Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Deep representational learning of the evolutionary DNA code in the vertebrate pallium (EvoDCode)

Framework: Horizon Europe — Excellent Science
Programme: Marie Skłodowska-Curie Actions (MSCA)
Theme: Marie Skłodowska-Curie
Destination: Postdoctoral Fellowships
Action type: Marie Skłodowska-Curie actions
Panel: Life Sciences
Countries involved: Belgium
Call: MSCA Postdoctoral Fellowships 2024 (HORIZON-MSCA-2024-PF-01, 2024)
Start date: 2025-04-01
End date: 2027-03-31
Duration (months): 24.0
Total project cost (EUR): 200400.0
EU funding (EUR): 200400.0
Participants: 1
Project status: SIGNED

Vertebrate genomes consist of tens of thousands of genes and yet they produce only a limited number of stable cell types. Our understanding of how cell types are encoded in the genome is still lacking. The expression of genes is controlled by gene regulatory elements, which are evolutionarily much less conserved than genes are and can be located far away in the genome. My main goal is to better understand how the genomic sequence underlies cell identity in the pallium across vertebrate species and I hypothesize that gene regulatory logic can be directly learned from the genomic sequence and used to predict cell types. Recent advances in the field of single cell sequencing have made the generation of large epigenomic datasets possible, while novel machine learning models like DNA language models are providing unprecedented insights into the regulatory logic of the genome. In addition, for many non-model species high quality reference genomes are becoming available as there is an increased awareness for the need to preserve biodiversity. I will conduct single cell multiome sequencing, supplemented with low-cost single-cell ATAC-seq using the HyDrop platform - developed in the host-lab - to profile regulatory elements across cell types in the pallium from multiple species, including mammals, birds, lizards and fish. My experience in generating and annotating single cell data from the brain will aid in the analysis and alignment of the generated datasets. Next, I will use this data to study the relationships between the genome of a species and the identified cell types by training species-aware DNA language models and using these models to identify species-specific and conserved regulatory logic. These models will not only be interesting from an evolutionary perspective, but also aid in ongoing efforts to develop synthetic enhancers used to target highly specific cell types, which can be applied in many therapeutic applications.

Keywords: machine learning convolutional neural networks phylogeny single cell sequencing scatac seq single cell multiomics molecular neurobiology enhancers gene regulatory network
Porous sensors for real-time monitoring of water quality risks (PROTEGE)

Framework: Horizon Europe — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Proof of concept grants
Action type: ERC actions
Countries involved: Portugal
Call: ERC PROOF OF CONCEPT GRANTS (ERC-2025-POC, 2025)
Start date: 2026-01-01
End date: 2027-06-30
Duration (months): 18.0
Total project cost (EUR): 150000.0
EU funding (EUR): 150000.0
Participants: 1
Project status: SIGNED

The unpredictable contamination of microbial communities in aquatic environments is a global concern for drinking water suppliers and aquaculture producers. Drinking water treatment expenditures, mainly caused by excessive proliferation of harmful cyanobacteria can cost over €150 million/year in European countries. The scenario aggravates when considering the debilitating attacks from pathogenic bacteria in aquaculture cages, generating global economic losses of over $25 billion. In both industrial sectors, the mitigation costs scales with microbial detection delay. Existent monitoring solutions for water quality mostly rely on time-consuming and operator-dependent measurements of nitrogen and phosphorus fractions, temperature and dissolved oxygen or in using chlorophyll a as a proxy. Yet, these approaches fail to deliver effective and real-time detection of microbial contamination. Within the ERC-funded GREEN project we have identified a promising commercial application which by means of ultrasensitive electrophysiology allows unprecedent real-time detection of harmful microorganisms in aquatic environments. An international patent has been filed and two research articles published. In addition, two distinct industrial partners and a state laboratory are committed to support and actively participate in PROTEGE. The breakthrough has been realised by the development of ultra-sensitive porous conducting polyurethane foams which exploits the large electrode area, maximizing the double-layer capacitance and concomitant microbial detection sensitivity. The main aim of PROTEGE is to demonstrate a working prototype in the industrial partners facilities, capable of real-time detection of cyanobacteria in water-supply reservoirs and pathogenic bacteria in aquaculture cages, and to develop a business and exploitation plan for technology commercialization of a market-oriented prototype with real-time telemetry data.
Regulation and modulation of the NALCN channelosome (TUNENALCN)

Framework: Horizon Europe — Excellent Science
Programme: Marie Skłodowska-Curie Actions (MSCA)
Theme: Marie Skłodowska-Curie
Destination: Postdoctoral Fellowships
Action type: Marie Skłodowska-Curie actions
Panel: Life Sciences
Countries involved: Denmark
Call: MSCA Postdoctoral Fellowships 2024 (HORIZON-MSCA-2024-PF-01, 2024)
Start date: 2025-06-01
End date: 2027-05-31
Duration (months): 24.0
Total project cost (EUR): 247553.28
EU funding (EUR): 247553.28
Participants: 1
Project status: SIGNED

The sodium leak channel (NALCN) is the ion-channel subunit of the NALCN channelosome, additionally containing UNC79, UNC80 and Fam155. NALCN controls the resting membrane potential (RMP) in excitable tissue (e.g. brain and myometrium) by an inward current of positively charged (sodium) ions that depolarizes the cell membrane, sensitizing the cell to excite (activate). NALCN is essential for survival. Mutations in the NALCN channelosome cause loss- or gain of function of NALCN currents which result in severe developmental disorders IHPRF and CLIFAHDD. Yet, NALCN channelosome physiology is largely unknown and no selective or specific drug-like compounds targeting the NALCN channelosome exist. I propose the objectives: I) to characterize regulation of the NALCN channelosome by endogenous protein partner interactions (PPIs), and II) to identify and characterize de novo designer proteins that modulate NALCN function. I anticipate that this can inform on NALCN physiology and future therapeutic strategies to counteract NALCN loss- or gain of function and other excitability-related disorders. I will perform the research at Copenhagen University in the lab of Professor Stephan Pless, an expert in the field. Objective I-II build onto novel in silico approaches where the Pless lab has identified PPIs based on protein co-evolution, tissue-co-expression, and disease association; and generated de novo designer proteins designed to bind the NALCN channelosome. I will elucidate the objectives experimentally by utilizing – and expanding – my experience in ion-channel research. In Objective I, I will use i) electrophysiology to study the functional impact of PPIs, ii) immunocytochemistry to interrogate sub-cellular localization and trafficking, and iii) biochemistry to determine direct interactions. In Objective II, I will perform electrophysiology on NALCN channelosome-expressing HEK cells and iPSC-derived neurons to find de novo designer proteins that inhibit or potentiate NALCN.

Keywords: ion channels,electrophysiology,de novo designer protein binders,pharmacology,cell biology,membrane protein regulation
Novel Biophysical Tools to Measure Multiple Parameters In The Same Cell (SameMultiPhys)

Framework: Horizon Europe — Excellent Science
Programme: Marie Skłodowska-Curie Actions (MSCA)
Theme: Marie Skłodowska-Curie
Destination: Staff Exchanges
Action type: Marie Skłodowska-Curie actions
Panel: Information Science and Engineering
Countries involved: Spain,Israel,Italy,France,United States,Chile,Canada
Call: MSCA Staff Exchanges 2022 (HORIZON-MSCA-2022-SE-01, 2022)
Start date: 2023-11-01
End date: 2027-10-31
Duration (months): 48.0
Total project cost (EUR): 179400.0
EU funding (EUR): 179400.0
Participants: 9
Project status: SIGNED

Biophysical biomarkers of cell state can reveal physiologically relevant changes that occur during disease progression. For example, cell deformability, cytoskeletal and nuclear organization, and macromolecular crowding are biophysical parameters implicated in migration and growth, which are essential processes for cellular functions. As biophysical parameters reflect physio-pathological cell states, they have the potential to be used as biomarkers for early diagnostics and clinical treatments in medicine. Current techniques based on microfluidics can be used to perform biophysical measurements in a high-throughput manner. However, these systems are not able to provide multiparameter, biophysical and same-cell measurements, making it difficult to find insightful relationships in heterogenous cellular mixtures. SameMultiPhys will develop and produce customized microfluidic systems to measure multiple features in the same cells and evaluate their potential applications as biophysical biomarkers. These new technologies will allow us to study multiscale biological questions of immune T cells from an interdisciplinary perspective and other cell lines. This project aims to facilitate the transfer of knowledge and resources between institutions with expertise in microengineering, materials science, chemistry, mathematics, biology, and biophysics to promote collaboration between researchers, and to develop innovative microfluidic technologies for mechanobiology. The project will involve state-of-the-art microfabrication techniques, deep-learning analysis of images, and computational modelling to develop and validate the technologies developed. The ultimate goal of this project is to gain a deeper understanding of the mechanobiology of cells, enabling progress toward more effective identification of biomarkers.

Keywords: mechanobiology cell mechanics biomarkers microfluidics microengineering cell biophysical properties cell label free biomarkers quantitative biology soft matter deformability physics of cells
Accelerating the transition to innovative and sustainable manufacturing by an AI-based software simulation that achieves first-time right printing of lightweight and complex of aluminium alloy parts. (AMA - AM meets AI)

Framework: Horizon Europe — Innovative Europe
Programme: European innovation ecosystems
Theme: Elevating the scalability potential of European business
Destination: Elevating the scalability potential of European business
Action type: Coordination and support actions
Countries involved: Germany
Call: Women TechEU (HORIZON-EIE-2021-SCALEUP-01, 2021)
Start date: 2022-06-01
End date: 2023-05-31
Duration (months): 12.0
Total project cost (EUR): 107142.86
EU funding (EUR): 75000.0
Participants: 1
Project status: CLOSED

Additive manufacturing holds important promises for sustainable engineering products and applications. Combining the capabilities of 3D printing in terms of bionic lightweight design with the lightweight nature of aluminium and its outstanding properties could lead to a revolution in the field of sustainable mobility. Despite the recent advances, 3D printing of aluminium alloys is a complex process that leads to many defects and a high scrap rate. This becomes a cost barrier to scale the technology especially in the sectors automotive and aerospace. AMA proposes to develop a machine learning based toolpath with process parameters that are optimal to achieve a component defect free and first-time right. In the context of the project, we will provide science-based life cycle analysis of the indirect impact of our technology in enabling competitive sustainable solutions to scale by reducing the cost barrier and also compare the parts before and after using our AI technology in cost, quality and environmental impact criteria. The technical objective will be achieved by designing a testbed demonstrator. For this, a specific Aluminium alloy (ALF357) and a representative geometry from the automotive industry will be selected. The AI process simulation algorithm will be trained with increasing geometry complexity. Once demonstrated the accuracy, the model will be used to achieve first-time right printing and avoid the traditional costly trial and errors. The success of the use case will provide 1000Kelvin with a unique demonstrator, showing the capability of our AI based APIs to solve some of the complex process challenges of the AM industry. This will help position our business as a leader technology provider and enhance our growth perspective to promote the role of women in leading tech start-ups and open the way for a more inclusive 3D printing ecosystem.

Keywords: ai based software solution in order to scale additive manufacturing
Building Conceptual and Methodological Expertise for the Study of Gender, Agency and Authority in Islam (BILQIS)

Framework: Horizon Europe — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Consolidator grants
Action type: ERC actions
Panel: Institutions, Governance and Legal Systems
Panel description: Political science, international relations, law
Countries involved: Ireland
Call: ERC CONSOLIDATOR GRANTS (ERC-2021-COG, 2021)
Start date: 2023-09-01
End date: 2028-08-31
Duration (months): 60.0
Total project cost (EUR): 1994249.0
EU funding (EUR): 1994249.0
Participants: 2
Project status: SIGNED

BILQIS emerges from a critical concern around Muslim women’s access to justice in Europe. BILQIS will be driven by methodological advances in Islamic feminism that the PI has been to the fore in delivering and will be primarily distinguished by its systematic and rigorous inquiries into questions of gender in relation to Islamic family laws (IFL) and IFL-related socio-religious and socio-legal power structures. The project will engage in a comparative study how Muslim women in Europe have navigated agency and authority over time from the long 19th century to the present day across diverse European peripheries, specifically the Ottoman Balkans, the post-Ottoman Balkans, and the territorial spaces that are currently governed by Bosnia and Herzegovina, Bulgaria, Greece, Ireland, Norway, and Sweden. BILQIS will interrogate how the gendered development of IFL in each of these peripheral contexts can be better understood in terms agency and authority through studies of legal texts and authorities (e.g., qadis, sijills, muftis, fatwas, istintâk, national court judgements) and will produce new critical, contextual, conceptual, and constructive knowledge in this regard. As a result BILQIS will break significant epistemic, conceptual and methodological impasses around shari’a, conflict of laws, and cultural pluralism in Europe. Finally, BILQIS will aim to use the sum of this new knowledge to construct a new methodological framework to transform the study of gender gaps and power imbalances related to agency and authority. This new methodology will direct the future of critical work on gender gaps across multiple disciplines (e.g., Islamic studies, Socio-legal Studies, Women’s and Gender Studies, European Studies, Near and Middle Eastern Studies, Cultural Studies, Political Philosophy, Government and Policy Studies).

Keywords: women s access to justice,islamic family laws,agency,authority,muftis,qadis,fatwas,ottoman archives
Biologging to inform Prevention of Seabird Bycatch (BioPSy)

Framework: Horizon Europe — Excellent Science
Programme: Marie Skłodowska-Curie Actions (MSCA)
Theme: Marie Skłodowska-Curie
Destination: Postdoctoral Fellowships
Action type: Marie Skłodowska-Curie actions
Panel: Environment and Geosciences
Countries involved: Ireland,New Zealand
Call: MSCA Postdoctoral Fellowships 2023 (HORIZON-MSCA-2023-PF-01, 2023)
Start date: 2024-11-01
End date: 2027-10-31
Duration (months): 36.0
Total project cost (EUR): 274426.08
EU funding (EUR): 274426.08
Participants: 2
Project status: SIGNED

As the global footprint of fisheries increases to match market demands, interactions between seabirds and vessels become more frequent leading to scavenging opportunities for many species, but also increase bycatch risk. Many seabird populations are in rapid decline, and bycatch in fishing gears has been identified as a leading cause. BioPSy is a global project, where the candidate will develop skills pertinent to seabird bycatch prevention in New Zealand, a country with an internationally recognised track record in applied conservation and seabird bycatch management. On the return phase, these skills will be applied to areas of Europe with severe seabird bycatch issues and little to no legislated corrective measures. Cutting-edge analyses will be developed and applied to seabird biologging data to design effective seabird bycatch prevention measures (SBPMs). BioPSy relies on stakeholder engagement for experimental design, with engagement skills and implementation focal point of the training program. New Zealand’s open fisheries practices and extensive observer data will be reviewed for SBPMs used, bycatch rates per hooks set, and efficacy of current SBPMs then estimated. Individuals of at-risk seabird species will be tagged with biotelemetry devices that record depth, location, and acceleration when at sea. This will reveal behaviour around vessels in the presence/absence of SBPMs, how deep birds dive to scavenge, and how this interacts with light availability. These behaviours will be placed in the context of current SBPM efficacy, and recommendations to improve SBPMs communicated to key stakeholders. The candidate will bring insights gained in New Zealand back to Europe, where observer coverage of fisheries most prone to seabird bycatch is minimal. The transferability of using biologging techniques to design SBPMs will be tested in a system with fewer sources of observer data, and practicable SBPMs recommended to policy makers.

Keywords: seabird bycatch,human wildlife interactions,scavenging,stakeholder engagement,marine policy,sustainable fisheries,applied conservation
Linkages of elements in soils and plants with mycorrhizae along Philippine and pantropical elevational gradients (PHILANTROPIC-ELEMYCO)

Framework: Horizon Europe — Excellent Science
Programme: Marie Skłodowska-Curie Actions (MSCA)
Theme: Marie Skłodowska-Curie
Destination: Postdoctoral Fellowships
Action type: Marie Skłodowska-Curie actions
Panel: Environment and Geosciences
Countries involved: Spain,Philippines
Call: MSCA Postdoctoral Fellowships 2024 (HORIZON-MSCA-2024-PF-01, 2024)
Start date: 2026-04-01
End date: 2029-03-31
Duration (months): 36.0
Total project cost (EUR): 305239.92
EU funding (EUR): 305239.92
Participants: 2
Project status: SIGNED

Tropical mountains are biodiversity hotspots where a zonation of biota occurs with environmental conditions as one ascends. Patterns of vegetation types are well documented, as is the decline of plant-available nitrogen (N) relative to phosphorus (P) with elevation. However, how absolute and relative availabilities of essential elements beyond the well-studied N, P and carbon (C) vary in such mountains remains poorly understood, despite evidence that base cations and micronutrients do indeed affect tropical forests’ and other ecosystems’ functioning. Potentially important but overlooked factors that may confound elevational patterns of elemental availabilities are the type, dominance and abundance of mycorrhizal fungi, which in turn are also affected by biogeochemical cycling, directly or through shifts in vegetation. Here, I address these knowledge gaps by investigating patterns of C, N, P, potassium (K), calcium (Ca), magnesium (Mg) and micronutrients, and their association with mycorrhizae across three distinct Philippine tropical mountains. While fungal and particularly plant biodiversity in these areas are well documented, biogeochemical patterns remain largely unexplored. PHILANTROPIC-ELEMYCO will test the hypothesis that absolute and relative availabilities of these elements are associated with both elevation and mycorrhizae. Specifically, the project will (1) analyze concentrations and stoichiometry of species- and community-weighted leaf, litter and soil elements along elevational gradients, (2) assess the co-occurrence thereof with association type, abundance and diversity of mycorrhizae, and (3) conduct a systematic review comparing mycorrhiza-nutrient relationships among tropical regions. By uniquely integrating expertise and approaches from tropical forest ecology, biogeochemistry, botany, mycology and molecular biology, I aim to contribute to an improved understanding of plant-soil-mycorrhiza-stoichiometry patterns in tropical mountains.

Keywords: tropical forests,elemental stoichiometry,soil,nutrients,mycorrhizae,elevational gradients,mountain ecology,plant biodiversity
Diabetic neuropathy: a study on the effects of insulin resistance on its pathophysiology and a randomized clinical trial to prevent neural loss (SenseDiabetes)

Framework: Horizon Europe — Widening Participation and Strengthening the European Research Area
Programme: Widening participation and spreading excellence
Theme: Attracting and mobilising the best talents
Destination: Attracting and mobilising the best talents
Action type: Marie Skłodowska-Curie actions
Panel: Life Sciences
Countries involved: Greece
Call: ERA Fellowships (HORIZON-WIDERA-2023-TALENTS-02, 2023)
Start date: 2025-01-02
End date: 2027-01-01
Duration (months): 24.0
Total project cost (EUR): 153486.72
EU funding (EUR): 153486.72
Participants: 1
Project status: SIGNED

We are facing a global epidemic of type 2 diabetes (T2D). Diabetic neuropathy (DN) is the most common complication of T2D affecting ~50% of patients with T2D. If not diagnosed early, DN may lead to further catastrophic complications. However, despite its potentially huge impact on patients’ quality of life, and burden imposed on healthcare systems, patients with T2D and practitioners are often unaware of the manifestations of DN. To make things worse, currently there are no approved treatments for DN. SenseDiabetes has several aims. First, we wish to increase our knowledge regarding the pathophysiology of DN, specifically assessing whether patients with T2D and DN have worse insulin resistance compared to patients with T2D without DN. While previous studies on DN have shown an effect of insulin resistance on DN, poor indexes of insulin resistance have been used. In SenseDiabetes we will use for the first time the gold standard method for the assessment of insulin resistance, i.e. the euglycemic insulin clamp. Second, we will assess the efficacy of two commonly used antidiabetic drugs in early DN. Patients with T2D and early signs of DN will be randomized to receive treatment for 9 months with either Semaglutide or Empagliflozin. The effects of these drugs on DN outcomes (small fiber density, cardiovascular autonomic function) and advanced glycation end-products will be assessed. Further, we will study with ex vivo experiments the effects of the two drugs of peripheral nerve density (obtained with skin biopsies), and in in vitro experiments we will study the exact mechanisms of action of Semaglutide on cultures of peripheral nerves. Along with the scientific part, SenseDiabetes has a dedicated WP to increase awareness of DN.SenseDiabetes may thus be pivotal for the development of new strategies to combat DN. Also, SenseDiabetes aims to promote awareness of DN and thus increase societal impact through early recognition of DN and prevention of further complications.

Keywords: diabetic neuropathy,insulin resistance,glucagon like peptide 1 receptor agonists,corneal confocal microscopy,lens fluorescence biomicroscope