Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Making more with less: intelligent wavefront design to enable high resolution images of unstable samples. (BeamSense)

Framework: Horizon 2020 — Excellent Science
Programme: Marie-Sklodowska-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Individual Fellowships (IF)-Reintegration panel
Action type: Marie Skłodowska-Curie actions
Panel: Physics
Countries involved: United Kingdom
Call: Individual Fellowships (H2020-MSCA-IF-2019, 2019)
Start date: 2020-11-01
End date: 2022-10-31
Duration (months): 24.0
Total project cost (EUR): 224933.76
EU funding (EUR): 224933.76
Participants: 1
Project status: CLOSED

The resolution of images formed using scanning transmission electron microscopes (STEMs) is no longer limited by optical limits of the microscope, but instead by sample damage during acquisition. The image is formed by a highly focused beam of electrons being scanned across the specimen, with diffraction intensities recorded at each probe position. However, the beam can also cause localised heating and rearrangement of the atomic structure – and it is this movement that ultimately limits the image quality. Electron-beam-induced specimen damage is particularly severe for weakly-bound compounds, such as battery materials, photovoltaics or pharmaceuticals. The inability to visualise the atomic structure of these materials easily is a severe impediment to research progress in their respective fields. Overcoming the beam-damage roadblock would have a profound impact across many scientific disciplines. This can be achieved by significantly reducing the number of electrons required to form an image. The mechanics of image formation in STEMs is largely unchanged since their first demonstration 80 years ago: the probe is formed by illuminating a circular aperture with a planar electron wave, brought to a focus on the sample and raster scanned. Portions of the scattered intensity are collected to determine the intensity of the pixel associated with each probe position. Electron detectors have developed significantly in recent years - while the probe-forming apertures have received less attention. A circular aperture creates a probe with broad tails, and an image with only weak contrast, thus requiring many electrons to achieve good signal-to-noise. I have previously developed methods to reshape the electron beam to generate angular momentum. In this work, I will apply related methods to increase the image contrast by intelligent shaping of the wave front. This will reduce the required electron dose, and thus enable atomic resolution STEM imaging of beam sensitive materials.

Keywords: transmission electron microscopy,phase contrast,beam shaping,ptychography
Advanced Reasoning in Arithmetic Theories (ARiAT)

Framework: Horizon 2020 — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Starting grants
Action type: ERC actions
Panel: Computer science and informatics
Panel description: Informatics and information systems, computer science, scientific computing, intelligent systems
Countries involved: United Kingdom,United Kingdom
Call: ERC Starting Grant (ERC-2019-STG, 2019)
Start date: 2020-01-01
End date: 2024-12-31
Duration (months): 60.0
Total project cost (EUR): 1481864.0
EU funding (EUR): 1421479.0
Participants: 2
Project status: SIGNED

Arithmetic theories are logical theories for reasoning about number systems, such as the integers and reals. Such theories find a plethora of applications across computer science, including in algorithmic verification, artificial intelligence, and compiler optimisation. The appeal of arithmetic theories is their generality: once a problem has been formalised in a decidable such theory, a dedicated solver can in principle be used in a push-button fashion to obtain a solution. Arithmetic theories are also of great importance for showing decidability and complexity results in a variety of domains. Decision procedures for quantifier-free and linear fragments of arithmetic theories have been among the most intensively studied and impactful topics in theoretical computer science. However, emerging applications require more expressive theories, including support for quantifiers, counting, and non-linear functions. Unfortunately, the lack of understanding of the computational properties of such extensions means that existing decision procedures are not applicable or do not scale. The overall goal of this proposal is to advance the state-of-the-art in decision procedures for expressive arithmetic theories. To this end, starting with a recent breakthrough made by the PI, we will develop novel and optimal quantifier-elimination procedures for linear arithmetic theories, which we plan to eventually integrate into mainstream SMT solvers. Furthermore, we aim to improve complexity bounds and push the decidability frontier of extensions of arithmetic theories with counting and non-linear operations. The proposed research requires to tackle long-standing open problems---some of them being decades old. In short, the project will lay algorithmic foundations on which next-generation decision procedures and reasoners for arithmetic theories will be built.

Keywords: logic in computer science,arithmetic theories,decision procedures,algorithmic verification,quantifier elimination,counter machines
What drives the RAN translation and why do we get neurodegenerative disease when it goes wrong? (Prot-RAN)

Framework: Horizon 2020 — Spreading excellence and widening participation
Programme: Widening participation and spreading excellence
Theme: Other Widening
Action type: Marie Skłodowska-Curie actions
Countries involved: Poland
Call: Widening Fellowships (H2020-WF-02-2019, 2019)
Start date: 2020-07-01
End date: 2023-03-24
Duration (months): 24.0
Total project cost (EUR): 149625.6
EU funding (EUR): 149625.6
Participants: 1
Project status: CLOSED

The short tandem repeats are common in human genome, but their uncontrolled expansions may lead to several inherited disorders. In Prot-RAN project, I will focus on the expansion of trinucleotide CGG repeats (CGGexp) in the 5’UTR of fragile X mental retardation 1 (FMR1) gene, which causes common neurodegenerative disease, known as fragile X-associated tremor/ataxia syndrome (FXTAS). The pathogenesis of FXTAS remains unclear, and one of the possible mechanisms, the repeat associated non-AUG initiated (RAN) translation, can be shared in majority of microsatellite expansion diseases, as it was already linked to 9 different disorders. In FXTAS, the CGGexp enhances RAN translation from the 5’UTR of FMR1 mRNA, what leads to the production of toxic polyglycine or polyalanine containing proteins. These aberrant products accumulate in nuclear inclusions in the brain of FXTAS patients, impairing the nuclear lamina architecture and leading to neuronal death. The RAN translation mechanism is still not well understood; therefore, in the proposed project I will identify and investigate the role of proteins implicated in RAN translation initiation/elongation. To achieve this goal, I will benefit from the synergy between my long-time experience in mass spectrometry and the expertise of the host lab in RNA biology, and I will bridge cutting-edge proteomics with RNA biology techniques. Briefly, I will employ the CGGexp RNA-targeting pull-down approaches combined with proteomic profiling, RNA mutagenesis, high throughput protein expression analysis and RNA/protein interaction studies in a context of their functional implications. The role of identified proteins will be then verified in other expansion disorders, e.g. Huntington’s disease, giving insight into more global view of the RAN translation. As a result, the discovered factors driving RAN translation and knowledge of mechanism of their action could be used as potential new targets for therapeutic strategies.

Keywords: fragile x associated tremor,ataxia syndrome,non aug initiated ran translation,microsatellite expansion disorders,cgg repeat expansion,rna protein interactions
Bringing a breakthrough e-nose solution on global markets for portable and reliable food safety and quality control (Global PERES)

Framework: Horizon 2020 — Industrial Leadership
Programme: Information and Communication Technologies
Action type: SME instrument
Countries involved: Lithuania
Call: Open Disruptive Innovation Scheme (implemented through the SME instrument) (H2020-SMEINST-1-2014, 2014)
Start date: 2014-10-01
End date: 2014-12-31
Duration (months): 3.0
Total project cost (EUR): 71429.0
EU funding (EUR): 50000.0
Participants: 1
Project status: CLOSED

Possibility for a reliable and effective food quality assessment at a consumer level would be of paramount importance both in industrialized and less developed countries as it will have tremendous implications in health (avoidance of food poisoning) and economic domains (avoidance of food waste). The issues of food poisoning and their consequences constitute a major social problem. According to the World Health Organization more than 200 diseases are spread through food. Furthermore, one person in three in industrialized countries may be affected by foodborne illness each year. The issue of proper assessment of food quality and whether it is still edible or already not is also of immense economic importance. According to the statistics of the European Commission, about 90 million tonnes of food is wasted annually in Europe. Currently, there is no single, portable device available to consumers that would support them in ascertaining in a reliable way: a) whether a food product is fresh, b) whether it might be potentially hazardous to health, c) whether there is a risk of food poisoning, and d) whether it is still safe to be consumed. Hence, the overall aim of this project is to provide a breakthrough solution to the above mentioned societal and economic challenges by delivering fully functional, market ready, unique and innovative at a world level electronic device (“electronic nose”) and mobile application to determine the quality and level of freshness of meat, poultry, fish and other grocery products. The PERES prototype has been developed and demonstrated to work. The expected, targeted outcome of this innovation project is a commercially mature, enhanced PERES device that will be subsequently demonstrated on the global markets.

Keywords: electronic nose,food safety,food quality control
DiseasE-FreE social life without Antibiotics resisTance (DEFEAT)

Framework: Horizon 2020 — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Consolidator grants
Action type: ERC actions
Panel: Environmental Biology, Ecology and Evolution
Panel description: Ecology, biodiversity, environmental change, evolutionary biology, behavioural ecology, microbial ecology, marine biology, ecophysiology, theoretical developments and modelling
Countries involved: Denmark
Call: ERC Consolidator Grant (ERC-2017-COG, 2017)
Start date: 2018-06-01
End date: 2023-11-30
Duration (months): 66.0
Total project cost (EUR): 1998809.0
EU funding (EUR): 1998809.0
Participants: 1
Project status: SIGNED

The application of antimicrobial compounds produced by hosts or defensive symbionts to counter the effects of diseases has been identified in a number of organisms, but despite extensive studies on their presence, we know essentially nothing about why antimicrobials do not trigger rampant resistance evolution in target parasites. In stark contrast to virtually any other organism, fungus-farming termites have evolved a sophisticated agricultural symbiosis that pre-dates human farming by 30 million years without suffering from specialised diseases. I will capitalise on recent pioneering work in my group on proximate evidence for antimicrobial defences in the termites, their fungal crops, and their complex gut bacterial communities, by proposing to develop the farming symbiosis as a major model to test three novel concepts that may account for the evasion of resistance evolution. First, the antimicrobial compounds may have properties and evolve in ways that preclude resistance evolution in pathogens. Second, resistance is only possible towards individual compounds and not natural antimicrobial cocktails. Third, pathogens can only successfully invade and proliferate if they bypass several consecutive lines of defence, analogous to the six hallmarks of metazoan defence against cancer development. Addressing these concepts will allow fundamental insights into the remarkable success of complementary symbiont contributions to defence, and they will clarify the forces of multilevel natural selection that have allowed long-lived insect societies to evolve sustainability. Documenting and understanding these disease management principles is fundamentally important for several branches of evolutionary biology, and strategically important for adjusting human practices for future antimicrobial stewardship.

Keywords: gut microbiota,metabolomics,metagenomics,metatranscriptomics,modeling,sustainable antimicrobial use
Next generation drug conjugates for cancer treatment (Syndivia)

Framework: Horizon 2020 — Societal Challenges
Programme: Health, demographic change and wellbeing
Theme: Treating and managing disease
Action type: SME instrument
Countries involved: France
Call: Supporting innovative SMEs in the healthcare biotechnology sector (H2020-SMEINST-1-2016-2017, 2016)
Start date: 2016-07-01
End date: 2016-11-30
Duration (months): 5.0
Total project cost (EUR): 71429.0
EU funding (EUR): 50000.0
Participants: 1
Project status: CLOSED

The optimal potential of chemotherapy, despite being the standard treatment, has not yet been achieved and instead it can lead to adverse toxicological effects as a result of off-target toxicity, as the drug cannot discriminate between healthy and cancerous cells. Small molecule prodrugs help solve this issue thanks to their high efficiency in targeting tumour cells. Syndivia have developed the next-generation Antibody Drug Conjugation platform for development of highly effective small molecule prodrugs for targeted cancer therapies. Two patented technologies are applied in the formulation of the prodrugs delivering higher plasma stability and controlled release at the tumour site resulting in a higher therapeutic efficiency and reduction of off-target toxicity of the chemotherapeutic. The pioneer product SDV1001 is specifically focused on treatment of pancreatic cancer, that accounts for the highest mortality rate among all cancers, over 74% of patients will not survive 1 year from time of diagnosis and 95% will die within 5 years. Preclinical trials have proven the efficacy of the product in which animals treated by SDV1001 displayed 92-100% tumour regression and no noticeable side effects. The Phase 1 project will be focused on establishing a complete and scalable supply chain, verifying the business model and commercialization strategy, planning new collaborations and partnerships, including the ones to implement the next clinical trials stage.

Keywords: cancer,pancreatic cancer,targeted therapy,bioconjugation,prodrug,antibody drug conjugate,drug development,healthcare,chemotherapy,clinical trial,citotoxin,pharmaceutical
Crosstalk between microbiota metabolites and immune cells, the missing link to brain damage. (MetaBiota)

Framework: Horizon 2020 — Excellent Science
Programme: Marie-Sklodowska-Curie Actions
Theme: Marie Skłodowska-Curie
Destination: Individual Fellowships (IF)-Standard European Fellowships
Action type: Marie Skłodowska-Curie actions
Panel: Life Sciences
Countries involved: Germany
Call: Individual Fellowships (H2020-MSCA-IF-2016, 2016)
Start date: 2017-05-01
End date: 2019-04-30
Duration (months): 24.0
Total project cost (EUR): 159460.8
EU funding (EUR): 159460.8
Participants: 1
Project status: CLOSED

Stroke is the second most common cause of death in Europe: accounting for almost 1.1 million deaths each year, with only 15% of stroke patients being eligible for a specific treatment. I have reported–in this year Nature Medicine’s April issue–that microbiota influences the severity of stroke injury through an impaired intestinal immune function. These findings revealed for the first time the critical implication of the microbiota as a novel and relevant prospective target for therapeutic strategies in stroke. However, the development of efficient therapies requires to identify which bacterial species and bacterial products are involved in the modulation of the immune response and thereby influence stroke outcome. To fill in this knowledge gap, my proposal aims to identify how metabolites derived from gut bacteria modulate the intestinal immune response and thereby influence the brain in the setting of stroke. To investigate this novel paradigm, I will use cutting-edge metabolomic tools to precisely analyze a large panel of metabolites, high-throughput sequencing to identify bacterial species, specific knock-out mice and mouse models of altered-microbiota available at the host institution and its established collaboration partners. This is the first attempt to discover a relationship between microbial metabolites, immune cell regulation and severity of ischemic stroke. Information derived from this project will have the potential to enable development of a “neuroprotective” microbiota–by diet intervention–and reduce the dramatic consequences of stroke. The Marie Sklodowska-Curie individual fellowship (MSC IF) will allow me to obtain the required methodological knowledge, access to critical infrastructure and collaboration partners in order to achieve this interdisciplinary and ambitious objective. My overall goal will be to gain this training fellowship to become an independent investigator and a leader in the field of stroke and microbiota biology.

Keywords: microbiota,metabolites,tryptophan,adaptive immunity,t cell polarization,stroke
Quantitative understanding of target recognition on DNA based on directional zipping processes (ZIPgeting)

Framework: Horizon 2020 — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Consolidator grants
Action type: ERC actions
Panel: Condensed matter physics
Panel description: Structure, electronic properties, fluids, nanosciences, biological physics
Countries involved: Germany
Call: ERC Consolidator Grant (ERC-2016-COG, 2016)
Start date: 2017-05-01
End date: 2022-10-31
Duration (months): 66.0
Total project cost (EUR): 2000000.0
EU funding (EUR): 2000000.0
Participants: 1
Project status: CLOSED

In the recent years a number of protein systems have been identified that recognize long (tens of base pairs) DNA sequences and allow flexible programmability of their target specificity. This promoted an enormous range of applications in genome engineering and synthetic biology. This project aims to decipher the mechanisms by which these proteins recognize their DNA targets in order to develop quantitative models/predictors for target recognition and to avoid off-target effects. To obtain detailed insight into the targeting mechanisms of different programmable systems in a “bottom-up manner”, cutting-edge single-molecule experiments, such as mechanical DNA twisting combined with single-molecule fluorescence detection will be employed. This will provide a fully quantitative characterization of the targeting process and insight into the mechanisms of allosteric regulation coupled to targeting. The quantitative data will allow to develop physics-based models of the target recognition process. In particular, we will focus on recognition through non-equilibrium, directional zipping along the target sequence – as recently revealed for CRISPR-Cas enzymes – as a promising unifying mechanism. To obtain precise targeting predictors our first-principle models will be tested and refined using high-throughput measurements on many different targets in parallel. Finally, the predictions will be used in order to understand target selection in live cells using single-molecule imaging. Within the project the following goals are defined: Goal 1: Quantitative understanding of target binding/degradation for CRISPR-Cas systems Goal 2: Detailed mechanistic insight into the target recognition process by TALEs Goal 3: Development of highly parallelized measurements on different target sequences down to the single-molecule level Goal 4: Target identification in the complex environment of live cells

Keywords: single molecule biophysics,force,torque spectroscopy,random walk model,crispr cas,dna recognition
Digital Assembly 2015 Riga (DA RIGA 2015)

Framework: Horizon 2020 — Industrial Leadership
Programme: Information and Communication Technologies
Action type: Coordination and support actions
Countries involved: Latvia
Call: ICT50 (H2020-Adhoc-2014-20, 2015)
Start date: 2015-04-01
End date: 2015-09-30
Duration (months): 6.0
Total project cost (EUR): 353955.0
EU funding (EUR): 141582.0
Participants: 2
Project status: CLOSED

The project is aimed at organisation and running of Digital Assembly in conjunction with EU in Riga, Latvia on 17th and 18th June 2015. The event will provide the opportunities to reflect on DSM strategy which will be published by the Commission in May and discuss possible barriers and challenges meeting its objectives. The overall aim of the Digital Assembly is to raise awareness of DSM strategy in EU Member States, to provide networking opportunities and showcase best practices.

Keywords: digital single market,e skills,e government,digital economy,cyber security,innovations,access,connectivity