Dragon09/odtu_chatbot huggingface dataset:
mineralization within macromolecular condensates the chemical playground of living cells

organisms form crystalline materials with superior structural and mechanical properties this arises from the ability of functional macromolecules to create intricate architectures via a multistep crystallization process current approaches to engineer bioinspired minerals focus on interactions between macromolecules and minerals in dilute aqueous environments rarely considering the emergent properties of macromolecular condensates however we and others showed that macromolecular crowding is intimately associated with biomineral formation in vivo in this project we will develop a new type of chemistrydensephase mineralizationto unlock the pathways mastered by natureour hypothesis is that weak polymerion interactions within dense phases tune the chemical landscape controlling the crystallization process and the properties of its products remarkably our preliminary results using the calcium carbonate system show that molarrange polymer concentrations four orders of magnitude denser than in previous works result in intricate crystals with lifelike properties we will investigate densephase mineralization in both synthetic and living systems relying on our unique expertise in cryoelectron and xray microscopies of hydrated biological samples in aim 1 we will grow crystals in a dense polymer phase and use the crowded environment to sculpt architectural motivesin aim 2 we will investigate the challenging phase separation regime and transform inorganic condensates into transient precursors for mineralizationin aim 3 we will elucidate how liquidliquid phase separation evolved by mineralizing organisms to regulate inorganic condensate formationthis project will open an uncharted chemical landscape to form and control bioinspired minerals the outcome will be a toolbox for process design that allows to optimize material properties the highest gain we can ask for in bioinspired mineralization
prostate cancer diagnostics using a noninvasive test based on innovative glycanbased scanning

prostate cancer pca is the 2nd most frequent cancer in men with 14m new annual cases and nearly 04m deaths worldwide in 2020 pca incidence is expected to increase to 21m cases and 06m annual deaths by 2035 statistically 1 in 8 men will get pca in their lifetime however nearly 50 of cancer deaths may be avoided if pca were detected at early stages survival is proportional to the stage reached at the time of diagnosis hence earlystage diagnostics is key to reduce mortality our aim is to clinically validate register proscan an affordable noninvasive nextgeneration liquid biopsy pca diagnostic test with a final accuracy of up to 90 the proscan is the first test for earlystage pca diagnostics based on glycan analysis in blood proscan will identify healthy men and those at risk of pca who need a confirmatory biopsy being so accurate proscan will eliminate 16 m of avoidable biopsies with the cost of 15bn in the eu and the us alone
deployment and assessment of predictive modelling environmentally sustainable and emerging digital technologies and tools for improving the resilience of iww against climate change and other extremes

ploto aims at increasing the resilience of the inland waterways iww infrastructures and the connected land infrastructures thus ensuring reliable network availability under unfavourable conditions such as extreme weather accidents and other kind of hazards our main target is to combine downscaled climate change scenarios applied to iww infrastructures with simulation tools and actual data so as to provide the relevant authorities and their operators with an integrated tool able to support more effective management of their infrastructures at strategic and operational levels towards this direction ploto aims to use high resolution modelling data for the determination and the assessment of the climatic risk of the selected transport infrastructures and associated expected damages use existing data from various sources with new types of sensorgenerated data computer vision to feed the used simulator utilize tailored weather forecasts combining seamlessly all available data sources for specific hotspots providing early warnings with corresponding impact assessment in real time develop improved multitemporal multisensor uav and satellitebased observations with robust spectral analysis computer vision and machine learningbased assessment for diverse transport infrastructures design and implement an integrated resilience assessment platform environment as an innovative planning tool that will permit a quantitative resilience assessment through an endtoend simulation environment running whatif impactriskresilience assessment scenarios the effects of adaptation measures can be investigated by changing the hazard exposure and vulnerability input parameters design and implement a common operational picture including an enhanced visualisation interface and an incident management systemthe ploto integrated platform and its tools will be validated in three case studies in belgium romania and hungary
synthetic and structural biology of rab gtpase networks

eukaryotic cells are characterized by their compartmentalization into hundreds of different membranebound organelles with unique biochemical identities small gtpases of the rab family play a central role in this organization but how they are able to generate spatiotemporal order in the complex cellular environment is currently not known most previous studies on rab gtpases have either relied on describing their behavior in living cells or in highly reductionist biochemical assays however neither of these two approaches can explain the dynamic activity patterns of rab gtpases associated with their cellular functions it has become clear that rab gtpases are controlled in sophisticated regulatory networks with emergent selforganizing properties to obtain a mechanistic understanding of these rab gtpase systems new experimental assays are now required in this proposal we will use a bottomup synthetic biology approach to rebuild the biochemical networks of rab gtpases from purified components and demonstrate their selforganization into spatiotemporal activity patterns in vitro we will combine these reconstitution experiments with cryoelectron microscopy to elucidate the structures of membranerecruited rab gtpase regulators finally we will use microfabrication and laser lithography to prepare a mimic for the compartmentalized cell and find out how rab gtpase signaling systems sense and process preexisting geometric and biochemical cues as in the living cell this project will provide novel quantitative information from different scales from the emergent ensemble behavior down to the molecular structure of protein complexes together this data will reveal how signaling systems of rab gtpases control membrane identities in space and time thereby improving our understanding of the intracellular organization of the eukaryotic cell
fluid gap electroactivepolymer machines for a new generation of mechatronic systems

while mechatronic solutions become increasingly pervasive there are areas such as the space or the ocean depths that are still difficult to reach and exploit through conventional technologies yet such areas represent an immense source of materials and energy a bottleneck is represented by actuationgeneration technologies which struggle in unconventional environments electrostatic drives based on electroactive polymers eaps have long been regarded as a potentially gamechanging solution as they rely on lightweight materials and feature no rigid moving parts but their applicability has been severely hindered by reliability and performance limitations recently fluidgap transducers fgts which leverage combinations of dielectric polymers and liquids have emerged as a breakthrough as they have shown potential for reaching significantly improved performance and lifetime with this project we will push fgts beyond their limits making them able to operate in low pressure atmospheres for space applications or underwater and at high pressures for application in the marine environment to achieve these goals we will 1 expand base knowledge on the working principle of fgts 2 develop new operating principle concepts based on highly unconventional material combinations enabled by our recent findings such as lowpressure airvacuum dielectric gaps or highpermittivity mildlyconductive leaky dielectric liquids 3 provide proof of concept and validation of such new paradigms in a number of relevant scenarios including fgtdriven robotic systems able to operate in vacuum for space applications or underwaterat high pressure and scaled prototypes of distributed energy harvesters from sea waves this project will mark a leap in the field of electromechanical drives and allow mechatronic devices to reach frontiers that are unthinkable with conventional technology
research entrepreneurship training ipexchange chip platform of europractice services

reticles will provide a platform that nurtures the growth of a design ecosystem in europe this will be achieved by building on the existing europractice platform sustaining its key elements and extending it with new services and technologies europractice is a wellestablished and widely used platform that provides european academia and smes with a full range of microelectronic services needed to design fabricate package and integrate microelectronic circuits this service includes affordable access to industrystandard design tools access to a wide range of fabrication technologies multiproject wafers and small volume production of asics photonics mems microfluidics etc full technical support and design methodology trainingby building on the europractice services the project will deliver impact already from the start the platform will then be extended to meet new technology challenges and further support semiconductor sovereignty for europe emerging technologies from european research centres and pilot lines will be added to the platform including those with lower trl design efficiency will be enhanced and supported through design reuse and establishing a design ip exchange repository efficient design at the smallest geometries will be enabled with advanced design tools and new cloud based solutions for highvalue ip the creation of smarter integrated systems will be stimulated through advanced system integration of dissimilar semiconductor technologies and chiplets a pipeline of talent for europe delivered through comprehensive upskilling and reskilling training courses and economic growth facilitated by supporting subsequent commercialisation of academic researchthrough advanced design tools leading edge semiconductor technologies and bespoke training reticles will provide a breeding ground for cuttingedge research deeptech startups and growth of the semiconductor design ecosystem in europe
profile nucleases and repurpose offtargets to expand gene editing

programmable nucleases reside at the nexus of advanced gene editing and microbial defense these nucleases degrade phage dna but avoid genomic dna to provide the microbe with adaptive immunity the standardbearer crisprcas9 relies on a guide rna grna its program to precisely cut a complimentary genetic sequence its target for precision gene editing these programmable nucleases deliver cure for genetic diseases like anemia blindness and cancer quick disease model development and diagnostics for viruses like sarscov2hunts across microbial genomes have exposed thousands of programmable nucleases each could be another valuable tool for genome engineers but we know just too little about them to use them safely even cas9 does not have guidetarget parity it cuts partially matched offtarget genome sites which can lead to dangerous side effects though we work hard to avoid offtargets partial matching may have a bright side what if we leverage it using it to make gene editing more predictableusing highthroughput biochemistry we will profile nucleases and repurpose offtargets to expand gene editing the protg research program will profile guidetarget parity specificity across promising newly discovered programmable nucleases it will deliver a toolset for assessing this critical safety feature rapidly and broadly finally we will test the hypothesis that purposefully misprogramming nucleases can direct specific repair outcomes we intended to benefit europe and the world community with safer and more diverse gene editing tools for achieving its horizon europe health technology and environmental goals
datadriven cancer genome interpretation for personalised cancer treatment

cgiclinics aims at improving personalised medicine in oncology by optimizing genomic data interpretation after sequencing and before advising on compatible targeted therapies interpretation is a bottleneck for the full deployment and broad accessibility of next generation sequencing ngs in cancer management the project tackles the 3 main hurdles in the interpretation of cancer mutations it is not systematic it deals with a majority of variants of unknown significance and it fails to empower patientsthe interpretation of tumor genomic data relies on the work of experts reviewing scattered databases and resources in a timeconsuming process that may lead to suboptimal clinical decisions cgiclinics will systematize the interpretation process by integrating relevant public and private databases hospitals in a onestop shop tool with the possibility to organize virtual molecular tumor boards cofacilitated by reference hospitals project will have three phases a setup assess needs validation pilot with the 9 clinical partners and replication 30 hospitals across eu it will enable democratization of genomic data interpretation independent of their size resources and profiling technology and provide health economics validationrelying on a systematic automatic learning platform gciclinics will increase the share of interpretable variants in tumors from the current 912 to at least 50 and features that constitute biomarkers of drug response the interpretation process is complex for most cancer patients alienating them from knowledge of their illness cgiclinics will build educgi an app to help them understand the information gained through interpretation of their tumors facilitating informed discussions with clinicians and sharing their data for research ultimately the project is built to inform policymakers on cancer management and empower patients
building climate resilience via large scale uptake of systemic solutions in agricultural ecosystems in the pannonian region

climapannonia is the coordinated effort of key stakeholders of the pannonian biogeographical area pbs towards strengthening the resilience of the agricultural sector and the regions community against climate change disastrous effects this will be achieved by enabling the widest possible uptake of tested and validated climate neutral solutions for four agriculture subsectors i waterfood nexus ii agroforestry iii organic crop production iv cattle productionclimapannonia aims to support pba agriculture sector in drastically improving its climate resilience by implementing innovative systemic solutions and fostering collaboration among the six countries within the pba hungary serbia croatia romania czechia and slovakia climapannonia will pave the way for a more sustainable and resilient agricultureby harnessing the knowledge and expertise of leading experts in pba and leverage the knowledge of partners from countries such as germany italy and france climapannonia seeks to ensure that the solutions implemented are innovative not only at pba level but also at european scale
simultaneous multiparametric mea based platform for invitro chronic cardiotoxicity assessment with livecell fluorescence imaging and electrophysiology

cardiac drugrelated adverse effects have been the major causes for the failure or withdrawal of drugs from the market with a growing global market cardiotoxicity still remains a bottleneck in the chain of drug development despite the large investments in drug discovery and development the number of approved drugs has been declining current invitro technologies assess functional cardiotoxicity relying on shortterm electrophysiological recordings detection of cardiac action potentials ap however drug toxic effects may manifest themselves in other ways such as morphological alterations toxic chemical species generation or metabolic dysfunction these effects are categorized as structural cardiotoxicitypresently functional and structural toxicities cannot be assessed simultaneously on the same cardiac cell culture in longterm experiments this represents a substantial barrier to a deeper toxicity assessmentsimultox addresses this need with a novel platform for multiparametric detection of cardiac functional and structural toxicity starting from the unique laserbased technology of foresee biosystems simultox aims at developing an invitro platform that exploits a combinatorial approach of ap recordings and livecell fluorescence imaging of the same cardiac cell culture more importantly it will provide these capabilities in extremely long tests more than 1 month that enable the assessment of chronic toxic effectsthe final objective is the commercialization of a platform that will reshape the market of invitro cardiotoxicity assessment the product will generate high demand for equipment in the markets of cardiac physiology safety pharmacology and drug development in perspective simultox will pave the way also to new products for assessing functional and structural neurotoxicities simultaneously allowing foresee biosystems to expand substantially its target market
resurrecting reevolving and reinventing rubisco from the evolutionary past of earths no 1 co2fixing enzyme to its synthetic future

can we reconstruct the engine of natural co2fixation rubisco catalyzes the key reaction in photosynthesis the capture and conversion of atmospheric co2 into biomass however despite billions of years of evolution the enzyme is still constrained by a tradeoff between co2fixation activity and co2specificity which limits photosynthetic carbon capture and thus directly agricultural yield in pro2neorubisco we will overcome this fundamental limitation of photosynthetic co2fixation with a completely fresh approach we will use an evolutionarysynthetic biology strategy to study the evolutionary history of rubisco derive a molecular understanding for the enzymes mechanism and develop highly efficient newtonature solutions that we will validate in a realworld context the living chloroplast we will use ancestral reconstruction to replay crucial steps in the evolutionary history of the enzyme we will resurrect the very first scaffolds that just learned to fix co2 protorubiscos and study rubisco ancestors that started to loosely interact with an accessory small subunit we will reevolve these ancestral enzymes and provide them with artificial small subunits to open up new evolutionary paths leading to improved variants these revolutionary studies will be complemented by synthetic biology efforts we will liberate rubisco from its entropic constraints by separating the complex multistep reaction onto different proteins that work in tandem and go even one step further by reinventing the enzymes scaffold finding a new home for the rubisco reaction and create a truly neorubiscocompared to many efforts in the field pro2neorubisco does not screen for existing rubiscos with improved kinetics or improving existing rubiscos in pro2neorubisco we aim at reexploring the history and evolutionary landscape of rubisco and delivering completely novel architectures for the key driver of the global carbon cycle
versatile printed solutions for a safe and highperformance battery system

in order to boost the transition to a climate neutral transport sector versaprint will bring innovations to the battery system to tackle safety issues enhance performances as well as decrease cost and environmental impact the versaprint technical solutions will be achieved mainly by 2d3d printing directly on battery components and will operate from the heart of the battery system i providing an efficient cell thermal regulation in order to reduce risk of thermal runaway tr and increase density and lifetime ii significantly improving the system thermal and safety management thanks to in operando sensoring iii adding thermal and safetyoriented functionalities on busbars iv allowing easy and safe dismantling and remanufacturing v lowering the casings weight without losing its capability to contain tr and while ensuring good recycling rate vi providing an advanced thermalfire response and vii controlling the exhaust gases released during a tr by cooling and evacuating them safelyversaprint will also implement a decision tool in order to choose the most optimised configuration for a given end application and will provide a validation at trl5 i at module level with two module prototypes for automotive and aeronautics as well as one virtual module prototype for waterway transport ii at system level through simulation for all these applications other applications such as bus nonroad mobile machinery and stationary storage will be explored as well through simulationversaprint aims to reach the cost and performances targeted in batteries europe 2030 kpis while increasing module density by 5 and significantly improving the battery system fire resistance and safety no fire outside module during tr sustainability will be assessed at all development stagesthe multidisciplinary consortium gathers 3 rtoacademic partners and 7 industrial partners 4 ind and 3 smes and is completed by 12 industrial advisory board members
toxicologytesting platform integrating immunocompetent in vitroex vivo modules with realtime sensing and machine learning based in silico models for life cycle assessment and ssbd

safe and sustainable by design approach requires an entire life cycle monitoring of toxicity of chemicals however current testing systems cannot mimic the exposure conditions related to each step and are not compatible with downstream in silico analyses new sets of instrumentation that enables modular testing capacities with integrated data bridging and progressive in silico model development systems are needed toxbox will provide a device based on a prototype developed in a h2020 project panbiora with a flexible microfluidic and instrument architecture to provide a plug and play testing platform to ease accessibility and interlaboratory validation the system will incorporate the following tests with modifications for each step of life cycle automated cytotoxicity and genotoxicity tests connected barriermetabolic tissue couples with cytokine and realtime electrochemical readouts flow cycle modules with environment mimicking conditions a testing module based on zebrafish embryo with mechanical stimuli the system will be validated using metallic 2d structures and nanoparticles biocides and known endocrine disruptors custom made functional polypeptides novel biocides will be used to cover the design phase progressive in silico models for long term effects will be iteratively developed and used to predict each new group to be tested until good predictability is achieved with new chemical formulations comprehensive risk assessment a data management platform that enables interfacing with the available databases will be developed after interlaboratory validation of the device by 4 partners a standardization folder will be prepared to make the device available for testing with accessibility at all stages of material life cycle assessment to different stakeholders toxbox aspires to bring forth an instrument that will provide reliable toxicity data in relevant conditions for each chemical and enable reliable in silico model development