM that function to suppress differentiation and to promote cell proliferation. Loss-of-function mutations in WUS or STM result in a lack of a self-maintaining meristem. I will combine affinity purification mediated by in vivo protein biotinylation together with high-throughput sequencing to map binding sites of WUS and STM. I will integrate the data to construct functional network required for carrying out stem cell and meristematic cell fate. I will use loss- and gain- of function approach to study the role of WUS and STM-binding in regulating expression and function of their targets

Keywords: arabidopsis,shoot apical meristem,stem cells,wus,stm,chip-seq
Coexistence of Ultra-Wideband and Licensed Systems (CUWLS)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Türkiye
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-11-01
End date: 2013-10-31
Duration (months): 36.0
Total project cost (EUR): 75000.0
EU funding (EUR): 75000.0
Participants: 1
Project status: CLOSED

Most of the communication systems that are in use today are licensed systems. Due to the spectrum getting crowded with many licensed systems, there is a need to consider future communication systems different from the current licensed systems in use. Ultra-wideband (UWB) communications is one of them. In UWB communications, due to the very low power spectral density (PSD) of the transmitted signal, the UWB system can operate as an underlay system in the same frequency band. Despite the low PSD of such systems, the European and Japanese regulatory agencies have made the implementation of detect-and-avoid (DAA) techniques mandatory in some common bands so as to protect the license rights of the licensed users. Therefore, the challenge here is to implement the new UWB systems so that they can coexist with the licensed communication systems peacefully. The main objective of this research is to investigate the coexistence of UWB systems with licensed systems. The research has two main parts; the implementations of detection and avoidance techniques considering practical scenarios. In the implementation of detection, the realistic case of active multiple systems with possible dependencies will be considered. This approach is different from the general approach that assumes the independence of the systems. In the implementation of avoidance, the linear combination of pulses with limited pulses will be considered as suggested by the IEEE 802.15.4a UWB standard. This approach is different from the general approach that assumes having enough number of pulses (i.e., filter coefficients). The main expected result of this research is to make suggestions for the coexistence of primary and secondary systems as a result of the considering the realistic cases. The research results are expected to provide benefit especially to the international communications research and development community and the European regulatory agency.

Keywords: technological sciences,ultra-wideband (uwb) communications,coexistence,detection and avoidance (daa),detection therory,pulse design
Computing in the dark sector: a Cactus toolkit for modified-gravity cosmologies (COSMOTOOLKIT)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Germany
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-06-01
End date: 2013-05-31
Duration (months): 36.0
Total project cost (EUR): 75000.0
EU funding (EUR): 75000.0
Participants: 1
Project status: CLOSED

Cosmology has entered a new era. After the surprising lessons learnt from recent observations and the ensuing revision of many traditional tenets, an entirely new set of questions has emerged in this field, and intensive theoretical searches are under way to find new physical mechanisms capable of answering them. Whilst intriguing ideas are continuously introduced, testing their consequences against the results of upcoming observative missions is a complex problem that requires accurate modelling of realistic scenarios, achievable only via numerical methods. The current modelling tools are, however, limited to simplified settings where the spacetime background is not evolved or heavy symmetry assumptions are made in order to reduce the dimensionality of the problem. In order to extend the domain of current codes, we intend to test cosmologically-relevant proposals using Cactus, a software framework for scientific codes inspired by software design concepts such as modularity, reusability and vast compatibilty across modern architectures. Cactus provides, among others, suites of tools for discretizing partial differential equations, handling parallel computations and concurrent I/O, and currently serves as a worldwide standard for three-dimensional, fully relativistic simulations of astrophysical-scale systems. In this proposal, we present an incremental plan for laying the foundations of a Cactus toolkit dedicated to cosmology; we will start out modelling the cosmic dynamics according to a selection of theories of gravity alternative to General Relativity.

Keywords: astrophysics,cosmology,computational physics,relativity
Re-creating the physics of astrophysical jets in laboratory experiments (LAB ASTRO JETS)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: European Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: United Kingdom
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2009-10-01
End date: 2012-09-30
Duration (months): 36.0
Total project cost (EUR): 45000.0
EU funding (EUR): 45000.0
Participants: 1
Project status: CLOSED

The observation of highly collimated jets is a ubiquitous phenomenon present in different types of astrophysical objects throughout the universe. These outflows have been observed in very different spatial scales, from large-scale jets emerging from black holes at the centre of galaxies, to smaller-scale jets observed in young stars. In recent years the study of these outflows has attracted the interest of the scientific community due to the possibility of performing laboratory experiments that can reach the extreme physical conditions relevant to these astrophysical processes. It has been demonstrated that despite the spatial and temporal scales being different by 15-20 orders of magnitude, it is possible to perform experiments that can reproduce the physics of these jets in a scaled way. The aim of this project is to perform experiments that are relevant to the dynamics of astrophysical jets, particularly focused in the study of (a) the launching mechanism and the subsequent collimation of a jet by the means of magnetic fields, (b) the formation of episodic outflows and the effect on the variability of the jet, (c) the propagation and interaction of the jet with the ambient medium. The experiments will be performed on the MAGPIE generator at Imperial College London. The use of present and new diagnostic techniques will allow measuring the physical conditions of the plasma during the experiments, allowing obtaining some parameters previously uncharacterized. Recent results have demonstrated that the &quot;magnetic tower&quot; scenario of jet formation can be reproduced from such experiments, in which the plasma is confined by a helical magnetic field, forming in this way a supersonic jet (Mach number~ 5-10). The ability of performing these experiments makes them of great interest in the field of laboratory astrophysics, and their continuation will contribute to a further understanding of the physical processes driving astrophysical jets.

Keywords: physical sciences,astrophysics,experimental physics,radiation physics
MIF genes: key regulators of floral meristem termination at the cross talk of multihormonal pathways (MIF/IMAGENE)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: France
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-05-01
End date: 2012-04-30
Duration (months): 24.0
Total project cost (EUR): 50000.0
EU funding (EUR): 50000.0
Participants: 1
Project status: CLOSED

Plants have the ability to form new organs according to an indeterminate growth that is ensured by pluripotent cells in organized structures called meristems. During floral induction the shoot apical meristem is converted into an inflorescence meristem, which gives rise to floral meristems (FM) leading to flower formation. This process called floral termination is under the control of the meristematic organizer gene WUSCHEL (WUS). The meristematic activity is intimately linked to hormonal signaling. However little is known about the integration of multi-hormonal signals during floral development. Recently, MIni Zinc Finger (MIF) proteins have been characterized in Arabidopsis, and shown to be involved in multiple hormonal regulations during plant development. Previously we isolated a gene named INHIBITOR OF MERISTEM ACTIVITY (IMA) as a tomato MIF ortholog. IMA was shown to regulate meristem activity by inhibiting the expression of WUSCHEL. Tomato plants overexpressing IMA exhibit a dwarf phenotype suggesting that IMA regulates negatively cell proliferation and expansion. A Two-Hybrid screen contributed to identify the COP9-signalosome subunit 5, as a strong interacting protein. The COP9-signalosome plays a conserved key role in the integration of endogenous and exogenous signals to regulate growth of eukaryotic organisms, including cancer development in human when a deregulation of this complex occurs. Our data suggest that IMA controls COP9-signalosome activity to modulate multihormonal responses during meristem development and floral termination. This project aims at understanding the molecular and genetic mechanisms by which IMA and more generally MIF proteins are involved in such regulatory pathways. In the context of fleshy fruit development, this innovative project will promote fundamental knowledge on an original model, but also will generate agronomical benefits through applications at the breeding and biotechnological level for fruit quality improvement.

Keywords: developmental biology,tomato,arabidopsis,floral meristem,mif genes,hormonal signaling
Protein SUlfenylation in Medicago truncatula – Sinorhizobium meliloti SYmbiosis (SUSY)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: European Re-integration Grants
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: France
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2009-10-31
End date: 2011-10-30
Duration (months): 24.0
Total project cost (EUR): 30000.0
EU funding (EUR): 30000.0
Participants: 1
Project status: CLOSED

It now appears that plants purposefully generate Reactive Oxygen Species (ROS) such as Hydrogen Peroxide (H2O2) as signalling molecules to control various processes. There is now compelling evidence that H2O2 is an important signal in plants; this has been particularly reported in the case of plant – pathogen interactions. Symbiosis between Legumes and Rhizobia is characterized by the formation of a new organ on the root able to fix atmospheric nitrogen. More recently, the involvement of ROS during the symbiotic interaction has also been highlighted where H2O2 production must contribute to the control of the establishment and/or functioning of the symbiosis, by exerting a positive effect on both partners. On the other hand, H2O2 is known to interact directly with protein thiols, leading to the formation of a sulfenic acid group (sulfenylation) which has been suggested as a widespread mechanism by which H2O2 might affect protein function. Thus, the goal of the project is to identify the model plant Medicago truncatula H2O2 targets proteins during its interaction with Sinorhizobium meliloti. The three objectives are: i) isolate specifically the sulfenylated proteins using an affinity purification followed by their proteomic identification, ii) map the H2O2 modified cysteins and validate their role in protein fonction and iii) characterise the role of the sulfenylation during the symbiotic interaction through a functional in planta analysis. The project aims at characterizing a completely new role for H2O2 as a signalling molecule in plants. The research programme will lead to the identification and the characterisation of H2O2-driven post-translational signalling. This will lead to important breakthroughs not only in the symbiotic field but also in compatible plant pathogen interaction and more generally of plant development. In this respect, it is expected to open new fields of investigation.
Change in Policy Fields: The Impact of International and Domestic Factors on Morality Policies in 25 OECD Countries Between 1980 and 2010 (MORAPOL)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Advanced grants
Action type: Support for frontier research (ERC)
Panel: Institutions, values, beliefs and behaviour
Countries involved: Germany,Germany
Call:  (ERC-2009-AdG, 2009)
Start date: 2010-09-01
End date: 2016-08-31
Duration (months): 72.0
Total project cost (EUR): 2056800.0
EU funding (EUR): 2056800.0
Participants: 2
Project status: CLOSED

MORAPOL pursues two basic objectives that entail both empirically and theoretically fundamental advances of the state-of-the-art. First, MORAPOL takes an innovative empirical focus. It is the first to provide systematic empirical knowledge on the development of morality policies. This policy area is so far unexplored from a policy-analytical perspective. The focus is on changing patterns of morality policy over time, across countries and policy subfields. The project compares morality policies in 25 OECD countries over a period of fifty years. It involves a comparison across nine different subfields of morality policy. Second, the project is conceptually innovative. The theoretical aim is to develop explanations and identify patterns of changes in policy fields rather than for individual policies or policy items. This holistic approach constitutes a path-breaking departure from existing concepts. This way, it is for the first time possible to develop theories that account for changes in whole policy fields or subfields. To systematically assess the influence of international and domestic factors on morality policy change, MORAPOL adopts a mixed-methods approach. In a first step, a macro-quantitative analysis is undertaken, based on legislative output data for the subfields and countries under study. This analysis is in a second step complemented with qualitative case studies. The case studies are selected on the basis of the results of the quantitative study, which turn out to be critical cases; i.e. cases that are apparently incorrectly predicted by the theoretical model.

Keywords: morality policy,change in policy fields,theories of policy change,comparative politics,comparative public policy
Morphology, Energy and Climate Change in the City (MECHANICITY)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Advanced grants
Action type: Support for frontier research (ERC)
Panel: Environment and society
Countries involved: United Kingdom
Call:  (ERC-2009-AdG, 2009)
Start date: 2010-07-01
End date: 2015-12-31
Duration (months): 66.0
Total project cost (EUR): 2336805.58
EU funding (EUR): 2336805.58
Participants: 1
Project status: CLOSED

Despite half a century of sustained research into the structure of cities, we still cannot answer the most basic questions of how their morphology is affected by the energy and income of their populations. We do not know if cities will become more compact or more spread out as energy usage changes due to global warming and as we switch to renewable energy sources. What we need is much more robust theory with applicable computer models for forecasting such impacts. Many of the rudiments involving agglomeration economics, growth theory, trade, nonlinear dynamics, and fractal geometry have already been put in place with the complexity sciences providing a framework for this new social physics. But so far, energy has been strangely absent. Here we will embrace this role, thus generating theory and models able to address what cities will look like if current predictions of climate change are borne out. We will organise the project into six related themes. First, we will extend theories of urban morphology based on fractals, scaling and allometry to incorporate energetics in analogy to transport and network processes. Second we will link these to statistical thermodynamics in spatial interaction and location modelling where energy, entropy, and accessibility are central. Third we will aggregate our theories to enable comparative analyses of city shape, compactness, energy use, and density. Fourth, we will explore different dynamic regimes building on self-criticality and bifurcation. Fifth, we will make these ideas operational building on our London Tyndall Centre model, and on related work in Phoenix and Shanghai. Last, we will construct a web-based laboratory for posing what if questions about climate change and energy balance using our theoretical and empirical models.

Keywords: urban models,complexity sciences,energetics,social physics