Data-Gouv-ML/pcri-actions-marie-curie-participations-et-projets-laureats huggingface dataset:
Projet CONTESSA (Horizon 2020, appel à projets 2014)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Information Science and Engineering
Statut du projet : CLOSED

The aim of this project is to develop methods for analysis of time-series based on count data. For example, detecting significant differences between two count data time series would distinguish between two different models: one in which the two time series are interchangeable, and one in which the second sample is a modification of the first, i.e. the two time series are non-interchangeable. This will broaden the target of my project to general analysis of count time-series data such as clustering, classification, perturbations inference and machine learning over sequential count data. The project will focus on count data sets from ribonucleic acid sequencing (RNA-seq) time course experiments. The method I plan to develop potentially has promising applications in a variety of multidisciplinary fields where event-counting is required, such as economics and biology. In economics, examples include the number of applicants for a job, or the number of labour strikes during a year. In biology, recent examples include high-throughput sequencing, such as RNA-seq and chromatin immunoprecipitation sequencing (ChIP-seq) analyses. These examples are especially relevant to this project because the method I will be developing enables various features of organisms to be compared through tag counts. I am enthusiastic about having the opportunity to be instrumental to a field where once developed this project will have a real impact in finding better treatments for patients with neurodegenerative diseases including amyotrophic lateral sclerosis (ALS), Alzheimer’s and Parkinson’s Disease. Professor Neil Lawrence will act as the supervisor of the fellowship and will take over responsibility for my training and development. My fellowship experience will be enriched further through a six month secondment period at University of Manchester with Professor Magnus Rattray and through the opportunity to collaborate with SITraN’s Professor Winston Hide and Biogen Idec Industry.

Mots clés : count data, time series, hypothesis testing, rna sequencing, chip sequencing, negative binomial

Participants :
- University of Sheffield (Royaume-Uni) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 195454.8 €
Projet DisMolGels (Horizon 2020, appel à projets 2016)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Chemistry
Statut du projet : CLOSED

The aim of this study is to develop molecular temporary hydrogels coupled to an energy dissipating chemical reaction (DisMolGels). Until now, most molecular self-assembled materials operate close to thermodynamic equilibrium, under static conditions, and are thus far from the interesting features biological living “materials” display. Biological materials are thermodynamically open and are kept far from equilibrium by a constant input of energy. This mode of self-assembly, one of the requirements of life, is referred to as dissipative or dynamic self-assembly. For this project I will focus on the recreation of part of such dissipative processes, and translating them to our current static hydrogel materials. With that, dynamic hydrogels with entirely new properties, most prominently their tunable lifetime and stiffness, will be developed. To do so, chemical fuels will be used as energy input and simple synthetic peptide derivatives will be constitute the self-assembling building blocks. Not only will this project result in hydrogels with a tunable lifetime and stiffness, it also aims at setting new design guidelines and requirements to develop dynamic systems. Thereby it aims at aiding the scientific community as such rules currently lack, hampering the development of these interesting systems. The ambitious research project builds on what I have already accomplished working on thermodynamically static self-assembled systems and the expertise that the host group offers in terms of dynamic materials approach. The research experience I will gain and all training received during the MSCA, will reinforce my expertise in this field and empower me to grow as an independent research leader.

Mots clés : dynamic supramolecular materials, supramolecular hydrogels, out of equilibrium systems

Participants :
- Technical University of Munich (Allemagne) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 159460.8 €
Projet AGRICADOPT (Horizon 2020, appel à projets 2015)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Social Sciences and Humanities
Statut du projet : CLOSED

Archaeologists have long debated the origins of settled farming communities, and their appearance across the world at vastly different times, attempting to establish why and how the earliest farming settlements occur where and when they do. This is particularly true for the western Nile Delta, the region within which this training-through-research project focusses, and where the first sedentary farming communities in Egypt appear at c. 5,000 BC, e.g. at Merimde Beni Salama (MBS). The proposed research will apply two key methods using sedimentary analysis to assess the local environment in the hinterland and wider regional around MBS, which will require training in 1) recording, interpretation and analysis of sediments, and 2) thin section micromorphology description and interpretation. The application of these methods aims, overall, to elucidate the environmental setting before, during and after the settlement at MBS, as well as examining climatic data to highlight changes in the suitability/necessity for permanent settlement in the area by c. 5,000 BC, addressing these aims through the questions: 1) To what extent does the transition to settled lifeways depend on the arrival of new human groups bringing with them domesticated species and new technical knowledge; 2) Are the ‘new’ Neolithic lifeways an adaptation of the preceding Epipalaeolithic way of life in the region with the integration of some new groups and new knowledge, within a changed climatic/environmental setting; and 3) was the local environment specific to the western Nile Delta fringes especially well suited for the adoption and success of agriculture. The focal time range is c. 8000-3000 BC, covering the period during which the mobile Epipalaeolithic communities were present in the region, through the Neolithic period to the end of the Predynastic period when MBS goes out of use. The research will involve comparative artefactual analysis and be set within a framework chronometric dating framework.

Mots clés : nile delta, environment, farming, neolithic, sedimentary, sedentary

Participants :
- University of Cambridge (Royaume-Uni) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 183454.8 €
Projet BARREN (Horizon 2020, appel à projets 2014)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Life Sciences
Statut du projet : CLOSED

Arid environments are habitats of energetic stringency because of extreme air temperatures and periods of decreased food and water abundance. Typically, birds confronted with these conditions reduce their energetic metabolism to be in balance with local resources. The ability to adjust energetic metabolism to face the harshness of arid habitats has been a significant question in ornithology and ecological physiology for decades. Recent evidence indicates the important role of the mitochondrial oxidative phosphorylation pathway – OxPhos – in this process. However, an effort to combine microevolutionary and physiology concepts remains to be attempted. The current advances in avian genomics combined with my background in ornithology, ecology and evolution provide the best opportunity to study adaptation to arid environments. In BARREN, I propose to integrate ecological properties of an arid environment with variation at OxPhos-related genes, and energy metabolism at cellular and organismal level in a sophisticated systems approach that, to the best of my knowledge, has never been attempted. Through placement at Copenhagen’s Centre for GeoGenetics, I will have access to one of Europe’s leading research groups in avian genomics. A short secondment at the University of Angers will confer additional training in avian physiology. BARREN offers an exceptional opportunity for me to expand on my previous knowledge through implementing a multidimensional and cutting-edge approach centred on genome-level data, in order to advance our understanding of bioenergetics in arid habitats. This project is not only pivotal for basic evolutionary research, but is relevant for one of the key issues of Horizon2020: prepare excellent scientists to address one of the major societal concerns: Fighting and adapting to climate change.

Mots clés : evolution, genomics, physiology, geospatial analysis, oxidative phosporilation pathway

Participants :
- University of Copenhagen (Danemark) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 200194.8 €
Projet END-osperm (Horizon 2020, appel à projets 2020)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Life Sciences
Statut du projet : TERMINATED

Around 60% of our daily diet is directly derived from cereal grains. In the grain, most nutrients are stored in a highly specialized reserve tissue called the starchy endosperm (SE). SE development ends by the execution of a controlled cell death program (PCD), which leaves the nutrient-filled cell corpses largely intact. PCD has been proposed to be crucial for storage compound preservation, but despite this potential importance, surprisingly little is known on the genetic regulation of SE PCD. In this project, I hypothesise that cereal SE PCD is controlled by a gene regulatory network that I propose to investigate in maize (Zea mays). To this end, I will combine the extensive knowledge I acquired during my PhD on maize kernel development with the well-documented expertise of the host lab in plant PCD analysis. I will first determine the spatio-temporal pattern of SE PCD under the growth conditions of the host institute and characterise its subcellular features in detail by ultrastructural analyses. As SE PCD is not executed homogenously in time and space, I propose to perform then a single-nucleus RNA-seq combined with a spatial transcriptomics approach on dissected endosperm tissue in order to obtain transcriptome profiles and developmental trajectories with single-cell resolution. Based on their expression profiles, I will finally select up to 20 PCD-associated candidate transcription factors and screen them for gain-of-function PCD phenotypes in transient expression systems. Promising candidates will be functionally analysed in maize SE via gain- and loss-of-function approaches. In the resulting maize lines, I will investigate the changes in PCD progression and use them to assess the physiological relevance of a correct PCD execution in the SE. In sum, this project will generate the first functional insights on the gene regulatory networks of cereal SE PCD and will provide new leads for future agronomic applications.

Mots clés : endosperm, programmed cell death, seed, grain, maize

Participants :
- Vlaams Instituut voor Biotechnologie (Belgique) — Coordinator, beneficiary, Recherche, subvention : 166320.0 €
Projet UNNAMEd-2 (Horizon 2020, appel à projets 2017)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Life Sciences
Statut du projet : CLOSED

Around 90% of all cancer-related deaths are due to metastasis. Understanding the process of cancer metastasis is therefore of urgent need to develop new treatments. Aberrant expression of the epidermal growth factor receptor (EGFR), or increased availability of its ligands promote tumour survival and metastasis in multiple cancers. As a result, several anti-EGFR therapeutics are in clinical use, but almost all patients will develop resistance against the treatment. Another strategy to treat EGFR driven cancers is to reduce the pool of available EGFR ligands. The crucial enzyme in EGFR ligand release is A Disintegrin And Metalloproteinase (ADAM) 17. I have unpublished data showing that depletion of ADAM17 significantly inhibits colon cancer growth and metastasis in vivo. However, anti-ADAM17 therapies have failed clinically and thus, we urgently need to understand the regulation of ADAM17. Recent discoveries by Dr. Kveiborg’s group, and collaborators showed that the protein phosphatase PP2A binds to ADAM17, and negatively regulates EGFR ligand release, thereby representing the first known negative regulator for ADAM17. Based on these novel findings, I hypothesize that the PP2A-ADAM17-EGFR axis has the ability to control cancer metastasis. To test this hypothesis, I aim to characterize the functional impact of the PP2A-ADAM17 interaction in cancer spread by creating ADAM17 mutants with different PP2A binding properties in colon cancer cells using CRISPR/Cas9 and functionally evaluate these cells in vitro and in zebrafish and mouse models. Moreover, I aim to unravel the molecular mechanisms of the interplay; applying SILAC coupled mass spectrometry and mutagenesis screening, to evaluate the mechanism by which PP2A affects ADAM17, and the signals involved in PP2A binding. This work will pave the way for the development of novel anti-cancer drugs and thereby expand the therapeutic choices for EGFR driven cancers and improve the patient survival.

Mots clés : pp2a, a disintegrin and metalloproteinase  adam, colorectal cancer, metastasis

Participants :
- University of Copenhagen (Danemark) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 200194.8 €
Projet PhyloPycno (Horizon 2020, appel à projets 2020)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Environment and Geosciences
Statut du projet : SIGNED

Arthropoda (e.g. insects, crustaceans, spiders and centipedes) comprises the majority of animal biodiversity and includes model organisms like the fruitfly Drosophila melanogaster. A rich fossil record, abundant genomic information, high morphological disparity, and unparallelled diversity, have made arthropods a key model system for macroevolution. Yet, our understanding of arthropod evolution remains incomplete. In part, this is because alternative interpretations of their morphology support different evolutionary hypotheses. For example, the phylogeny of total-group Chelicerata (i.e. the living chelicerates – e.g. sea spiders, horseshoe crabs, spiders and scorpions – and all fossils more closely related to these than to any other arthropod) depends on alternative interpretations for the origin of the chelicerae. These pincer-like first head appendages are found in all living chelicerates, but it is unclear whether they are primitive, derived, or converging characters. Central to this debate are the sea spiders (Pycnogonida), a poorly-understood, marine, chelicerae-bearing lineage, dissimilar in many respects to other chelicerates. It has been suggested that pycnogonids might not be chelicerates and that chelicerae might be convergent or a primitive trait for Arthropoda, which would necessitate a reassessment of early arthropod evolution. Here, I will use a cutting edge computed tomography approach to provide the first detailed study of fossil pycnogonid morphology, and to generate a new morphological dataset spanning all key arthropod taxa. Bayesian and Maximum Likelihood-based total evidence approaches will then be used to combine the new morphological dataset with genomic data and test hypotheses of (1) chelicerate and arthropod relationships, (2) the evolution of the arthropod body plan, (3) the origin and diversification rate of the highly divergent Pycnogonida, and (4) to estimate an evolutionary timescale for Pycnogonida and Chelicerata.

Mots clés : pycnogonida, chelicerata, total evidence phylogeny, phylogenomics, diversification, tree dating, evolutionary timescales, tomography

Participants :
- University of Bristol (Royaume-Uni) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 212933.76 €
Projet GreenML5G (Horizon 2020, appel à projets 2019)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Information Science and Engineering
Statut du projet : CLOSED

Artificial Intelligence (AI) is revolutionising a wide range of industries. Wireless networks with emerging high dimensional challenges are set to benefit from data-driven deep learning optimisation across layers. In particular, we expect that the deep supervised and deep reinforcement learning modules can resolve high-dimensionality inputs, achieve near optimal solutions, and efficiently scale via confederated learning. However, what is not well understood is the energy cost and carbon footprint of AI in future wireless networks. The danger is that intelligent networks are not green networks and that the recent progress made in green communication risk being undermined by the new breed of AI-based wireless communication. Here, in this project, we propose to develop green machine learning algorithms for radio resource management. This will lead to a future of intelligent and sustainable wireless networking.

Mots clés : resource management, energy efficiency

Participants :
- Cranfield University (Royaume-Uni) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 224933.76 €
Projet PhotoArM (Horizon 2020, appel à projets 2018)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Chemistry
Statut du projet : CLOSED

Artificial metalloenzymes have recently emerged as powerful tools to address the ever-growing requirements of chemistry to become more efficient and sustainable. This methodology involves anchoring a reactive transition metal catalyst within a protein to exploit the secondary coordination sphere created around the new active site, which can induce selectivity in reactions and improve turnover numbers. Concomitantly, photoredox and metallophotoredox catalysis, where a small quantity of a light sensitive compound allows non-traditional reactivity though open shell reactive intermediates, has also developed dramatically in recent years. The impressive reaction repertoire is especially synthetically attractive due to the mild conditions required and the ability to activate abundant and generally more inert functional groups. However, the current drawback to this methodology is the high levels of control needed to give the reactions their full synthetic potential. This is where the two fields display complementarity with an unexplored interface: Photoredox Artificial Metalloenzymes. By anchoring a nickel catalyst inside an enzyme pocket with a nearby photocatalyst, it should be possible to control catalytic reactivity by mutagenesis of residues in the secondary coordination sphere. In the proposed case of an sp3-sp3 cross-coupling reaction between a racemic amino acid derivative and bromoalkane, this could potentially allow control over both new stereocentres independently to achieve stereodivergent catalysis. It is subsequently proposed that this methodology could be adapted to include intramolecular cross-coupling reactions, which would beneficially allow access to the valuable monocyclic β-lactam scaffold from suitably functionalised linear substrates. If possible, this may allow efficient access to diastereoisomers potentially difficult to access by other means, which may hold unexplored pharmaceutical potential.

Mots clés : artificial metalloenzymes, directed evolution, stereodivergent catalysis, biocatalysis, nickel, high throughput screening

Participants :
- University of Basel (Suisse) — Coordinator, beneficiary, Enseignement supérieur ou secondaire, subvention : 191149.44 €
Projet TPANN (Horizon 2020, appel à projets 2016)
Action : Postdoctoral Fellowships - European Fellowships
Panel : Information Science and Engineering
Statut du projet : CLOSED

Artificial neural networks have been shown to offer a powerful computing approach to encounter many classification problems as in synthetic vision (e.g. autonomous driving) and artificial intelligence (e.g. AlphaGo). While their implementations are often based on power-hungy CPU- and GPU-installations, first researchers have delivered initial application-specific solutions that demonstrate FPGAs to be a feasible and efficient alternative. This proposal aims at providing a generic reference implementation of ANNs on FPGAs that is tunable towards various application needs by parametrization. Since individual FPGA designs establish enormous costs of entry due to a higher engineering effort on a lower abstration level, an IP core that is available out of the box is a great R&D incentive that enables more researchers and engineers to embrace the emerging efficient heterogeneous computing more quickly and produce innovations and more compact and more efficient products on this basis. Besides this technological advance, this proposal enables a researcher with an enormous experience in mapping computations into FPGA hardware to make a valuable industrial experience in an international context with the major company in this domain. His expertise is ideally complemented with the application experience available at Xilinx who will benefit from opening a new growing market for manufactured FPGA devices. The development of the researcher's skill set is explictly addressed by complementing his academic background with industrial experience and scheduled cooperate trainings. As part of the dissemination activities, his network into the FPGA community is strengthened and approaches towards the ANN community are made.

Mots clés : heterogeneous computing, fpga, artificial neural networks, cognitive computing, ip core

Participants :
- Xilinx (Ireland) (Irlande) — Coordinator, beneficiary, Organismes privés (hors enseignement), subvention : 93933.0 €