Data-Gouv-ML/pcri-informations-sur-les-projets-laureats huggingface dataset:
Functional dissection of X-linked regulatory DNA: unravelling the impact of genome topology on transcriptional regulation (eXcape3D)

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-2018, 2018)
Start date: 2019-04-01
End date: 2021-10-01
Duration (months): 24.0
Total project cost (EUR): 174806.4
EU funding (EUR): 174806.4
Participants: 1
Project status: CLOSED

Mammalian genomes are structurally organized into sub-chromosomal self-interacting domains called topologically associating domains (TADs). Functionally, genes embedded within the same TAD appear to be co-regulated by their shared regulatory landscapes, suggesting the tendency of the genome to be divided into discrete regulatory domains. Although disrupting TAD boundaries has been shown to result in aberrant patterns of gene expression, whether TAD organisation is cause or consequence of transcriptional activity remains largely unknown, as well as the regulatory elements that direct TAD formation and long-range chromatin interactions within TADs. This project aims to define the exact functional link between genome topology and transcriptional regulation by exploiting the mammalian dosage compensation mechanism X-Chromosome Inactivation (XCI) as a model system. First, I will identify the combination of regulatory elements that allow a subset of X-linked genes to resist the transcriptional silencing of one entire X chromosome in female cells. Then, I will characterise their functional and structural relevance by combining advanced epigenetic tools for the manipulation of complex regulatory networks with transcriptomic analysis and chromosome conformation capture, an innovative method that allows to define the 3D structure of chromosomes within the nucleus. This project represents a unique opportunity to enhance our understanding of genome topology, providing valuable insights into the roles of the non-coding genome in gene regulation. Considering my personal professional background, and the outstanding level of scientific excellence of the host institution, this project promises a great potential of radically advancing the field and, in addition, will provide the European Research Area with a highly-qualified expert scientist who has the technical and complementary skills to successfully lead a European research team.

Keywords: x chromosome inactivation,gene regulation,chromosome conformation,chromatin structure,chromatin loops,genome topology,dna regulatory elements,crispr cas9,embryonic development
Introducing preventive management of chronic thyroid conditions through patient empowerment and a ML-powered mHealth solution (BOOST HEALTH)

Framework: Horizon 2020 — Industrial Leadership
Programme: Innovation in SMEs
Action type: SME instrument
Countries involved: Germany
Call: SME instrument (H2020-SMEInst-2018-2020-1, 2019)
Start date: 2019-05-01
End date: 2019-10-31
Duration (months): 6.0
Total project cost (EUR): 71429.0
EU funding (EUR): 50000.0
Participants: 1
Project status: CLOSED

VLM Health UG is improving the life of people affected by chronic autoimmune conditions by 1. facilitating earlier diagnoses 2. enabling preventive disease management and 3. improving the patient-doctor relationship. Chronic autoimmune conditions affect 800 million people and cost €400bn a year because of too-late diagnosis and the absence of prevention. The best way to minimize the effect is by creating positive lifestyle habits, improving conversations with doctors, and increasing knowledge through collaboration with biomedical research. VLM Health UG combines peer-reviewed science on thyroid autoimmune conditions with data science in the BOOST Thyroid app. This reduces health complications and creates a valuable solution for patients: “This app had made a difference. I know what to focus on and already see my bad habits! This is an excellent tool for anyone with a thyroid condition or Hashimoto’s. Thank you!” During Phase 1 we will work on assessing the feasibility of methods which facilitate patient’s understanding preventive management of own health: 1. Empowering patients through regularly delivered summaries and analysis of their health and well-being 2. Validate in clinical setting 3. Delivering a prototype of an ML/AI-assisted individualized patient health plan In summary, we are will engage patients to understand how to preventively manage their own health, and enable free access to medically validated information at their convenience in an empathic product making people feel assured, positive, and motivated to improve their health. We have been instrumental in building the successful startups Clue and Wrapp, leading tech, product and science teams. We have over a decade of experience in academic research and patient experience, and share a passion for empowering people to improve own health.

Keywords: mhealth,patient empowerment,clinical practice,preventive health management
A mechanistic approach to understand microbiome-viriome dynamics in nature (DYNAMIC)

Framework: Horizon 2020 — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Advanced 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: France,France
Call: ERC Advanced Grant (ERC-2019-ADG, 2019)
Start date: 2021-01-01
End date: 2023-12-31
Duration (months): 36.0
Total project cost (EUR): 1886516.25
EU funding (EUR): 1706212.5
Participants: 2
Project status: SIGNED

Facing the therapeutic impasse of antibiotics, farming systems, among which aquaculture, should consider the extraordinary resource of phages, the natural bacterial predators, for environmental friendly practices. It is, however, crucial to understand how phages can control pathogens in a sustainable and safety manner. The goal of this project is to shed light on key ecological and evolutionary processes underlying phage-bacteria dynamics in the marine environment. An oyster bacterial pathogen, Vibrio crassostreae and its infecting phages will be used as model system to investigate the molecular bases and evolution of phage infections in nature. Based on a field approach, we will determine whether phages influence V. crassostreae dynamics in the wild by reducing bacterial density via predation and if co-evolution applies in this natural system. Combining comparative and functional genomics we will identify genes involved in the phage host range, host resistance, and phage–host coevolution. Exploring phage-vibrio interactions in culture, we will analyze whether fitness costs can constrain evolution of resistance in oyster hemolymph. We will identify vibrio virulence genes that are negatively selected by phages. In addition we will study whether phages in combination act synergistically to control V. crassostreae. Focusing on a T4-giant phage as a model, we will assess the molecular mechanisms underpinning its broad host range and decipher its potential to spread bacterial genes by horizontal gene transfer. We will finally revisit the phylogenomics of T4-related phages, and reconstruct the T4-giant phage ancestral genome to determine how the ability to infect multiple hosts has evolved in this group. This project has significant potential to make truly ground breaking discoveries on phage-bacteria coevolution providing new and major knowledge for the future generation of phage therapy in aquaculture.

Keywords: vibrio,phage,aquaculture,evolution ecology,trade off,synergy,horizontal gene transfers
Dynamic Microfluidic Structures for Analysis of Single Cell Systems (MetamorphChip)

Framework: Horizon 2020 — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Starting grants
Action type: ERC actions
Panel: Physical and analytical chemical sciences
Panel description: Analytical chemistry, chemical theory, physical chemistry/chemical physics
Countries involved: Israel
Call: ERC Starting Grant (ERC-2015-STG, 2015)
Start date: 2016-04-01
End date: 2021-03-31
Duration (months): 60.0
Total project cost (EUR): 1744056.0
EU funding (EUR): 1744056.0
Participants: 1
Project status: CLOSED

The interaction and communication between individual cells plays a central role in virtually all fields of biology, from the cooperative work of cells in the immune system, through the differentiation of stem cells, and to the proliferation of cancer cells. In recent years it has been shown that these processes are fundamentally coupled to cell-to-cell heterogeneity and variability. Despite the fact that studying cellular ensembles obscures these fundamental biological processes, most current studies consider cell populations, largely due to technological limitations in the ability to dynamically compartmentalize, manipulate, and analyze single cells. We propose to develop and demonstrate a new concept for a single-cell-level bioanalytical workspace that is dynamically configurable in real time. Making use of electrokinetically driven surface deformations, a physical mechanism recently invented in my lab, the MetamorphChip will be able to dynamically modify its own microfluidic structure, thus allowing complete freedom in the manipulation of individual cells and their environment, in real time. The project is divided into 5 aims: 1. Deepening our physical understanding of electrokinetically driven surface deformations, and using it to create a “library” of fundamental dynamic elements. 2. Designing, building, and testing the first prototype MetamorphChip. 3. Demonstrating the ability of the MetamorphChip to manipulate single cells and their microenvironment. 4. Performing advanced biochemical analysis on single cells using the chip. 5. Demonstrating the use of the MetamorphChip for experimental study of immune cell interaction. I strongly believe that successful implementation of this project would fundamentally change the way in which single-cell experiments are conceived and performed.

Keywords: electroosmotic flow,electrokinetics,lab on a chip,microfluidic chip,single cell analysis,cell communication,immunology,t cell,cytokines
Translating rewards to eye movements (iMove)

Framework: Horizon 2020 — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Starting grants
Action type: ERC actions
Panel: Neuroscience and Disorders of the Nervous System
Panel description: Nervous system development, homeostasis and ageing, nervous system function and dysfunction, systems neuroscience and modelling, biological basis of cognitive processes and of behaviour, neurological and mental disorders
Countries involved: Israel
Call: ERC Starting Grant (ERC-2017-STG, 2017)
Start date: 2018-07-01
End date: 2024-06-30
Duration (months): 72.0
Total project cost (EUR): 1570000.0
EU funding (EUR): 1570000.0
Participants: 1
Project status: SIGNED

The drive for rewards controls almost every aspect of our behavior, from stereotypic reflexive behaviors to complex voluntary action. It is therefore not surprising that the symptoms of neurological disorders that interrupt reward processing, such as those stemming from drug-abuse and depression, include deficits in the capacity to make even simple movements. Accordingly, how do rewards drive and shape movements? The brain uses two major subcortical networks to drive behavior: the basal ganglia and the cerebellum. Both areas are essential for the control of movement as damage to either structure leads to severe motor disabilities. Research on the basal ganglia has highlighted their importance in the control of reward-driven behavior-but how the reward information interacts with sensorimotor signals to drive the motor periphery is unknown. By contrast, research on the cerebellum has focused primarily on how sensory error signals are used to optimize motor commands but has mostly ignored the modulatory factors that influence behavior, such as reward. My goal is to unify research on the basal ganglia and cerebellum in order to understand how the computations underlying the influence of reward on action are implemented in the brain. I hypothesize that rewards drive and shape the motor commands in both subcortical networks, albeit with differing behavioral functions. While in the basal ganglia, information about reward is used to mediate selection between multiple actions; I predict that, in the cerebellum, reward potentiates movements to drive more accurate behavior. I will use the monkey smooth pursuit eye movement system as a powerful model motor system to study the neural mechanisms by which reward influences motor processing. I will combine the use of novel behavioral paradigms together with novel application of neural recording and optogenetic stimulation in primates to probe activity of neurons in the cerebral cortex, basal ganglia, and cerebellum.

Keywords: eye movements,basal ganglia,cerebellum
Mathematics of Density Functional Theory (MDFT)

Framework: Horizon 2020 — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Consolidator grants
Action type: ERC actions
Panel: Mathematics
Panel description: All areas of mathematics, pure and applied, plus mathematical foundations of computer science, mathematical physics and statistics
Countries involved: France
Call: ERC Consolidator Grant (ERC-2016-COG, 2016)
Start date: 2017-09-01
End date: 2023-02-28
Duration (months): 66.0
Total project cost (EUR): 1534159.0
EU funding (EUR): 1534159.0
Participants: 1
Project status: CLOSED

Density Functional Theory (DFT) is one of the most famous methods used in quantum physics and chemistry to describe matter at the microscopic scale. The purpose of the proposal is to investigate the mathematical foundations of this theory. The questions which have to be solved involve advanced tools from nonlinear analysis, partial differential equations, spectral theory, optimal transport, and numerical analysis. Several have stayed unsolved for many years. The project is prone to have an impact in many areas of mathematics, as well as in physics and chemistry. The proposal is divided into three main tasks. The first is focused on some important questions on the foundations of DFT, including excited states, its time-dependent formulation, and the local density approximation based on the uniform electron gas model. DFT can be formulated as an inverse problem, the main question being to find the external potential knowing only the density of particles in the system. We will investigate the invertibility of the potential-to-density map, both in the stationary and time-dependent cases. The second task deals with the derivation of simple DFT models from the true Schrödinger equation, a problem which has been largely discussed in the literature. We will work on the most challenging open questions, including for instance the relativistic Scott correction, or the proof of Bose-Einstein condensation for an infinite Bose gas in the mean-field limit. Finally, in the last task we study some particular DFT models, which are particularly challenging from the mathematical point of view. This includes for example a highly nonlinear model for neutrons and protons, infinite crystals with deterministic and random perturbations, and a time-dependent electromagnetic field solving Maxwell's equations coupled to the quantized Dirac quantum vacuum.

Keywords: density functional theory,variational methods,quantum theory,numerical analysis
Mapping Dispersion Spectroscopically in Large Gas-Phase Molecular Ions (BALANCE)

Framework: Horizon 2020 — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Advanced grants
Action type: ERC actions
Panel: Physical and analytical chemical sciences
Panel description: Analytical chemistry, chemical theory, physical chemistry/chemical physics
Countries involved: Switzerland
Call: ERC Advanced Grant (ERC-2018-ADG, 2018)
Start date: 2019-05-01
End date: 2024-04-30
Duration (months): 60.0
Total project cost (EUR): 2446125.0
EU funding (EUR): 2446125.0
Participants: 1
Project status: SIGNED

We use IR spectroscopy of trapped ions in a cryogenic FT-ICR spectrometer to probe non-covalent, “dispersion” interactions in large, gas-phase molecular ions. We will measure conformational equilibria by N-H frequency shifts, and correlate gas-phase IR frequency to the N-H-N bond angle in an ionic H-bond. Substituents on “onium” cations can adopt various conformations, whose energies map interaction potentials. Substituents on their proton-bound dimers interact non-covalently through dispersion forces, whose quantitative evaluation in large molecules has remained difficult despite dispersion becoming increasingly cited as a design principle in the construction of catalysts and materials. The non-covalent interactions bend the N-H-N bond, leading to large shifts in the IR frequency. The proton-bound dimer acts like a molecular balance where the non-covalent interaction, is set against the bending potential in an ionic hydrogen bond. Despite encouragingly accurate calculations for small molecules, experimental benchmarks for large molecules in the gas phase remain scarce, and there is evidence that the good results for small molecules may not extrapolate reliably to large molecules. The present proposal introduces a new experimental probe of non-covalent interactions, providing a sensitive test of the diverging results coming from various computational methods and other experiments. The experiment must be done on isolated molecules in the gas phase, as previous work has shown that solvation substantially cancels out the attractive potential. Accordingly, the proposed experimental design, which involves a custom-built spectrometer, newly available tunable IR sources, chemical synthesis of custom substrates, and quantum calculations up to coupled-cluster levels of theory, showcases how an interdisciplinary approach combining physical and organic chemistry can solve a fundamental problem that impacts how we understand steric effects in organic chemistry.

Keywords: infrared spectroscopy,mass spectrometry,non covalent interactions
Inclusive Public Space: Law, Universality and Difference in the Accessibility of Streets (InclusivePublicSpace)

Framework: Horizon 2020 — Excellent Science
Programme: European Research Council (ERC)
Theme: European research council
Destination: Advanced grants
Action type: ERC actions
Panel: Institutions, Governance and Legal Systems
Panel description: Political science, international relations, law
Countries involved: United Kingdom
Call: ERC Advanced Grant (ERC-2017-ADG, 2017)
Start date: 2019-01-01
End date: 2024-12-31
Duration (months): 72.0
Total project cost (EUR): 2499672.0
EU funding (EUR): 2499672.0
Participants: 1
Project status: SIGNED

This project considers the accessibility of public space – focusing on pedestrian access to streets. It explores law’s engagement with the exclusion which occurs when streets are designed, operated or managed so as to deny access to pedestrians whose bodies, minds or life circumstances do not ‘fit’. Such exclusion is damaging both to individuals and communities. With a view to understanding how states and the EU can more effectively ensure that public space is inclusive, the project aims to deepen understanding of what physical features of streets are experienced as exclusionary in 5 countries and by whom; how effectively law is used to challenge such exclusion in these countries; and how the problem is perceived and politically challenged. It also aims to foster shared concern about this form of exclusion, in the 5 countries and beyond, and to raise awareness of how law can be used to challenge it. The methodology will be comparative, transdisciplinary and participatory in nature. It will develop innovative videovoice techniques for data gathering. It will also develop groundbreaking awareness-raising tools – such as software to simulate experiences of pedestrian exclusion – as well as digital story telling and legal orientation guides. Theoretical context and framing will be provided by an innovative blending of Martha Fineman’s universal vulnerability thesis with the social model of disability. The project will be the first to bring a multinational sociolegal perspective to bear on this significant social justice problem. It is timely - given concerns about the move in EU countries (often supported by EU funding) toward streets in which space is shared by vehicles and pedestrians; and the ratification (including by the EU) of the UN Convention on the Rights of Persons with Disabilities, which is the first such treaty to include provisions on the accessibility of public space.

Keywords: human rights,exclusion,inequalities,diversity,transportation and mobility,ageing,disability,universal vulnerability,accessibility,streets,urban studies,design,sociolegal,comparative
Accelerating the commercialisation of a disruptive analytical technology which enables the biopharmaceutical industry to manufacture drugs faster, cheaper and with greater regulatory confidence (BIOSIM)

Framework: Horizon 2020 — Societal Challenges
Programme: Health, demographic change and wellbeing
Theme: Treating and managing disease
Action type: SME instrument
Countries involved: Ireland
Call: Supporting innovative SMEs in the healthcare biotechnology sector (H2020-SMEINST-2-2016-2017, 2017)
Start date: 2017-10-01
End date: 2019-05-31
Duration (months): 20.0
Total project cost (EUR): 2029325.0
EU funding (EUR): 2029325.0
Participants: 1
Project status: CLOSED

The global Biologic drug [including Vaccines] market exceeds €500 bn with an annual growth of 8%. Biopharmaceutical companies need to be able to produce these new biologic drugs faster and cheaper to meet the needs of patients, regulators and the governments and insurance companies who are paying for these high cost therapies. Valitacell is an Irish SME which currently supplies this market and is a validated supplier to a growing number of market leaders including GE Healthcare & MedImmune. BIOSIM will accelerate the commercialisation of our ChemStress technology platform for this industry. Scientifically these tests measure a cell’s performance when exposed to small molecule chemicals which simulate the stresses that the cell will experience in the scaled-up manufacturing process. When applied together they can reduce the average Cell Line Development stage of drug manufacture from 16 to 6 months and reduce the average cost from €2.3million to €1.1 million. BIOSIM will support: the demonstration of ChemStress at 4 leading biopharmaceutical manufacturing sites resulting in the generation of a customer endorsed value proposition; productise the ChemStress platform for the Biopharmmaceutical industry; refinement, scale-up and validation of the product manufacture; priming the sales & marketing for product launch. . ChemStress will realise €40m of end-user product sales and support 50 jobs in the 5 years following the project. ChemStress will provide EU Biomanufacturers with the opportunity to maintain their leadership position by implementing this disruptive innovation and realizing cost reductions. ChemStress will reduce the cost of biological drugs through lower manufacturing costs so enabling EU governments to provide these drugs to EU citizens at a lower cost.

Keywords: clone selection,cell line development,bioreactor simulation,process analytical technology,phenotypic fingerprinting