Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Noncoding RNA Comparative Searching System (NARCISUS)

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: Poland
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-11-01
End date: 2012-10-31
Duration (months): 24.0
Total project cost (EUR): 30000.0
EU funding (EUR): 30000.0
Participants: 1
Project status: CLOSED

Beside these well-known molecules there is a vast unknown world of tiny RNAs (RiboNucleic Acids) that might play a crucial role in a number of cellular processes. Those elements are named noncoding RNAs (ncRNA) and they play their function without transcription to the protein product. Here is proposed development of integrated bioinformatics platform that is specifically addressed for detecting, verifying, and classifying of noncoding RNAs. This complex approach to &quot;Computational RNomics&quot; will provide the pipeline which will be capable of detecting RNA motifs with low sequence conservation. It will also integrate RNA motif prediction which should significantly improve the quality of the RNA homolog search. The first commercial application is the integrated system for detection of new regulatory elements located in the non coding genome parts. Up to now numerous human disorders have been found to be related to some of the noncoding RNA’s The second application of the project is so called RNA nanotechnology. It is designing of artificial nanoparticles, which are assembled mainly from ribonucleic acid which possess both the right size and ability to gain entry into cells and halt viral growth or cancer&apos;s progress or deliver drugs. The project will benefit from latest achievements in High Performance Computing and General-Purpose computing on Graphics Processing Units and Graph theory.

Keywords: bioinformatics,noncoding rna,hpc,high performance computing,gpgpu,general-purpose computing on graphics processing units. molecular biology
Design and development of novel reagents, tools, and techniques targeting human glutamate carboxypeptidases II and III (GCPII_SYSTEM)

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: Czechia
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-11-01
End date: 2014-10-31
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

Glutamate carboxypeptidase II (GCPII) is a membrane-bound metallopeptidase with a vast pharmacological potential. Given the intimate involvement of the enzyme in neurotransmission under normal physiological conditions, it is not surprising that GCPII-specific inhibitors are neuroprotective in multiple preclinical models of neurodegeneration. Additionally, the cancer-associated form of GCPII is exploited as a target for immunotherapy/imaging of prostate cancer as well as neovasculature of solid tumors. Despite of its utilization in (pre)clinical settings, the physiological function of GCPII in the latter tissues is unknown and the whole picture is further complicated by the existence of GCPIII, a close GCPII homolog. The main goals of this proposal focus on the identification and development of novel reagents, tools and techniques associated with the GCPII/GCPIII system that may help addressing questions pertaining to the fundamental (patho)physiological roles of GCPII/GCPIII. We will use information from X-ray structures of GCPII/GCPIII complexes to modify and improve characteristics of small-molecule ligands currently used in experimental models of prostate cancer. Secondly, will develop an activity assay based on fluorescence polarization that, in turn, will be exploited for the identification of novel inhibitor scaffolds targeting GCPII/GCPIII. The physicochemical properties of the lead-like compounds will be further optimized to develop isoform (GCPII vs. GCPIII) specific reagents. Such compounds are not available at present and their availability is crucial for dissecting potentially diverse physiological functions of GCPIII and GCPII with implications for GCPII/III associated pathologies. Lastly, we will try to gain insight into non-enzymatic (receptor-like) properties of GCPII by identifying physiological interaction partner(s) of the enzyme using a tandem affinity purification approach.

Keywords: glutamate carboxypeptidase ii,prostate-specific membrane antigen,metallopeptidase,x-ray crystallography,structurally-based drug design,inhibition,prostate cancer,tandem affinity purification
The role of Salmonella Pathogenicity Islands in salmonellosis outbreaks and invasive disease (ROLE OF SPIS)

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: 2010-02-01
End date: 2014-01-31
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

Non-typhoid Salmonella (NTS) enterica is a major cause of foodborne infections in industrialized countries and a leading cause of hospitalization and death among bacterial foodborne pathogens. The vast majority of the Salmonella virulence factors are encoded within horizontally acquired discrete regions along the chromosome known as Salmonella Pathogenicity Islands (SPIs). SPIs are crucial for Salmonella virulence. Herein we propose to study the role of 17 SPIs and associated virulence loci in different aspects of NTS pathogenicity including the ability to cause outbreaks, host-to-host transmission, and manifestation of invasive disease. In the first stage of the study we will map and characterize the distribution of these virulence loci across various outbreak and bacteremia isolates. This analysis will provide a broad view over the distribution of SPIs in highly virulence isolates, which are clinically relevant in Israel and Europe. Based the collected data, we will develop a Quantitative Microbial Risk Assessment approach for detection of virulent Salmonella strains in food, environmental and livestock samples. In addition we are interested in investigating the potential contribution of SPIs to the oral-fecal route of transmission. To do so, we will use the persistent mouse model and study the ability of Salmonella strains, harboring SPIs deletions to transmit the disease over time. The gained data are expected to yield a broader understanding about the role of primary virulence loci in the pathogenesis and epidemiology of Salmonella and will shed light on the evolution of pathogenic Salmonella serotypes. Understanding these mechanisms will contribute to our knowledge about host-pathogen interactions and the molecular basis of outbreaks. Deeper understanding about these processes could lead to better prevention and treatment of infectious diseases and may provide new therapeutic targets for the development of novel antimicrobial chemotherapies and vaccines.

Keywords: health sciences,salmonella,pathogenicity islands,virulence factors,infectious diseases,medical sciences
Study of mechanisms underling the balance between inflammatory and regulatory immune response in Multiple Sclerosis (IMMUNO BALANCE MS)

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: Italy
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-01-01
End date: 2012-12-31
Duration (months): 36.0
Total project cost (EUR): 45000.0
EU funding (EUR): 45000.0
Participants: 1
Project status: CLOSED

Multiple sclerosis (MS) is an autoimmune disease whose pathology is directly mediated by inflammatory autoimmune T cells. The mechanisms determining the initiation of inflammation by T cells are still unknown. Since antigen presenting cells (APC) play a crucial role in the activation of T cells, their involvement in directing the quality of T cell responses in MS is likely. Thelper (Th) 17 type of immune response is responsible for mediating pathogenesis during autoimmunity. In contrast, Tregulatory (Treg) cells suppress the functions of effector T cells, thereby protecting tissues from the devastating damage inflicted by non-specific inflammation. A delicate balance of soluble factors is involved in the differentiation of naïve T cells into either polarized inflammatory Th17 or suppressive Treg cells. Moreover, the increase of Th17/Treg ratio in MS patients suggests a functional antagonism between Th17 and Treg cells, and a dichotomy in their generation as well. In this project we aim to characterize the involvement of APC in the Th17/Treg balance during MS disease. We will purify primary APC subsets and we will stimulate them ex vivo with Toll like receptor (TLR) agonists. A specific transcriptional profile of APC purified from MS patients versus healthy donors will permit to select genes differentially expressed and potentially involved in the activation of T cells. In order to clarify the role of selected APC molecules, we will block them before coculture APC with naïve/memory T cells. Differentiation of T cells will be analysed through the measurement of Th17- and Treg-specific features and in vitro functional assays. These results will clarify whether the signals originating from APC in MS patients underlie the Th17/Treg imbalance. Moreover, the characterization of molecular mechanisms adopted by APC in controlling T cell response in MS disease, will be important to pharmacologically influence the immunity towards an anti-inflammatory response in MS patients.

Keywords: immunology,multiple sclerosis,antigen presenting cells,dendritic cells,t helper 17,t regulatory cells,balance
Systems biology of Pseudomonas aeruginosa in biofilms (SYSBIOFILM)

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: Iceland
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-03-01
End date: 2014-02-28
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

Systems biology is a new and rapidly growing discipline. It is widely believed to have a broad transformative potential on both basic and applied studies in the life sciences. In particular, metabolic network reconstructions are playing a key role as they provide a framework for investigation of the mechanism underlying the genotype-phenotype relationship. Pseudomonas aeruginosa is an opportunistic pathogen of clinical relevance with an increasing resistance against available antibiotics, which is partially attributed to its ability to form biofilms. The proposed project will construct a comprehensive biofilm model of P. aeruginosa using a recently published metabolic reconstruction. The biofilm model will represent typical micro-habitats. Hence, it will give insight into distinct metabolic difference of planktonic and biofilm-associated bacteria and may further our understanding as to why biofilm bacteria are resistant to antibiotics. Metabolomic, patient samples will be integrated with the biofilm model which is expected to yield insight into conditions associated with disease progression and manifestation. The biofilm model will also be employed to predict new strategies for therapeutic interventions through in silico gene deletion studies. The project will include the development of relevant reconstruction and analysis methods. This work will set new standards in reconstruction, analysis, and modeling techniques and will build the first large-scale bacterial-community-based network. Gained knowledge will be directly applicable to other single or multi-species bacterial communities. The proposed project will be carried out within the Center for Systems Biology at the University of Iceland. Lastly, the project is well placed within the recent European efforts to apply systems biological approaches towards improving early diagnosis and accelerating the discovery of novel interventions.

Keywords: natural sciences,biological sciences,molecular biology,systems biology,biofilm,pseudomonas aeruginosa,metabolic reconstruction,constraint-based modeling,mathematical modeling
Contradicting responses to multiple stressors reduce the resilience of zooplankton community (CONTRASTRESS)

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: Poland
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2010-06-01
End date: 2013-05-31
Duration (months): 36.0
Total project cost (EUR): 45000.0
EU funding (EUR): 45000.0
Participants: 1
Project status: CLOSED

The aim of the project is to find out what happens within zooplankton communitiy when various chemicals (cyanotoxins and infochemicals) force organisms to use contradictory strategies. Aquatic ecosystems are subject to many anthropogenic stressors, which includes eutrophication with toxic cyanobacterial blooms, chemical pollution (e.g. pesticides) and invasive species linked with climate change. These factors modify populations and whole lake ecosystem as well. Also natural factors like predation, resource competition and food quality may cause substantial changes in populations and communities. Organisms need to use different strategies to cope with these stressors and these strategies exclude each other. This situation may lead to losses in genetic biodiversity or even to exclusion of a species. Zooplankton plays important role in aquatic food webs and it is crucial to know how chemical interactions affect population dynamics and community structure. The aim of this study is to check what are the strategies of individuals to cope with such contrasting conditions and what is their role in biodiversity loss. To answer these questions several approaches will be used to bring together paleolimnology, evolutionary ecology and ecotoxicology. Molecular biology will be included as well in order to asses the genetic biodiversity and to develop a new tool for testing the response of an organism to chemical stressors. Two main hypotheses will be tested (1) Hormesis of a trait is maladaptive (i.e. strategy ‘bigger is better’ decreases fitness and hence indicates a negative response), (2) Interaction of cyanotoxins (hormesis) with fish infochemicals can induce developement of a new zooplankton community. Based on these working hypotheses we set several objectives: - to describe the effects of contradicting chemical signals on life history traits, - testing hormetic effects on several clones of Daphnia adapted to ‘good’ and ‘bad’ conditions, - reconstruct zooplankton com

Keywords: aquatic ecology,ecotoxicology,biodegradation,ecosystem impact (climate change),anthropogenic impact on ecosystems,fresh water ecosystems,causes and mechanisms of loss
Precision Spectroscopy of the 1S-2S Optical Clock Transition in Atomic Hydrogen (HYDROGEN 1S-2S)

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: Germany
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

Field of optical atomic standards is rapidly developing. In 2008 optical atomic clocks surpassed the precision of microwave atomic clocks for the first time. The applicant continues to work at Max-Planck Institute of Quantum Optics (MPQ) on the same project as during the MC IEF with the goal to further improve the precision of the 1S-2S optical transition frequency in hydrogen and deuterium. These are the simplest atoms that have always been in the center of quantum mechanics. At MPQ a new hydrogen experimental setup is being constructed with a novel magnetic coil gun slower that will allow further improvement of the spectral resolution of the hydrogen line. This spectrometer will be able to run continuously and is important for collaborators at CERN who want to compare the optical transition frequency in antihydrogen with that of hydrogen. A novel optical fiber link scheme between MPQ and the German time keeping institute PTB in Braunschweig is set up that will allow to measure the laser frequency stabilised to hydrogen atoms with the best optical atomic clocks at PTB. This fiber link will allow to improve measurements of the H 1S-2S transition without borrwing a portable Cs fountain clock from Paris. Optical frequency distribution via an optical fiber network among the metrology institutes in European countries is presently one of prioritary tasks as it will allow to compare the clocks much faster. Better clocks will allow to search for a possible variation of fundamental constants, make faster telecommunication networks and more precise satellite navigation. Participation in these new developments increases the potential of Dr. Alnis to pursue his carrier in research in the field of optical atomic standards. The experience of the applicant on making some of the worlds most stable lasers used for the hydrogen 1S-2S experiment is now used in two other projects where applicant’s knowledge transfer to the PhD students is very important.

Keywords: atomic physics,spectroscopy,metrology
A Novel Mathematical Framework for the Modelling and the Analysis of Transportation Networks (MANTRAS) (MANTRAS)

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: Netherlands
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

Transportation networks are ubiquitous nowadays: people move over transit links (airspace, highway systems, networks of subways and railways), trade goods through industrial networks (logistics and production networks, manufacturing systems) and assets through financial networks (market and banking systems), support their lifestyle via distribution networks (power, energy, food and water distribution systems), and communicate and exchange knowledge through information networks (based on telephone lines, satellite stations, optical grids, cable and wireless internet, postal networks and the media). A reliable, resilient, secure, efficient, and effective operation of these networks is of paramount importance both when the systems are operated to the limits of their performance during critical situations, as well as under regular operating conditions. The quest for a quantitative understanding of these networks and their properties necessitates the development of descriptive formal models to represent, analyze, and control them. Discrete Event Systems (DES) and Stochastic Hybrid Systems (SHS) are general mathematical models that, while rather different in nature, by virtue of their structural properties and dynamical features are both particularly suitable at modelling transportation networks. This project has two original objectives. The first major goal is theoretical, and is aimed at the introduction of a formal mathematical framework that is capable of connecting between the theory of DES and that of SHS. The second objective deals with the applications of this novel formal model in the description, analysis, and control of classes of transportation networks (road traffic networks and railway systems). This innovative project is expected to yield theoretical results that will be foundational for further investigations, and to originate compelling and relevant practical outcomes of considerable industrial, economic, societal, and environmental impact.

Keywords: engineering mathematics,systems and control theory,automation,hybrid systems,probabilistic models,control of transportation networks
Role of serpinB1 in cellular homeostasis in the bone marrow and the lung (SERPINB1)

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: Switzerland
Call:  (FP7-PEOPLE-2009-RG, 2009)
Start date: 2009-10-01
End date: 2013-09-30
Duration (months): 48.0
Total project cost (EUR): 100000.0
EU funding (EUR): 100000.0
Participants: 1
Project status: CLOSED

Neutrophils are short-lived leukocytes with vital functions in host defense. Neutrophils are massively recruited to extravascular sites in response to danger signals. This immediate, life saving, inflammatory response can turn against the host if its intensity and duration are dysregulated leading to tissue injury and/or failed immune response to pathogens. The dual protective/pathologic role of neutrophils is reflected by the functions of neutrophil serine proteases, potent granule enzymes that hydrolyze other proteins. Neutrophil serine proteases (or NSPs) directly kill pathogens after fusion of the NSP-rich granules with the microbe-containing phagosome. However, when released extracellularly and in excess of the anti-protease shield, NSPs are harmful by fueling the inflammatory response and by destroying extracellular matrix proteins and immune defense proteins. The aim of the proposed work is to investigate the regulation of NSPs by the serpin (SERine Protease INhibitors) family of proteins in health and disease. Specifically, we will study the role of serpinB1, one of the best inhibitors of the three NSPs: neutrophil elastase, cathepsin G and proteinase-3. We have previously shown that (i) serpinB1, a cytoplasmic inhibitor of NSPs carried at high levels in neutrophils, provides a physiological and vital shield against pathologic actions of NSPs during lung infection, and (ii) serpinB1 prevents the early death of neutrophils during infection. Our preliminary data now indicates that serpinB1 is required to preserve the size of the neutrophil reservoir in bone marrow and protects lung epithelial cells against NSPs. The proposed work will elucidate the protective functions of serpinB1 in myeloid cells and lung epithelial cells. Overall, these studies will provide highly significant advances in understanding pathologic mechanisms due to excess NSPs in bone marrow homeostasis and pulmonary disease.

Keywords: immunology,haematology