Data-Gouv-ML/pcri-erc-participations-et-projets-laureats huggingface dataset:
Projet ERC : NextWheat (Horizon Europe, appel 2024, Advanced grants)
Domaine scientifique : Life Science
Panel : Biotechnology and Biosystems E ngineering
Entité participante : Institut Weizmann — Pays : Israël — Rôle : PI
Acronyme de l'entité : WIS
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2498500.0 €

Addressing the challenge of food security during the current environmental crisis will necessitate rapidly breeding a new generation of adapted cultivars. Genetic diversity and selection of natural variants are key to advances in breeding. However, there is a need for better tools to predict how natural variation impacts plant performances, to improve the precision and efficiency of gene modification, and transfer from wild relatives to crops. We will focus on wheat, one of the most important staple foods of humanity, and on the broad genetic pool of its wild relatives. Our goals are to develop a computational tool to analyze genetic variation in the genomes of modern and wild wheat and to identify deleterious mutations that impair fitness. We will build genomics tools for effective genotyping of deleterious mutations in classical breeding and we will test their effect on yield. Then, we will use genome editing tools to increase diversity via the precise transfer of genes from the wild into the domestic background and for targeted repair of deleterious mutations towards wheat improvement. We plan to achieve this by developing a machine-learning algorithm to predict the presence of deleterious mutations in whole genomes (WP1). Then, we will test how such mutations can affect crop fitness by designing a genotyping microarray for simple identification of deleterious mutations in segregating populations for use in classical breeding (WP2). We will also harness new breeding technologies to increase the genetic diversity in wheat through the precise transfer of genes or chromosomal segments from close and distant chromosomes of wild relatives to modern wheat and for repairing deleterious mutations through modification of the relevant genes (WP3). This project should provide a new understanding of how genetic diversity affects plant fitness and how better to exploit it in plant breeding. All materials and tools developed through this work will be freely available.

Mots-clés : plant breeding,inter species gene transfer,dna recombination,food security,sustainability
Projet ERC : SteadyNMR (Horizon Europe, appel 2024, Advanced grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Physical and Analytical Chemical Sciences
Entité participante : Institut Weizmann — Pays : Israël — Rôle : PI
Acronyme de l'entité : WIS
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2498142.0 €

Pulsed Fourier-transform (FT) has reigned supreme in nuclear magnetic resonance (NMR) for over 50 years, standing at the core of numerous analytical, pharmaceutical, materials, biophysical and medical applications. However, if spectral information is not a must, FT NMR is not necessarily the optimal way for maximizing sensitivity: when, as often happens, spin relaxation times are long and T1≈T2, steady-state free-precession (SSFP) experiments can provide a higher sensitivity per unit time. SSFP NMR applies a train of closely spaced pulses and works only at suitable offsets, and has therefore been assumed impractical when seeking high resolution among multiple chemical sites. We have recently found a way to break this limitation, enabling SSFP-based schemes to resolve multiple sharp peaks spread over arbitrarily large bandwidths. We have also devised routes that can incorporate J-driven polarization transfers onto these sequences. On the basis of such findings, we propose here a series of SSFP-based developments, that in numerous heteronuclear NMR applications should provide sensitivities exceeding by sizable margins those afforded by FT NMR. SteadyNMR presents preliminary experiments and calculations substantiating such claim (see below an example on a mix of aromatic hydrocarbons in chloroform), and builds on them to: devise optimal spectral reconstruction algorithms translating SSFP’s enhancements into high-resolution methods opening new frontiers in chemical and biomolecular research; exploit these methods potential to monitor dynamics on thermal and on hyperpolarized samples; develop new families of metabolic 13C spectroscopic imaging experiments that are both 1H- and SSFP-enhanced, serving as basis for potentially superior ways of detecting cancer and metabolic abnormalities on widely available MRI platforms; combine these and other principles into new approaches complementing –and eventually improving– existing FT-based 2D NMR schemes.

Mots-clés : nmr,mri,polarization transfer,spectroscopic imaging,chemical exchange,multidimensional spectroscopy,hyperpolarization,spin spin couplings
Projet ERC : STAGE (Horizon Europe, appel 2022, Advanced grants)
Domaine scientifique : Social Sciences and Humanities
Panel : Texts and Concepts
Entité participante : Université Rennes 2 — Pays : France — Rôle : PI
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2487306.0 €

Digital sources are one of the most significant challenges facing performing arts historiography. At the intersection of history, epistemology, and digital humanities, STAGE’s key goal is to move performing arts studies into a digital context to establish a new historiography of mise en scène and their creative processes in Europe since WWII. It proposes a groundbreaking theoretical and methodological framework merging culture analytics, actor-network theory, data modeling, and computer vision to challenge conventional approaches to the paradigm shift of digital traces in performing arts studies. I call this new field “performing arts analytics.” STAGE will allow a Copernican revolution of our methodologies combining close reading with distant reading and distant viewing; hypothesis-driven with data-driven analysis; hermeneutics with artificial intelligence, computer vision, and digital humanities; qualitative interpretation with quantitative evidence. STAGE will build from the Avignon festival collection before opening to larger corpora to scale up our results and expand our analysis. Through the two prisms of influence and collaboration, STAGE will reveal creation contexts and networks, aesthetic influences, and creative process models in an unprecedented way. It will make it possible to test new algorithms for medium-sized corpora; to develop a new approach to studying collaborations over time through digital traces; to demonstrate the potential of a data-driven approach and interdisciplinary research in humanities; to create accessible corpora for future research; to demonstrate the importance of digital traces for cultural heritage and research projects. STAGE is transferable in that it will create widely open science tools, methodologies, and theoretical frameworks. It will be of value to historians and art historians who explore digital traces of the past, promising a potential impact beyond performing arts studies.

Mots-clés : performing arts,digital humanities,culture analytics,mise en sc ne,influence,collaboration,computer vision,creative process
Projet ERC : GI-DYNAMICS (Horizon Europe, appel 2024, Advanced grants)
Domaine scientifique : Life Science
Panel : Integrative B iology : from Genes and Genomes to S ystems
Entité participante : Institut Weizmann — Pays : Israël — Rôle : PI
Acronyme de l'entité : WIS
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2500000.0 €

The gastrointestinal (GI) tract undergoes significant changes during post-natal development and in response to various diseases. Single-cell atlases are static and therefore fail to capture the dynamic changes occurring within the GI tract. We have devised a method to transcriptomically profile cells that are naturally shed into the GI tract. Contrary to earlier beliefs, we found that shed cells remain viable and can robustly be measured in fecal samples. Shed cell transcriptomics enables non-invasive tracking of cellular states throughout development and disease progression. Moreover, discrepancies between transcriptomic profiles of shed cells and tissues can identify which cell types are preferentially shed or retained, revealing cell turnover patterns. Our objective is to combine shed-cell and spatial transcriptomics to achieve basic and biomedical discoveries that were not possible before: 1. To study the developmental changes in the neonatal human GI tract. This will include longitudinal acquisition and in-depth analysis of shed cell transcriptomic and proteomic data in stool samples obtained from babies. 2. To characterize turnover of cells in colorectal cancer (CRC). We will combine shed cell transcriptomics in stool and blood with spatial transcriptomics of tumor biopsies to spatially map the cancer cells that resist death/shedding and examine their interactions within the tumor microenvironment. 3. To investigate cellular dynamics and tissue adaptations in Celiac disease. This will involve shed cell transcriptomics and high-resolution spatial transcriptomics to thoroughly understand the turnover rates of various enterocyte sub-populations and tissue adaptations during the disease. Our innovative use of shed cell transcriptomics will add a dynamic dimension to human cell atlas reconstruction efforts, enriching our understanding of tissue processes in health and disease.

Mots-clés : spatial transcriptomics,intestine development,cancer heterogeneity,celiac disease
Projet ERC : VIBES (Horizon Europe, appel 2021, Advanced grants)
Domaine scientifique : Life Science
Panel : Environmental B iology, Ecology  and E volution
Entité participante : Institut Weizmann — Pays : Israël — Rôle : PI
Acronyme de l'entité : WIS
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2500000.0 €

The fate of carbon in marine environments is influenced by associations between heterotrophic bacteria and phytoplankton, mediated by chemical communication and metabolic exchange. Deciphering the nature of these associations is critical given the impact of marine plankton on biogeochemical cycling and climate regulation. Viral infection is a prevalent mortality agent of algal blooms in the ocean, leading to massive release of biomass to the dissolved organic matter (DOM) pool, one of the largest global inventories of carbon. This process, termed the ‘viral shunt’, is a key ecosystem process, but remains unquantifiable and mechanistically enigmatic. Furthermore, the metabolic composition of the DOM released following viral infection (vDOM) and its role in shaping microbial communities are largely unknown. In the VIBES project, we will disentangle the complexity of the viral shunt, and elucidate its impact on microbial lifestyles (mutualism and pathogenicity) during algal bloom demise. We will generate experimental approaches to study these bacterial lifestyles, and uncover the chemical language that mediates them. Our expertise in marine microbial chemical ecology, using single-cell transcriptomics to quantify host-pathogen interactions, and metabolomics to identify the chemical signals that govern microbial interactions, will pave the way for unprecedented quantification of the viral shunt. We will investigate the molecular and metabolic basis of virus-derived microbial lifestyles and their consequence for the flow of carbon in the ocean, both under controlled lab-based experiments and during complex interactions in the ocean. We will investigate how microbial lifestyles that specialize on vDOM can determine the partitioning of carbon between the dissolved and particulate fractions, representing carbon cycling and export, respectively. Ultimately, VIBES will enable to evaluate the importance of microscale interactions to the cycling of carbon in the ocean.

Mots-clés : algal blooms,marine viruses,microbial chemical ecology,environmental metabolomics,emiliania huxleyi viral shunt,infochemicals,algal viruses,phytoplankton bacteria interactions
Projet ERC : MOLECULAR MUCUS (Horizon Europe, appel 2022, Advanced grants)
Domaine scientifique : Life Science
Panel : Molecules of Life: B iological  Mechanisms , Structures  and Functions
Entité participante : Institut Weizmann — Pays : Israël — Rôle : PI
Acronyme de l'entité : WIS
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2162383.0 €

Our bodies produce copious mucus daily to shield vulnerable epithelial cell surfaces in the lungs, intestines, and other organs. Mucus is crucial for defense against pathogens and other environmental hazards, but the mechanisms by which mucus hydrogels assemble and execute their functions are poorly understood. The main obstacle has been that the enormous, heavily glycosylated, and flexible mucin proteins constituting mucus are not readily amenable to structural and molecular approaches. However, I contend that mucin glycoproteins have exquisitely specific abilities and interactions that are ultimately understandable on the molecular level. By carrying out the research plan described herein, we will crack the code that transforms the primary building blocks of mucins into diverse three-dimensional, dynamic, and active hydrogels. Specifically, we will test the hypothesis that glycosylated mucin regions are tunable entropic spacers that influence the positioning and adhesion of neighboring folded domains, thereby controlling mucin assembly and hydrogel formation. We will solve the first high-resolution structures of respiratory mucins and will develop an experimental and theoretical framework for analyzing the spans and dynamics of O-glycosylated mucin domains. Perhaps most exciting is our recent discovery that the redox set-point of the Golgi apparatus influences sialic acid decoration of O-glycans during mucus biosynthesis, with potential implications for mucus biophysics and viral penetration. We will explore the benefits of this regulatory pathway for mucin self-assembly, hydrogel properties, and mucus barrier function. Together, this work will pave the way toward rationally manipulating mucus hydrogels, offering new avenues for the treatment of inflammatory, fibrotic, and infectious diseases.

Mots-clés : mucus,mucins,sialic acid,cryo em,filament,polymer,disulfide bonds,colon,lung,fret,qsox1,glycosyltransferases,natively disordered proteins
Projet ERC : ISoSCOPE (Horizon Europe, appel 2023, Advanced grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Earth System Science
Entité participante : Institut Weizmann — Pays : Israël — Rôle : PI
Acronyme de l'entité : WIS
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2499928.0 €

Dissimilatory S metabolisms impart large S and O isotope fractionations, which are modulated by a suite of (bio)chemical reactions and physical processes (i.e., diagenesis) and ultimately preserved in the reduced and oxidized products of sedimentary S cycling (e.g., pyrite, carbonate-associated sulfate). The multi-isotope composition of such compounds encodes valuable information about microbial activity, environmental conditions, and elemental cycles. Robust interpretation of these signals requires mechanistic understanding of both the metabolic isotope fractionation itself and the impacts of diagenesis on its ultimate preservation. Such understanding is currently limited by simplified models of isotopic fractionation in dissimilatory S metabolisms, and by difficulty in capturing spatio-temporally heterogeneous diagenesis in reaction-transport models. We pioneered metabolic-isotopic models (MIMs), which account for the thermodynamics and kinetics of enzymatic reactions and turn empirical multi-isotope correlations into causal relationships. Here, I propose to develop and apply novel, experimentally-validated MIMs of the three most ecologically important S metabolisms—sulfate reduction, reduced S oxidation, and S disproportionation. By embedding these MIMs in a hierarchy of ecosystem models of increasing dimensionality and sophistication, and comparing the results to microfluidic experiments and environmental data, we will gain quantitative, nuanced insight into: (i) the controls on multi-isotope fractionation in metabolic S cycling, (ii) its heterogeneous manifestation in aqueous and solid compounds, and (iii) the use of these compounds' isotopic compositions to robustly probe S cycling on microscopic to global scales, microenvironmental conditions, and depositional parameters, in both modern and ancient settings. With S as a test case, we blaze a path to similar treatment of the processes that govern the isotopic composition of many other natural materials.

Mots-clés : biogeochemical cycles,sulfur cycle,stable isotope fractionation
Projet ERC : LEAP (Horizon Europe, appel 2023, Advanced grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Computer Science and Informatics
Entité participante : Institut Weizmann — Pays : Israël — Rôle : PI
Acronyme de l'entité : WIS
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2105840.0 €

This proposal aims to delve further into the study of Probabilistically Checkable Proofs (PCPs), a cornerstone of modern theoretical computer science, that exhibits some of the most powerful local to global behavior. Any NP proof can be written in a format that is locally testable, meaning that local pieces of the proof imply very rich global structure. This theory is strongly tied to hardness of approximation and has significant applications in cryptography. A major goal is to develop simpler and more efficient PCP constructions, with better parameters, as well as to deepen our understanding of robust encodings with local to global features, such as PCPs. The main methodology of this exploration will be through harnessing the power of the beautiful emerging theory of high-dimensional expansion (HDX). Generalizing the concept of expander graphs to higher dimensions, HDX emerge as an exciting cross-disciplinary theory with roots in group theory, number theory, algebraic topology, combinatorics, and theoretical computer science. The HDX theory is characterized by a local-to-global principle, which allows inferences about the global structure based on local link properties. This principle bears significant potential for areas like property testing and it has already shown its power with the construction of C^3 locally testable codes. As these are very closely connected to PCPs, we seek to harness HDX towards advancing our understanding of more general local-to-global encodings, and potentially paving the way for novel PCP constructions.  The research directions outlined in this proposal cover a wide array of goals, including the exploration of the HDX theory, the construction of new PCPs, inapproximability, and the creation of novel error-correcting codes. These directions seek to bridge various areas of mathematics and computer science, promising to contribute significantly to the field and open up new horizons for further research and applications.

Mots-clés : error correcting codes,high dimensional expansion,local testability,pcps,robustness
Projet ERC : DarkSHunt (Horizon Europe, appel 2024, Advanced grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Fundamental Constituents of Matter
Entité participante : Université de Bologne — Pays : Italie — Rôle : PI
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2470366.0 €

There is incontrovertible evidence that the Standard Model is not the ultimate theory of particles and interactions: it cannot explain neutrino masses, dark matter, our own existence (i.e. the Universe baryon asymmetry). A New Standard Theory must exist.  The key question is: what is the new physics scale? In the past decades, a formidable effort took place to explore the TeV scale, culminating in the LHC experiments, but no evidence of new physics has been found.  A change of paradigm may be required. New physics at low masses, the so-called dark sectors, offers a viable alternative. Their theoretical study and experimental searches are blooming.  The next 5 years offer a unique window of opportunity. New experiments will be taking data opening the possibility to search for dark sectors with unprecedented sensitivity and novel strategies: from the SBN programme, to ProtoDUNE, NA64, KM3Net, complemented by beam-dump, collider, sub-GeV dark matter, high energy neutrinos and gravitational wave searches. DarkSHunt ultimate aim is to exploit this opportunity to uncover hints (or evidence) of Dark Sectors, collaborating directly with leading experimentalists to perform dedicated analysis. It will focus on the most promising experimental strategies to search for heavy neutral leptons, dark photons, sub-GeV dark matter. It will adopt a phenomenological approach, necessary to combine information from diverse experiments, and will complement it with theoretical and astroparticle/cosmological considerations. It will focus specifically on rich (i.e. non-minimal) dark sectors at the GeV scale. Thanks to their multiple particles and interactions, they have strong theoretical motivation, can explain the 2023 discovery of nanoHertz gravitational waves and have nearly-unexplored phenomenology.  If DarkSHunt achieves its ultimate goal, it would have a groundbreaking impact on our understanding of fundamental particles and interactions, paving the way to new research directions.

Mots-clés : dark or hidden sectors,neutrinos,neutrino and dark sector phenomenology,feebly interacting particles
Projet ERC : EYAWKAJKOS (Horizon Europe, appel 2021, Advanced grants)
Domaine scientifique : Physical Sciences and Engineering
Panel : Mathematics
Entité participante : Lyon-I université — Pays : France — Rôle : PI
Acronyme de l'entité : Lyon I
Type d'entité : Enseignement supérieur ou secondaire
Financement ERC de l'entité : 2016000.0 €

The project deals with the so-called Jordan-Kinderlehrer-Otto scheme, a time-discretization procedure consisting in a sequence of iterated optimization problems involving the Wasserstein distance W_2 between probability measures. This scheme allows to approximate the solutions of a wide class of PDEs (including many diffusion equations with possible aggregation effects) which have a variational structure w.r.t. the distance W_2 but not w.r.t. Hilbertian distances. It has been used both for theoretical purposes (proving existence of solutions for new equations and studying their properties) and for numerical applications. Indeed, it naturally provides a time-discretization and, if coupled with efficient computational techniques for optimal transport problems, can be used for numerics. This project will cover both equations which are well-studied (Fokker-Planck, for instance) and less classical ones (higher-order equations, crowd motion, cross-diffusion, sliced Wasserstein flow...). For the most classical ones, we will systematically consider estimates and properties which are known for solutions of the continuous-in-time PDEs and try to prove sharp and equivalent analogues in the discrete setting: some of these results (L^p, Sobolev, BV...) have already been proven in the simplest cases ; the results in the classical case will provide techniques to be applied to the other equations, allowing to prove existence of solutions and to study their qualitative properties. Moreover, some estimates proven on each step of the JKO scheme can provide useful information for the numerical schemes, reducing the computational complexity or improving the quality of the convergence. During the project, the study of the JKO scheme will be of course coupled with a deep study of the corresponding continuous-in-time PDEs, with the effort to produce efficient numerical strategies, and with the attention to the modeling of other phenomena which could take advantage of this techniques.

Mots-clés : optimal transport,gradient flows,functional inequalities,network simplex,diffusion