Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Prediction of protein flexibility and its role in protein-protein interactions and binding specificity (PROTFLEXPRED)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: United Kingdom
Call:  (FP7-PEOPLE-2007-2-1-IEF, 2007)
Start date: 2008-07-01
End date: 2010-06-30
Duration (months): 24.0
Total project cost (EUR): 161225.98
EU funding (EUR): 161225.98
Participants: 1
Project status: CLOSED

Recent studies show that protein function is not only determined by the static folded three-dimensional structure, but also by the distribution of the populations of its conformational sub-states within different environments. A detailed investigation of interacting protein interfaces requires - beyond the knowledge of their structure - information about their flexibility and the range of accessible conformations of the native state and complexed states. Additionally, successful protein structure prediction has demonstrated the suitability of “building blocks” (prototype fragments) as embodiment of local biological and physicochemical features. It is expected that the overall dynamics of protein structures can similarly be assembled from fragment flexibilities embedded in a known protein fold. Therefore this proposal focuses on developing a fast fragment-based method to predict the dynamics of a native or designed protein structure, which will be used to determine or define function in interaction networks and binding specificity in protein-ligand complexes. Specifically, the dynamics of prototypical fragments from a representative protein set will be sampled by molecular simulations; a flexibility predictor will be designed, implemented using Hidden Markov Model (HMM) and trained on dynamic profiles of the prototypical fragments; by using the flexibility predictor protein-protein and protein-ligand interactions will be investigated. For protein-protein interactions the flexibility of all known high-resolution protein structures will be predicted and made publicly available. To study flexibility as determinant of ligand-binding specificity, comparisons between the conformational sub-space of protein-ligand complexes and the space of all accessible conformations of the unbound components will be performed.

Keywords: computational biology,structural biology,molecular simulations,protein interactions,protein flexibility prediction
Conflict Management, Cross-border relations and the Struggle for maritime Hegemony in the North Atlantic (XVIth-XVIIth centuries) (MARITIME HEGEMONY)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: France
Call:  (FP7-PEOPLE-2007-2-1-IEF, 2007)
Start date: 2008-09-01
End date: 2010-08-31
Duration (months): 24.0
Total project cost (EUR): 154911.75
EU funding (EUR): 154911.75
Participants: 1
Project status: CLOSED

War between the French and Spanish crowns, the two Grand Powers of the sixteenth century, had important consequences in shaping collective identities and cross-border relations of frontier communities of both monarchies. That was the case of the Basque maritime provinces of Guipúzcoa in Spain, and Labourd in France. The hostility between these two frontier communities was not limited to the borderland region but in fact extended to the high-sea and beyond. The conflict embraced the Atlantic, not only in European waters but also in distant places like the Spanish-American colonies and especially the important Newfoundland fisheries. My research on the frontier-like confrontation between Guipúzcoa and Labourd corsairs/fishermen at home and in the rich fisheries of Newfoundland is relevant to explain progressive decay of the Spanish maritime policy, and so the ascension of the English and French in North-America. In this sense the study of judicial trials and local “peace treatises” (tratados de buena correspondencia, lies et passeries or lines of amity) between maritime communities constitues a perfect source to analyze the link between “public” and “private” warfare and the interplay between global strategy and local interests on important matters for both the crown and the communities such as fisheries, course, commerce and the navy. The aim of this project is to go further in the comprehension on the use of royal institutions and military apparatus by local communities in order to implement their own power strategies in relation with rival communities across the border and to what extent were royal authorities, both in the territory and the court, conscious of this fact. In the same fashion it is very important to understand the king’s interests at local level as well as his concern on political, social and economic stability in borderlands.

Keywords: early modern history,political history,maritime history,transnational history,sea-frontiers and borderlands,cross-border relations,ius in bello
Identification and characterization of primate-specific duplications and an assessment of intra-specific patterns of selection and copy-number variation (IDCHPRIMATESDS)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Outgoing Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Spain
Call:  (FP7-PEOPLE-2007-4-1-IOF, 2007)
Start date: 2008-06-01
End date: 2010-11-30
Duration (months): 30.0
Total project cost (EUR): 233921.24
EU funding (EUR): 233921.24
Participants: 1
Project status: CLOSED

Segmental Duplications (SDs) can be defined as blocks of DNA ranging from 1-400kb in length with copies found in multiple sites and typically share high sequence similarity (>90%). Studies based in both experimental and computational analyses show that ~5% of the human genome is composed of duplicated sequences. More generally, primate genomes have been found enriched for this complex patterns of interspersed segmental duplications.This 5% of euchromatin differs in structure and content between closely related primates and is not easily resolved by whole-genome shotgun sequence assembly methods.This proposal focuses on this 5% of the genome that historically has been the most difficult for sequence and assembly.The aim of this research is to reconstruct the evolutionary history of all primate segmental duplications in 6 species of primates (Human, Chimpanzee, Orangutan, Gibbon and Macaque and Marmoset) and to understand gene innovations that have emerged within these dynamic genomic regions. The Main goals of the proposal are: 1.SDs detection and analysis of non-human primate genomes. 2.SDs validation (by means of FISH and CGH arrays hybridizations) 3.Analyze species-specific functional elements and their polymorphism and divergence patterns The proposed work not only can assist/direct efforts in these regions but serve as a benchmark of the quality of the final sequenced genomes, and, as such, benefit the genomics/evolutionary/genetics community as a whole. The long-term goal is to create an integrated view of the evolution of primate segmental duplications by studying changes in the composition, frequency, size and location at the major branchpoints in the primate phylogeny. This work has the ancillary benefit that it will provide inssight the origin of SD structure associated with genomic disease and characterize lineage-specific genes relevant to realization of these primates as models of human disease and to the adaptation of these species.

Keywords: health sciences,genomics,segmental duplication,disease,evolution,primates,genomics
The Evolution of Evolvability: How Natural Selection Shapes Itself (SELFREF)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Hungary
Call:  (FP7-PEOPLE-2007-2-1-IEF, 2007)
Start date: 2008-04-01
End date: 2010-03-31
Duration (months): 24.0
Total project cost (EUR): 74573.2
EU funding (EUR): 74573.2
Participants: 1
Project status: CLOSED

The objective of this research is to understand how a metabolic system undergoing natural selection can transform into a template-based system undergoing natural selection. This is an example of an early major transition in evolution. Answering this question will contribute to our understanding of the origin of life, the self-referential nature of embodied evolution, the evolution of evolvability, evolutionary algorithms in engineering, and combinatorial chemistry. We build upon our published papers on natural selection at the extremes: evolution of complex metabolic organizations by natural selection; and the evolution of non-enzymatic template replicators. We build a model that can bridge the gap between our previous two models. A new algebraic representation describes an abstract chemical structure to function map that can represent the behaviour of both autocatalytic metabolities undergoing macromutation, and nucleotide based templates undergoing micromutation. This unified model can then be simulated and explored to understand the transition from limited to unlimited heredity. We test the hypothesis that second-order selection (i.e. selection for variability properties) acting on metabolic organizations enclosed in compartments was the driving force for the evolution of nucleotides. Although the work is a natural and well-defined extension of our previous results, we believe it will produce the first model of a physically embodied evolutionary algorithm capable of open-ended evolution.

Keywords: evolutionary biology,computational biology,cybernetics
Generation of stable transgenic embryonic stem cell lines (TRANSHESC)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: United Kingdom
Call:  (FP7-PEOPLE-2007-2-1-IEF, 2007)
Start date: 2008-09-01
End date: 2010-08-31
Duration (months): 24.0
Total project cost (EUR): 243268.29
EU funding (EUR): 243268.29
Participants: 1
Project status: CLOSED

Human embryonic stem cells (hESC) are pluripotent cells derived from blastocyst stage early embryos. Since the original publication a vast number of studies have described the differentiation of hESC and their potential in regenerative medicine. It is now well known that hESC might be used in cell replacement therapies in a number of severe degenrative diseases like Type I diabetes or Parkinson’s disease. In addition, hESCs and their derivatives could be used as tools in discovering new drugs and in understanding mechanisms of genetic diseases. HESC applications could also be used in toxicological studies reducing the need of animal experiments. Genetic manipulation of hESC will be a crucial issue in a variety of future studies. To elucidate the role of any given gene for example in directed differentiation or pathogenesis the loss- and gain-of gene function approaches are of major importance. Also, considering the potential therapeutic applications of the hESC their genetic modifications may be necessary. The first part of this proposal is designed to improve and test novel efficient and safe transposon-based gene transfer method in generating conditional transgenic hESC lines. Of special interest is the use of insulator elements around transgene to assure nonbiased expression of the integrated sequences. Several reports have indicated that in long term hESC cultures the cells aquire chromosomal aberrations. The observed karyotypic changes probably reflect the progressive adaptation of self-renewing cells to their culture conditions. This process has parallels with malignant transformation. Changes observed in hESC in culture reflect tumorigenic events that occur in vivo, particularly in testicular germ cell tumors (TGCT). A recent report indicated the formation of a chromosomal homogeneous staining region (HSR) in some hESC lines, a feature almost a hallmark of cancer cells. The HSR represents an amplified small chromosomal region most likely containing gene

Keywords: human embryonic stem cells,transgenic,adaptation,self-renewal
Effect of Inhomogeneous Parallel Flow on Plasma Waves and Instabilities (SPACE PLASMA FLOW)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Incoming Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: United Kingdom
Call:  (FP7-PEOPLE-2007-4-2-IIF, 2007)
Start date: 2008-12-01
End date: 2010-11-30
Duration (months): 24.0
Total project cost (EUR): 235103.34
EU funding (EUR): 235103.34
Participants: 1
Project status: CLOSED

The prevalent theories of parallel flow have considered plasma waves and instabilities in the presence of only flow shear. As a result, these theories have predicted only excitation (destabilization) of instabilities which has lead to the well-known hypothesis that `parallel flow shear is the origin of many space oscillations and instabilities'. However, here we propose to develop a model of space plasma oscillations and instabilities in the presence of a more realistic flow profile including both flow shear and flow curvature. Now, with the inclusion of flow curvature the stability picture is expected to be changed drastically. The flow curvature, contrary to the flow shear, can actually STABILIZE the modes which is rather opposite to the well-know hypothesis of the generation of space fluctuations by the parallel velocity shear. Furthermore, the new model of space oscillations in the presence of both flow shear and curvature, being more realistic, is expected to produce results which should fit better with the spacecraft data. These results are also expected to have important implications in the communication systems and space weather technologies. Apart from the space plasma and fluid dynamics community, the theory proposed to be developed here will also have application in the plasma and fusion energy technology.

Keywords: space plasma,ionosphere,magneosphere,waves and instabilities
Analysis and Management of Wireless Networks with Selfish Users (WNET-GT)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Outgoing Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: Israel
Call:  (FP7-PEOPLE-2007-4-1-IOF, 2007)
Start date: 2008-03-25
End date: 2011-05-31
Duration (months): 36.0
Total project cost (EUR): 229988.46
EU funding (EUR): 229988.46
Participants: 1
Project status: CLOSED

The emerging use of wireless technologies for data communication has brought to focus novel system characteristics, such as power control, time variation in the channel quality and mobility of the network users. In addition to diversity in these physical parameters, mobile users are heterogeneous with regard to their Quality of Service (QoS) criteria, differently evaluating delay, throughput and power. Distributed mechanisms for wireless medium-sharing, branching from the celebrated Aloha protocol, have gained prominence due to their relative simplicity. However, Aloha-based protocols (such as 802.11x) are not fully adjusted to the distinctive features of the wireless channel. Moreover, the parameters of these protocols are identically configured among users, not allowing for QoS differentiation. Centralized scheduling algorithms, on the other hand, have been designed in order to consider the wireless specific features and to support QoS. Yet, high-quality schedulers require substantial data and computational resources, and might become hard to implement. Our research attempts to find a middle ground between fully distributed mechanisms and centralized scheduling algorithms, by allowing users to adjust their protocol parameters in order to accommodate their individual QoS requirements. Under the above framework, users can be seen as competing for scarce network resources. Accordingly, this research will employ (non-cooperative) game-theoretic tools for the analysis of multiple access wireless networks. Based on the analysis, we shall design distributed protocols, which allow users to obtain their required QoS, and still preserve network-wide objectives such as fairness. At a higher level, we shall develop efficient management schemes, with the objective of bringing network interference to a minimum. Finally, the designed protocols and management schemes will be evaluated under current network standards.

Keywords: technological sciences,telecommunications engineering,wireless networks,mac protocols,channel fading,quality of service,nash equilibrium,best-response dynamics,multi-packet reception,management
Investigation of electron induced chemical control using momentum imaging of negative ions from dissociative electron attachment (MIND)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: International Incoming Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: United Kingdom
Call:  (FP7-PEOPLE-2007-4-2-IIF, 2007)
Start date: 2009-01-05
End date: 2011-01-04
Duration (months): 24.0
Total project cost (EUR): 243268.29
EU funding (EUR): 243268.29
Participants: 1
Project status: CLOSED

This proposal aims at investigating chemical control using electrons by studying the dynamics of the dissociative electron attachment in gas phase molecules of practical interest using ion momentum imaging. These experiments will be complemented by measurements on molecules condensed on surfaces using electron beam irradiation as well as scanning tunneling microscopes. The proposal is motivated by the recent observations by several groups on molecules in gas and condensed phases that dissociative attachment allows control of electron induced processes. In particular, the group led by the applicant showed that functional group dependence exists in dissociative attachment allowing site/bond selective fragmentation of organic molecules using electron energy as a control parameter. They further investigated the dynamics of this process in selected small molecules using a novel technique developed by them for ion momentum imaging in low energy electron collisions. This technique allows characterization of the intermediate resonant state, the fragmentation pattern and the energy partitioning in the product channels. It is proposed to set up a similar experiment for ion momentum imaging arising from dissociative attachment and polar dissociation in molecules relevant to nanolithography, astrochemsitry and radiation biology at the host institution. These experiments will be complemented by experiments on molecules condensed on surfaces by electron beam irradiation and by using scanning tunneling microscopes with a view to correlate the energy partitioning in the dissociative attachment process and the reactivity of the products. While the applicant brings in expertise on gas phase measurements like absolute partial cross section measurement and ion momentum imaging, the host group and his collaborators provide necessary expertise and facilities for complementary experiments in condensed phase and on surfaces.

Keywords: physical sciences,chemistry,reaction mechanisms ands dynamics,physical chemistry
Investigating the fern diversity of the Mascarene Islands using phylogeographic approaches (MASCARENES FERNS)

Framework: FP7 — People
Programme: Marie-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Intra-European Fellowships
Action type: Support for training and career development of researchers (Marie Curie)
Countries involved: United Kingdom
Call:  (FP7-PEOPLE-2007-2-1-IEF, 2007)
Start date: 2008-06-01
End date: 2009-08-31
Duration (months): 15.0
Total project cost (EUR): 161364.33
EU funding (EUR): 161364.33
Participants: 1
Project status: CLOSED

The South West Indian Ocean islands are an official hotspot of biodiversity and endemism (Myers et al., 2000). Among these islands, the Mascarenes consist of three main islands: La Reunion, Mauritius and Rodrigues. These islands differ in size, elevation profile, age, distance to the next larger land mass (Madagascar) and biodiversity. The Mascarenes are particularly rich in plants species, with about 1,300 vascular plants, of which 585 are endemics. Ferns form an important flora component in the very diverse biotas of the islands, especially in tropical forest. Most ferns disperse easily via their spores, allowing frequent colonization from Madagascar but also exchange among the Mascarene islands. We propose to perform an integrated phylogeographic study of selected groups of ferns with a view to elucidating the processes creating these islands diversity. To this end, we will integrate ecological data to explore the biotas of each island, population genetics, and cytological data to explore polyploidy. The study will also take into account the fern gametophytic phase, too often neglected in fern studies. We will particularly investigate the importance of apomixis. This study is expected to help identify characteristics that allow ferns to successfully colonize islands.

Keywords: systematic botany,biogeography,biodiversity status and trends