Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Large scale interactions in brain networks and their breakdown in brain diseases (BRAINSYNC)

Framework: FP7 — Cooperation
Programme: Health
Destination: Translating research for human health
Action type: Collaborative project
Countries involved: Italy,Belgium,Netherlands,France,United Kingdom,Spain,Czechia,Germany
Call:  (FP7-HEALTH-2007-A, 2007)
Start date: 2008-03-01
End date: 2011-02-28
Duration (months): 36.0
Total project cost (EUR): 3933811.0
EU funding (EUR): 2978242.0
Participants: 8
Project status: CLOSED

The long-term goal of this project is to understand how neuronal assemblies exchange information (functional or neuronal communication), and how variability in neuronal communication explains variability in behavioural performance, both in the intact and injured brain. Communication involves temporal interactions between neuronal assemblies either locally within an area or large-scale between areas. We concentrate on large-scale interaction that occur at two different temporal scales: 'slow' (<0.1 Hz) fluctuations of the blood oxygen level dependent (BOLD) signal easily measured with functional magnetic resonance imaging (fMRI), and 'fast' (1-150 Hz) neuronal oscillations measured at high (multi-unit activity (MUA), local field potential (LFP)) or low (electroencephalography, EEG; magnetoencephalography, MEG) spatial resolution. We wish to demonstrate that these two phenomena are mechanistically linked and are behaviorally significant. A potentially important clinical application is the development of easy-to-use diagnostic measures of neuronal communication for many brain diseases such as stroke, traumatic head injury, multiple sclerosis, and Alzheimer's disease.

Keywords: cortical dynamics,neuronal coding,oscillations,functional connectivity,fmri,local field potential,vision,attention,behavior,microstimulation,tms,modeling,multiple sclerosis,schizophrenia
Exploring applications of spatial-map and velocity-map imaging mass spectrometry (IMAGEMS)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Physical and Analytical Chemical sciences
Countries involved: United Kingdom
Call:  (ERC-2007-StG, 2007)
Start date: 2008-06-01
End date: 2013-05-31
Duration (months): 60.0
Total project cost (EUR): 1499969.0
EU funding (EUR): 1499969.0
Participants: 1
Project status: CLOSED

Our aim is to develop a next-generation mass spectrometer with unique imaging capabilities. For each mass, the new instrument will image the complete velocity or spatial distribution of the ions at their point of formation. The velocity distributions of fragment ions are highly sensitive to the detailed dynamics of the fragmentation process, such that in velocity imaging mode the new instrument will provide a powerful alternative to conventional tandem mass spectrometry approaches for fragmentation studies. In addition to the mechanistic and structural information encoded the images, the set of photofragment velocity distributions constitutes a unique ‘fingerprint’ for the parent molecule that may be used in molecular identification. In spatial imaging mode, there are clear applications in the areas of surface analysis and high throughput sampling, both of which will be explored over the course of the project. The spectrometer will utilise the method of velocity/spatial-map imaging, a technique originally developed for studying the photofragmentation dynamics of small molecules. A standard velocity-map imaging measurement yields the detailed speed and angular distributions for a single fragment. However, by employing advanced detector technology, our instrument will be capable of recording such distributions for all fragments simultaneously, opening the way for the study of much larger molecules with complex fragmentation pathways. A working prototype of the spectrometer will be constructed within the first year of the project, with further developments and improvements taking place over the remaining four years. The instrument will be calibrated using results from previous studies, and its capabilities in both spatial and velocity-map imaging modes will then be explored using a number of carefully chosen chemical systems. These include fundamental dynamics studies, ultraviolet photodissociation of peptides, and imaging of biomolecules and single cells on surfaces.

Keywords: mass spectrometry,imaging
Genotype-To-Phenotype Databases: A Holistic Solution (GEN2PHEN)

Framework: FP7 — Cooperation
Programme: Health
Destination: Biotechnology, generic tools and medical technologies for human health
Action type: Collaborative project
Countries involved: United Kingdom,Germany,Spain,Netherlands,France,Sweden,Greece,Finland,Portugal,South Africa,India,Switzerland,United Kingdom,Germany,Iceland,Belgium,Greece,Sweden,Netherlands
Call:  (FP7-HEALTH-2007-A, 2007)
Start date: 2008-01-01
End date: 2013-06-30
Duration (months): 66.0
Total project cost (EUR): 14816974.92
EU funding (EUR): 11889367.0
Participants: 23
Project status: CLOSED

The GEN2PHEN project aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and to link this system into other biomedical knowledge sources via genome browser functionality. The project will establish the technological building-blocks needed for the evolution of today’s diverse G2P databases into a future seamless G2P biomedical knowledge environment. The project will then utilise these elements to construct an operational first-version of that knowledge environment, by the projects end. This will consist of a European-centred but globally-networked hierarchy of bioinformatics GRID-linked databases, tools and standards, all tied into the Ensembl genome browser. The project has the following specific objectives: 1) To analyse the G2P field and thus determine emerging needs and practices; 2) To develop key standards for the G2P database field; 3) To create generic database components, services, and integration infrastructures for the G2P database domain; 4) To create search modalities and data presentation solutions for G2P knowledge; 5) To facilitate the process of populating G2P databases; 6) To build a major G2P internet portal; 7) To deploy GEN2PHEN solutions to the community; 8) To address system durability and long-term financing; 9) To undertake a whole-system utility and validation pilot study GEN2PHEN Consortium members have been selected from a talented pool of European research groups and companies that are interested in the G2P database challenge. Additionally, a few non-EU participants have been included to bring extra capabilities to the initiative. The final constellation is characterised by broad and proven competence, a network of established working relationships, and high-level roles/connections within other significant projects in this domain.

Keywords: genetic variation,genotype to phenotype,database integration,grid,biomedical knowledge,disease genetics,model organisms,genome browser,bioinformatics,association studies,clinical diagnostics
Innovative contrast imaging by non-linear optics (NLO) for the observation of biological tissues in vivo and in real time, at cellular and molecular levels (CARS EXPLORER)

Framework: FP7 — Cooperation
Programme: Health
Destination: Biotechnology, generic tools and medical technologies for human health
Action type: Collaborative project
Countries involved: France,Belgium,Germany,United Kingdom
Call:  (FP7-HEALTH-2007-A, 2007)
Start date: 2008-03-01
End date: 2011-08-31
Duration (months): 42.0
Total project cost (EUR): 4701881.0
EU funding (EUR): 3091129.0
Participants: 7
Project status: CLOSED

The CARS EXPLORER seeks to demonstrate the concept of innovative light-based contrasting technologies for functional in situ imaging in life science and biomedical research. Our ultimate goal is to develop an endoscope based on non-linear optics (NLO) and laser pulse phase shaping. Non linear laser pulse interactions with living tissues provide unique possibilities, such as an absence of sample preparation, direct multiparametric visualization with molecular specificity and cellular resolution, and deep sample penetration. Nevertheless, the effective transfer of NLO to biomedical applications faces major technological challenges related to the delivery of ultra-short laser pulses, the weakness of the signal produced in biological samples and the difficulty in interpreting generated contrasts. Therefore, the CARS EXPLORER interdisciplinary consortium includes partners with expertise ranging from optical physics to the clinic. The work plan is split into 5 RTD workpackages: three are intended to overcome specific technological problems with (1) the development of dedicated methodology using phase shaping for NLO imaging of deep biological tissues, (2) the development of specific photonic crystal fibre optics for the excitation, delivery and collection of NLO signals, and (3) the extraction of relevant information from NLO signals generated in biological tissues. The two other workpackages will determine the assets and constraints in NLO imaging through appropriate experimental biological models. These models will also assess each technological improvement made on the microscope and endoscope prototypes. Last, to bring the concept to the diagnostic level, we will explore the molecular and morphological NLO signatures associated with tumor development in skin cancer. In addition to the challenge of developing pulse shaped NLO-based endoscope technology, this project will have strategic and economic impact by providing a non-invasive functional exploration method.

Keywords: non-linear optics,photonic crystal fibres,pulsed shaping techniques,endoscopy,animal model of cancer
A combined experimental and computational approach for quantitative and mechanistic understanding of transcriptional regulation (TRANSCRIPTION_REG)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Genetics,Genomics,Bioinformatics and Systems Biology
Countries involved: Israel
Call:  (ERC-2007-StG, 2007)
Start date: 2008-07-01
End date: 2013-06-30
Duration (months): 60.0
Total project cost (EUR): 1005600.0
EU funding (EUR): 1005600.0
Participants: 1
Project status: CLOSED

The complex functions of a living cell are carried out through the coordinated activity of many genes. Since transcription is a key step in establishing such coordinated activity, much effort was devoted to its study, and tremendous progress was made in identifying many of the transcription factors and regulatory DNA elements involved in the regulation of specific systems. However, very few attempts were made at going beyond these phenomenological and qualitative descriptions. Consequently, we are far from a quantitative and predictive understanding of transcriptional regulation. Through this program, I aim to develop a mechanistic understanding of transcriptional regulation, and for the first time model the entire process. We wish to go much beyond identifying and qualitatively describing the involved components, and arrive at a quantitative understanding of how transcriptional programs are encoded in the DNA sequences. To this end, my team and I will first work to mechanistically understand various building blocks of the transcriptional system, including: mechanisms of activation and repression; binding cooperativity; binding competition; transcription factors and chromatin interplay; architectural features of promoters that are important for its function; and the transcription functions “computed” by promoters. Since existing data are clearly insufficient for addressing such questions, I have opened an experimental lab and began to assemble a multidisciplinary team of scientists whose expertise span the experimental biology, computer science, physics, statistics, and mathematics disciplines, that will work synergistically to generate the appropriate data, analyze it, and use it to construct and experimentally validate models for the above transcriptional building blocks. We will then integrate all the insights gained into unified and quantitative models that should significantly enhance our understanding of the mechanistic workings of transcriptional regulation.

Keywords: probabilistic models,chromatin and transcription regulation
Affording Recovery In Stroke (ARISE)

Framework: FP7 — Cooperation
Programme: Health
Destination: Translating research for human health
Action type: Collaborative project
Countries involved: Germany,Finland,Sweden,Germany,Spain,United Kingdom,France,Switzerland,Poland,Belgium,Denmark,Germany,Germany,Germany
Call:  (FP7-HEALTH-2007-A, 2007)
Start date: 2008-03-01
End date: 2013-08-31
Duration (months): 66.0
Total project cost (EUR): 16246309.14
EU funding (EUR): 11246776.0
Participants: 17
Project status: CLOSED

Stroke poses a massive clinical, social and economic burden, yet we have very limited effective therapies. This inadequacy is in spite of intensive research efforts and numerous failed clinical trials. Leading European stroke researchers and clinicians with a track record of established cooperation will share their complementary expertise, and team up with SME partners with high profile R&D and ongoing, promising clinical trials. Based on a thorough reexamination of the failures and bottlenecks of previous attempts to develop effective therapies for stroke, the ARISE consortium proposes an integrative and innovative approach to overcome the translational roadblock. ARISE research will result in a number of novel, promising therapies, including safer thrombolytics, modulators of the immune system and inflammation, compounds inducing or mimicking endogenous neuroprotection, therapies to induce repair of lost function, as well as a fast way to selectively cool the brain. We will work on a common model and methods platform, in which for the first time relevant comorbidities, gender, age, and long term outcomes will be investigated. Training of young researchers will lead to a standardisation and harmonisation of laboratory practices within the consortium, and implement the standard operating procedures generated by the consortium. Importantly, the ARISE consortium combines expertise in clinical as well as preclinical stroke research. To obtain clinical proof of principle and to translate our findings into effective therapy of stroke, ARISE is conducting clinical trials and has established a dedicated clinical platform to (1) provide advice to the basic researchers of the consortium with regard to clinically relevant questions and modelling, (2) to periodically review the ongoing development of innovative therapies, and to (3) ultimately take the most promising preclinical strategy developed by the ARISE consortium into a multicenter randomized clinical trial.

Keywords: stroke,clinical,neuroprotection,preclinical,recovery,regeneration,therapy,translational research
EUROpean consortium on NEUTralising antibodies using gp41 (EURONEUT-41)

Framework: FP7 — Cooperation
Programme: Health
Destination: Translating research for human health
Action type: Collaborative project
Countries involved: France,Germany,Spain,Germany,Denmark,France,United Kingdom,Austria,Hungary,France,United Kingdom,France,France,Haiti,Switzerland
Call:  (FP7-HEALTH-2007-A, 2007)
Start date: 2008-01-01
End date: 2014-03-31
Duration (months): 75.0
Total project cost (EUR): 15922033.23
EU funding (EUR): 11966082.0
Participants: 19
Project status: CLOSED

There is now an increasingly solid body of scientific evidence which demonstrates that the binding of small molecular weight compounds, peptides and antibodies (Abs) to fusion-intermediate conformations of gp41 leads to an inhibition of HIV cell entry. The principal aim of this project is to exploit this information by establishing a platform where gp41-derived vaccine candidates will be designed to elicit neutralising Abs. Several families of immunogens which mimic gp41 in its fusion intermediate conformations are already available and others will be designed using modelisation approaches. Candidates will be submitted to a thorough biophysical characterisation followed by a preclinical development in order to identify the most promising for clinical evaluation. A crucial selection parameter is the capacity of antigens to elicit neutralising Abs using internationally standardized assays. Since sexual transmission accounts for more than 90% of HIV infection, the capacity of Abs to inhibit infection at the mucosal level will also be determined. This cross-disciplinary project gathers top European scientists with expertise in protein engineering and characterisation, adjuvantation, formulation for systemic and mucosal delivery, evaluation of functional antibody response, efficacy testing in animal models, medium to large scale vaccine production as well as conduct of clinical trials in both developed and third-world countries. In contrast to previous more empirical attempts, this project is based on the rational exploitation of the knowledge on the mechanism of HIV entry and is thus a promising approach to generate a protective vaccine. It will be the first European project targeting intermediate conformations of gp41 and it could complement/synergize other international strategies focusing on the membrane proximal region of gp41 or gp140 trimer to induce neutralising Abs or aiming at reducing the viral load by eliciting a cellular immunity against HIV.

Keywords: gp41fusion-intermediate,gp41 hybrid proteins,neutralising antibody,systemic and mucosal immunity
Paediatric European Network Treatment AIDS Laboratory Network (PENTA LABNET) (PENTA-LABNET)

Framework: FP7 — Cooperation
Programme: Health
Destination: Translating research for human health
Action type: Coordination and support actions
Countries involved: Italy,United Kingdom,France,Netherlands,United Kingdom,Netherlands,Italy,France,Switzerland
Call:  (FP7-HEALTH-2007-A, 2007)
Start date: 2008-05-01
End date: 2012-07-31
Duration (months): 51.0
Total project cost (EUR): 1132977.4
EU funding (EUR): 1000000.0
Participants: 12
Project status: CLOSED

PENTA-LABNET(PL) is a coordination action aimed at improving the range of products and clinical use of antiretrovirals(ARVs) in HIV-infected children in resource-rich and resource-limited countries. This will be achieved through building capacity of laboratories to undertake co-ordinated studies on pharmacokinetics, pharmacodynamics and pharmacogenetics of new formulations and dosing and studies of viral and immune responses to novel regimens and strategies for using ARVs in children. PL forms a logical, necessary and cost-effective addition to the clinical-trial-focused research activities of the longstanding PENTA network, building on its existing operational infrastructures and expertise. To respond to emerging needs identified by EU as priority areas, the aim of PL is the development of a “drug centred” research platform, which will provide a complimentary range of activities focussed on supporting the rational selection of optimal dosage and delivery forms of ARVs, and providing the lab basis for evaluating new ARVs strategies in children. The definition, organisation and management of integrated pharmacological and viro/immunological studies to better characterise the concentration-exposure-effect relationship will be a central activity of PL. In support of these studies, standardised data collection systems will be established enabling linkage of clinical and laboratory data. In addition a central biobank will be set up to provide rapid identification of samples to be used for research. The laboratory and paediatric expertise generated in PL will support rapid assessment of new and existing individual and combined ARVs. The WHO will be a key partner of PL to define research priorities in ARV drug development and (also through PENTA’s extensive international links) to rapidly disseminate results to a range of stakeholders (e.g. EMEA and industries) and support the rapid translation of research findings into guidelines and practice for children in all settings

Keywords: coordination,penta,hiv/aids,paediatrics,pharmacology,pharamcokinetics,viroimmunology,formulations,drug formulations
The interaction and the genetic basis of naturally versus sexually selected traits in the adaptive radiations of cichlid fishes (INTERGENADAPT)

Framework: FP7 — Ideas
Programme: European Research Council
Theme: European research council
Destination: Starting grants
Action type: Support for frontier research (ERC)
Panel: Neurosciences and neural disorders
Countries involved: Switzerland
Call:  (ERC-2007-StG, 2007)
Start date: 2008-08-01
End date: 2013-07-31
Duration (months): 60.0
Total project cost (EUR): 750000.0
EU funding (EUR): 750000.0
Participants: 1
Project status: CLOSED

The question of how variation in the DNA translates into organismal diversity has puzzled biologists for decades. Despite of recent advances in evolutionary and developmental biology, the molecular mechanisms that underlie diversification, adaptation and evolutionary innovation remain largely unknown. The exceptionally diverse species flocks of cichlid fishes in the East African Great Lakes are textbook examples for adaptive radiations, and emerge as excellent model systems to study the genetic basis of biodiversity. East Africa’s hundreds of endemic cichlid species are akin a natural mutagenesis screen and differ greatly in ecologically relevant and, hence, naturally selected characters such as mouth morphology, but also in sexually selected traits such as coloration. Here, I propose to study the relative adaptive relevance and the molecular basis of characters that contributed to the origin of the cichlids’ astonishing species-richness, making the underlying genetic pathways prime targets in the quest of “speciation genes”. Specifically, I aim to focus on three unique characters of cichlids: (i) thick lips that evolved independently in different cichlid assemblages; (ii) the highly adaptable pharyngeal jaw apparatus; and (iii) egg-dummies on the anal fins of male haplochromines, which play an important role in the breeding cycle of these mouthbrooding fishes. A major goal of this project is to test whether the same developmental and genetic pathways are involved in the origin of evolutionary parallelisms in cichlid radiations. To this end, I will use gene expression, RT-PCR and in situ hybridization experiments to compare thick-lipped species, parallel pharyngeal jaw morphologies and similar color patterns on fins of cichlids of different assemblages, as well as the egg-spots of haplochromines to those of unrelated ectodine cichlids, in which similar dummies have evolved independently and on a different fin. Finally, I intend to compare the genes underlying these characters in an evolutionary genomic framework in order to evaluate the relative strength and the type of selection that has acted on loci involved in the morphogenesis of naturally versus sexually selected traits in cichlid adaptive radiations.

Keywords: evolutionary genomics