Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Genotyping using solid-state nanopores and Pepetide Nucleic Acid markers – a new tool for single-molecule molecular diagnostics (GENOTYPING NANOPORES)

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-2010-RG, 2010)
Start date: 2011-03-01
End date: 2015-02-28
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

The rapidly decreasing costs of DNA sequencing have made the genomic sequences from thousands of pathogens broadly accessible. The utilization of this new knowledge in clinical practice, however, critically depends on the availability of new analytical tools and techniques that could quickly and efficiently detect the presence of specific genomic variants of pathogens. Some recent examples include the outbreak of H1N1 (Swine flu) and HIV-AIDS. Current approaches rely on costly and time-consuming Polymerase Chain Reaction (PCR), to achieve the specificity and quantity required by standard means of detection. Here I propose to develop a radically low-cost, single-molecule, genotyping method based on nanopore sensing of Peptide Nucleic Acids (PNA) markers. This method is designed to yield an extremely low cost, single-molecule detection of viral infections. Nanopores are emerging single-molecule sensors, where an electrophoretic force threads DNA or RNA biopolymers, into a nanoscale aperture made in a thin film. The threading process uncoils the biopolymers, as they move from one side of the film to the other. Molecules entering the nanopore occlude some of the free ions in the solution from the pore volume, thus permitting real-time electrical detection of the local cross-section of the biopolymer. We propose to develop this method to permit the rapid detection of sequence-specific PNA markers, known to invade double-stranded DNA and form bulges at the points of invasion. We recently showed that PNAs can be detected using tiny solid-state nanopores. To transform this discovery into a robust analytical tool, extensive studies are now required to critically improve the nanopore fabrication, the signal over noise of the measurements, and the biomolecular strategies for efficient PNA invasion. Our studies will ultimately enable the development of low-cost, portable, and high-throughput devices for a broad range of genome based molecular diagnostics.

Keywords: physical sciences,natural sciences
Investigating the genetic architecture and pathogenesis of of Herpes Simplex encephalitis susceptibility (HSEPID)

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-2010-RG, 2010)
Start date: 2012-01-12
End date: 2014-01-11
Duration (months): 24.0
Total project cost (EUR): 30000.0
EU funding (EUR): 30000.0
Participants: 1
Project status: CLOSED

Childhood herpes simplex encephalitis (HSE) is a potentially life-threatening complication of primary infection by herpes simplex virus-1 (HSV-1), a common virus that is innocuous in most children. HSE is the most common sporadic viral encephalitis in Western countries and acyclovir-treated patients often suffer from severe neurological sequels. The pathogenesis of HSE remained unknown until the recent discoveries of Mendelian single-gene mutations specifically impairing immunity to HSV-1 at least in a subset of children suffering from HSE. We have identified mutations in TLR3, UNC93B, TRIF and TRAF3 in patients with isolated HSE, suggesting that impaired type I interferon (IFN) production upon stimulation of TLR3 by dsRNA viral intermediates in the CNS underlies the pathogenesis of HSE in these patients. Despite the identification of these genes, only a minority of the patients tested carried these genetic defects. Hence we hypothesize that childhood HSE is a genetically heterogeneous disease and that other single gene inborn errors of immunity may explain HSE in other patients. As a first objective, we hope to identify novel HSE-causing genes following a candidate gene approach in patients with a cellular phenotype. The TLR3-IFN pathway will be tested and the known genes sequenced. For those without any mutations in known genes, alternative approaches such as cDNA complementation and RNA sequencing will be carried out. In addition, we also aim to understand the cellular basis of the pathogensis of HSE as most our studies have been carried out on patients’ fibroblasts. We hope to characterize the TLR3-dependent type I IFN production in response to dsRNA and HSV-1 in CNS resident cells by differentiating patient-derived fibroblast induced pluripotent stem (iPS) cells into neurons, oligodendrocytes, and astrocytes. Investigating the anti-HSV-1 immunity in the relevant CNS cells types will be important in furthering our understanding of HSE pathogenesis.

Keywords: health sciences,genetics,virology,immunology,infections
IMPROVEMENT OF NOx EMISSIONS THROUGH SATELLITE NO2 RETRIEVALS AND GROUND OBSERVATIONS (IMNOXE)

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-2010-RG, 2010)
Start date: 2011-05-02
End date: 2015-05-01
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

Recent developments in the remote sensing allow acquiring vertical column information of NO2 as well as other air pollutants in the atmosphere with the use of electromagnetic radiation. The availability of these state-of-the-art retrievals as tropospheric NO2 columns with comparable spatial resolutions to regional air quality models and global coverage within days including remote areas where other means of measurements are not available are long-needed additions to the sparse ground-based observations. Using satellite observations to improve our scientific understanding of atmospheric processes by integrated analysis of satellite, and ground-based observations with regional air quality models is the starting point of this research. The improvement of NOx emissions via satellite NO2 retrievals is one of the emerging research areas with the development and availability of the remote sensing retrievals. The overall objective of the research presented here is to improve the NOx emission inventories by integrating observations from satellite retrievals, and ground observations with regional air quality modeling which is in line with the EU Seventh Framework (FP7) Environment theme where Earth observation and assessment tools are given as one of the emphasized research areas and it is also related to the Space theme, where an emphasis is given to the research area of Space-based applications serving European society. One of the important endpoints of this research is informing the decision-makers in their design of environmental policy in the area of NOx emissions. The proposed research program is a multidisciplinary topic which combines environmental sciences, modeling, remote sensing and environmental policy. The novelty of this project that distinguishes it from similar research in Europe is its focus area. Here, NO2 satellite retrievals will be used to improve NOx emissions in and around Turkey where the emission inventories have less detail and higher uncertainties.

Keywords: environmental science,air pollution,no2,nox emissions,remote sensing,inverse modeling
Multiple-Access Quantum Key Distribution Networks (MULTIPLE-ACCESS QKD)

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: United Kingdom
Call:  (FP7-PEOPLE-2010-RG, 2010)
Start date: 2011-05-01
End date: 2015-04-30
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

I propose the theoretical study of multiple-access quantum key distribution (QKD) networks. Quantum cryptography is an emerging interdisciplinary field of science and engineering with developing commercial applications. It is one of the objectives of the work programme to provide European citizens with the security level that the quantum technology offers. Multiple-access QKD networks make us one step closer to this goal, and open up new marketing opportunities by introducing more flexible configurations as compared to the current point-to-point QKD links. In a multiple-access network, every two users can use a shared channel to exchange a secure key without trusting any other users. This shared channel can be used, possibly, at the same time, by other pairs of users who also wish to create secure keys. Such an advantage becomes possible by employing the well developed multiple-access techniques in classical optical communication networks. In particular, I intend to study the three schemes of wavelength, code, and time division multiple access, in which, respectively, each user is assigned a particular wavelength, code, or time slot. The main question to answer is how the interference caused by other users will affect the rate of secure key generation in a multiple-access QKD setup. It is also important to compare different network configurations in terms of their architecture and cost. Finally, I would like to investigate the possibility of extending the ideas relevant to local and metropolitan area networks, to wide area networks, where we need to employ quantum repeaters for the secure exchange of the key. Experimental demonstration of such networks will also be pursued via finding other sources of funding or in collaboration with other research groups.

Keywords: quantum mechanics,quantum cryptography,optical communication networks,multiple-access techniques,quantum key distribution,quantum repeaters,cdma,wdma
DEVELOPMENT OF TWO COMPLEMENTARY SYSTEMS FOR THE STUDY OF RECOMBINATION AND PACKAGING OF HEPATITIS C VIRUS GENOMIC RNA USING FLUORESCENT PROTEINS AND LIVE IMAGING (HCVPACK)

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: Denmark
Call:  (FP7-PEOPLE-2010-RG, 2010)
Start date: 2011-04-01
End date: 2015-03-31
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

The Hepathitis C Virus (HCV) infects more than 150 million people worldwide and is the major cause of hepatic cirrhosis and hepatocellular carcinoma. Current available treatment options have limited efficacy and result in effective viral suppression only in about 50% of treated patients. In addition, HCV exhibits an extremely high genetic variability, mainly due to lack of proofreading activity of the viral RNA polymerase and its ability to generate recombinant genomes. Genetic diversity allows the virus to evolve variants capable to escape immune response and drug pressure and hampers the development of effective vaccines. Research of novel specific drugs is hindered by our limited understanding of several key steps of the viral life cycle. To clarify different aspects of HCV RNA biology, we propose the development of two new assays based on detection of fluorescent proteins. Our first objective is to use the reconstitution of a GFP protein to measure native recombination capability of HCV under different infection conditions. This part will clarify the relative importance of several factors in the generation on new recombinant forms. Subsequently, we will deploy a system to visualize genomic RNA and viral Core protein simultaneously in live cells. By fusing different fluorophores to RNA-binding proteins and to the Core, we will be able to measure packaging and copackaging efficiencies of HCV. Lastly, we will trace the pathway of RNA molecules and Core using live imaging. This will help identifying the sites of recombination, dimerization and packaging in the cell. Taken together, the data produced will help clarify several important aspects of the viral replication cycle, and identify possible new targets for antiviral intervention. Moreover, the systems proposed represent novel approaches to the study of RNA biology in HCV, providing the Copenhagen Hepatitis C Program with advanced and competitive know-how in the field of HCV research.

Keywords: virology,molecular biology
Group-based Dynamics on Complex Networks (GRODYNET)

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: Spain
Call:  (FP7-PEOPLE-2010-RG, 2010)
Start date: 2011-03-01
End date: 2015-02-28
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

Cells, ecosystems and economies are examples of complex systems. In complex systems, individual components interact with each other, usually in nonlinear ways, giving rise to complex networks of interactions that are neither totally regular nor totally random. Partly because of the interactions themselves and partly because of the interaction topology, complex systems cannot be properly understood by just analyzing their constituent parts, which poses important challenges from both a fundamental perspective and an "application" perspective. The structure of the network of interactions was traditionally ignored and approximated by one of two limiting cases: a regular low-dimensional lattice or a completely random uncorrelated graph. It wasn't until recently that the scientific community, spearheaded by physicists, started to look for universality on the statistical description and classification of networks. Although significant progress has been made since then, we are still far from the ultimate goal of developing a general theory decribing the impact of network structure on the dynamics of complex systems. The general aims of the project are: (i) to develop a general theoretical framework, based on the mesoscopic structure of networks, to understand the interplay between network structure and system dynamics; and (ii) to apply this framework to biological and socio-economic systems of interest.

Keywords: complex networks,complex systems,systems biology
ADVANCEMENT OF SATELLITE RAINFALL APPLICATIONS FOR HYDROLOGIC MODELING WITH EMPHASIS ON FLOOD MONITORING (FLOODSAT)

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-2010-RG, 2010)
Start date: 2011-04-01
End date: 2014-03-31
Duration (months): 36.0
Total project cost (EUR): 75000.0
EU funding (EUR): 75000.0
Participants: 1
Project status: CLOSED

Floods are the most widespread and frequent natural disaster responsible for significant loss of lives and property each year. The European Environmental Agency estimated that floods in Europe between 1998 and 2002 caused about 700 deaths, the displacement of about half a million people and at least 25 billion Euros in insured economic losses. As such, one of the four priority areas in FP7 has been identified as triggering factors and forecasting and mitigation strategies for natural hazards. Flood early warning systems are the most effective way to mitigate flood induced hazards. The reliability of such systems depends on the availability of timely and good-quality rainfall estimates. Although many of the regions in Europe are equipped with dense rain gauge networks, the station density varies greatly from country to country, which can affect the quality of the model simulations. Hence exploiting alternative ways, such as satellite-based products, for estimating rainfall having continuous spatial coverage and short latency will be potentially beneficial for mitigating flood risks. The overall goal of this project is to “advance the utility of satellite-based rainfall estimates for hydrologic modeling, specifically for flood monitoring”. The expected outcomes of this research are: 1) a large database of dynamic and static datasets for the Western-Black Sea basin, Turkey, 2) A methodology for adjusting satellite-based rainfall estimates, 3) intercomparison study revealing the degree of agreement between rain gauge and satellite-based rainfall products over the study area before/after the adjustment, 3) A hydrologic model that is implemented for the study basin using rainfall estimates from rain gauges and existing/adjusted satellite rainfall products, 4) An improved methodology for calibration and evaluation of hydrological models, 5) An analysis providing insights into the value of existing/adjusted satellite-based rainfall estimates for streamflow simulations.

Keywords: flood forecasting,hydrology (water science)
Finding order to harness chaos: A new approach to understanding and controlling high Reynolds-number wall-bounded turbulence. (WBT)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Products and process engineering
Countries involved: United Kingdom
Call:  (ERC-2011-StG_20101014, 2011)
Start date: 2012-01-01
End date: 2017-12-31
Duration (months): 72.0
Total project cost (EUR): 1486500.0
EU funding (EUR): 1486500.0
Participants: 1
Project status: CLOSED

The enormous impact and significance of high Reynolds-number wall-bounded turbulence in various applications ranging from transportation and energy generation systems to meteorology and oceanography cannot be understated. However, almost all existing ideas in modelling and controlling wall-bounded turbulence are based on our limited understanding of low Reynolds-number flows. In higher Reynolds-numbers, we simply assume the existence of mutual independence of the large-scales located farther away from the wall from the small-scales near the wall and vice-versa. However, this notion of independence is incorrect. In fact, multiscale interactions between large- and small-scales play a significant role in various turbulent transport processes in practical situations. Consequently, our predictive models and control schemes that cannot account for or take advantage of these interactions have very limited success. Therefore, the central question posed in this research project is: What is the physics of scale interactions at higher Reynolds-numbers and how do we take advantage of it? The aim is to explore the essence of scale interactions and develop fundamental understanding by performing novel experiments in high Reynolds-number boundary layers. New control methodologies based upon the existence of interactions between large- and small-scales will be devised and applied to reduce skin-friction drag. Additionally, unconventional, yet highly innovative experiments will be devised to ``simulate'' essential aspects of high Reynolds-number scale interactions in a controlled laboratory environment. State-of-the-art laser diagnostics techniques including tomographic PIV and multiple-plane PIV will be performed together with other methods such as hot-wire/laser anemometry to study the physics of scale interactions in these flows. The ultimate goal is to develop new initiatives aimed at predicting and controlling wall-bounded flows in order to meet current and future challenges.

Keywords: wall-bounded turbulence,scale interactions,flow control,advanced diagnostics
Application Performance Optimisation and Scalability-EU (APOS-EU)

Framework: FP7 — Cooperation
Programme: Information and Communication Technologies
Destination: International Cooperation
Action type: Collaborative project
Countries involved: United Kingdom,France,Poland,France,Germany
Call:  (FP7-ICT-2011-EU-Russia, 2011)
Start date: 2011-02-01
End date: 2013-01-31
Duration (months): 24.0
Total project cost (EUR): 1596629.0
EU funding (EUR): 1200000.0
Participants: 5
Project status: CLOSED

The objective of APOS-EU is to develop optimised versions of scientific and industrial codes which are scalable and portable across heterogeneous and homogeneous architectures. Codes will be chosen from the areas of seismic processing, magneto-hydrodynamics, percolation, molecular modelling and CFD. Scalability to thousands of cores will be a principal goal of the work. In parallel with the development of the codes, prototype tools, starting from the current state of the art, will be interactively developed, deployed and refined. The proposal falls within Part C of the call Objective ICT-2009.10.2 EU-Russia Research and Development Cooperation. This proposal is a small, but important step on the road to innovative, advanced simulations and tools to support their development. Real-world applications will be used to test and evaluate methodologies for developing massively parallel, highly scalable applications and for testing relevant tools. This will provide an important reference to code owners both ISVs and those with in-house codes. It will provide important feedback to tool developers on the requirements of porting real applications to the new generations of machine. The successful outcome of the project will constitute an important advance in the state of the art and will have immediate industrial and economic impact. The work in APOS-EU will be complemented by that in the Russian proposal APOS-RU which addresses two important application areas namely high-resolution 3-D seismic processing and atomic simulation codes based on many-body interatomic potentials. Both these areas create opportunities for common work between the EU and Russian consortia on the development of algorithms and on the use and development of tools for parallelisation.

Keywords: hpc russia