RCaz/eu-funding-proposals-sft huggingface dataset:
system: You are an expert grant writer specializing in European Union research funding proposals. You write compelling, well-structured proposal sections that demonstrate excellence, impact, and implementation quality, using precise EU terminology and following best practices for Horizon Europe, Horizon 2020, and earlier framework programmes.

user: Compose the 'State of the Art and Innovation' section for a Horizon 2020 proposal on 'Translating the Global Refined Analysis of Newly transcribed RNA and Decay rates by SLAM-seq'.

assistant: **Innovation**

I propose to introduce novel analysis tools via a platform for three recently developed RNA sequencing (RNA-seq) mI propose to introduce novel analysis tools via a platform for three recently developed RNA sequencing (RNA-seq) methods (SLAM-seq, TimeLapse-seq and TUC-seq). All three methods enable the direct detection of new RNA transcribed by cells in a defined window of time within the pool of total cellular RNA. This is achieved by the introduction and subsequent detection of base-mismatches in newly transcribed RNA using RNA-seq. The ability to differentiate “new” from “old” RNA greatly increases the temporal resolution of RNA-seq experiments. In the frame of my ERC CoG grant “HERPES”, we developed a computational approach (an algorithm) termed GRAND-SLAM (Globally Refined Analysis of Newly transcribed RNA and Decay rates using SLAM-seq; patent application filed) to reliably define the relative contributions of “new” and “old” RNA. GRAND-SLAM not only directly computes the contribution of “new” and “old” RNA but also provides credible intervals that allow to judge the precision of the obtained ratios for each gene. GRAND-SLAM thereby provides novel means to identify perturbations in RNA synthesis and decay. Furthermore, GRAND-SLAM directly reduces experiment costs by eliminating the need for control samples to determine sequencing error rates.In conclusion, SLAM-seq will become the new standard for gene expression profiling worldwide and GRAND-SLAM the computational tool to analyze the respective data. Within this PoC-project, we will present the GRAND-SLAM analysis platform and prepare its introduction on the market with prospective customers in three areas: next-generation-sequencing companies, pharmaceutical industry, and research institutes.  We will validate th
system: You are an expert grant writer specializing in European Union research funding proposals. You write compelling, well-structured proposal sections that demonstrate excellence, impact, and implementation quality, using precise EU terminology and following best practices for Horizon Europe, Horizon 2020, and earlier framework programmes.

user: Draft the 'Objectives and Scope' section of a Horizon Europe proposal for the project 'Hybrid Winding Traction Drive Unit for Sustainable Electric Mobility'.

assistant: **Objectives**

Objective. Develop and validate a compact, high-efficiency electric drive unit (EDU) for battery-electric vehicles that delivers higher continuous power, lower losses and can be manufactured at scale in Europe. The project addresses today’s main bottlenecks: copper AC loss in hairpin windings, thermal hot spots, and control strategies that optimise the inverter and motor separately.How it will be achieved. Five coordinated work packages will deliver: (1) a hybrid hairpin–Litz winding produced with continuous wave winding and additively manufactured joints to keep a high slot fill while cutting high-frequency loss; (2) direct oil cooling of both stator end windings and rotor to remove heat uniformly and raise continuous power; (3) a multiphysics co-design framework linking electromagnetic, thermal, mechanical and fluid models with explicit design-for-manufacture rules; (4) co-optimisation of a silicon-carbide inverter and the machine using hybrid PWM and variable switching frequency, verified on a hardware-in-the-loop bench; and (5) system integration and testing of a full-scale prototype under realistic drive cycles. Open science practices include a data-management plan, open models and code, and early dissemination.Relevance to the Work Programme. The fellowship supports the European Green Deal and Fit for 55 by improving EV efficiency and affordability and by strengthening Europe’s industrial base. Expected outcomes are a validated EDU prototype and an open toolchain (models, data and software) that enable up to 10% lower vehicle energy use, a 10–15% reduction in EDU manufacturing cost and higher production efficiency. The project will generate exploitable intellectual property, high-quality publications and targeted training, advancing skills and competitiveness in E
system: You are an expert grant writer specializing in European Union research funding proposals. You write compelling, well-structured proposal sections that demonstrate excellence, impact, and implementation quality, using precise EU terminology and following best practices for Horizon Europe, Horizon 2020, and earlier framework programmes.

user: Write the concept and methodology overview for 'Tokens and their Cultural Biography in Athens from the Classical Age to the End of Antiquity' under Horizon 2020.

assistant: **Concept**

The project ‘Tokens and their Cultural biography in Athens from Classical Age to the End of Antiquity’ provides the first in depth analysis of tokens and the roles they played in the world’s first democracy. Tokens are small, coin like objects made either from metal or clay. They bear images and devices which can intrigue the modern day researcher with their complexity and originality. The inscriptions they carry - most often abbreviated references to little known Athenian institutions and practices - are quite as intriguing. A primary objective of the project is to reach a universally accepted definition for Athenian tokens and to provide scholarship with the first synthesis of this material. The project will also explore the roles played by tokens in two major sectors of Athenian democracy: the Assembly and the Jury Courts. Tokens are the material manifestations of practices and institutions that enabled the solidarity and cohesion of the citizen body, safeguarded legal and political equality, and were key parts in transcending knowledge and expertise. Primary research on the tokens themselves, material which is abundant but under examined and most often mislabeled, as well as library research, will chart the images on Athenian tokens by discerning categories, types and subtypes. Plotting the tokens against their find spots - most notably the sites where the affairs of the world's first democracy were run - will visualize the remarkable social and political network enabled by tokens. Tokens are unassuming objects that support community and participation in civic life, providing a model for the challenges of the modern day.
system: You are an expert grant writer specializing in European Union research funding proposals. You write compelling, well-structured proposal sections that demonstrate excellence, impact, and implementation quality, using precise EU terminology and following best practices for Horizon Europe, Horizon 2020, and earlier framework programmes.

user: Describe the specific objectives and expected outcomes for 'Long-term Serial Multi-contrast Quantitative MR Imaging and Volumetry' in the context of a Sixth Framework call.

assistant: **Objectives**

Magnetic Resonance Imaging (MRI) is an essential tool for both clinical diagnosis and cognitive research. Nevertheless, it is not yet fully exploited, because a lot of information is not available to the clinician. In fact, data are acquired on various sca nners, with various scanning properties and at various times, and a full analysis of these data requires to put them all in the same referential. This project addresses the problem of registering these data acquired with various scanning characteristics, a t several time steps and on different scanners, for longitudinal analysis and quantitative MRI. Thus, longitudinal analysis gives information on deforming processes of brain structures, that can occur in several neurological disorders. Quantitative MRI giv es information on volumes and tissue characteristics, to study pathological evolution compared to normal one, and improve diagnosis quality.Finally, to undertake long term serial studies, an analysis of true changes when comparing scans acquired with diffe rent scanners will be considered. This will be of major importance due to the apparition of new scanners of higher magnetic fields, that are characterised by different geometrical distortions and intensity distributions with respect to traditional scanners .Various registration methods will thus have to be considered, combined with automatic segmentation algorithms, allowing to obtain quantitative information on volume changes and on tissue changes in longitudinal analysis, with data acquired with various sc anners.
system: You are an expert grant writer specializing in European Union research funding proposals. You write compelling, well-structured proposal sections that demonstrate excellence, impact, and implementation quality, using precise EU terminology and following best practices for Horizon Europe, Horizon 2020, and earlier framework programmes.

user: Write clear, measurable objectives and define the scope for the project 'Ca2+ homeostasis and oxidative stress in muscular dystrophy - mitochondria as a potential target of the necrotic /apostosis cascade' (1994-1998) under Fourth Framework.

assistant: **Objectives**

It is widely thought that in Duchenne's muscular dystrophy, the muscular cells death is linked with disruption of Ca2+ homeostasis and oxidative stress. The permeability transition pore is an inner membrane channel inhibed by Cyclosporin A which might participate to mitochondrial Ca2+ homeostasis and which is a target of oxidative stress. The irreversible opening of permeability transition pores leads to a collapse of ATP synthesis and induces cell death. Mdx mice is an established animal model of Duchenne's muscular dystrophy. We intend to (1) investigate intracellular Ca2+ homeostasis in two types of muscle fibers: skeletal muscle which will undergo cell death, and extraocular muscle which is spared by the disease; (2) find out whether mitochondrial function is differentially regulated in these two types of muscle fibers; (3) study the effects of Cyclosporin A on the response of the permeability transition pore to conditions of oxidative stress and Ca2+ overload.
system: You are an expert grant writer specializing in European Union research funding proposals. You write compelling, well-structured proposal sections that demonstrate excellence, impact, and implementation quality, using precise EU terminology and following best practices for Horizon Europe, Horizon 2020, and earlier framework programmes.

user: Compose the 'Concept and Approach' section for a Horizon 2020 proposal on 'Republics on the Stage of Kings. Representing Republican State Power in the Europe of Absolute Monarchies (late 16th - early 18th century)'.

assistant: **Concept**

RISK investigates Republican pageantry and encomiastic production from late 16th- to early 18th-century Europe, with regard to the Italian city-states that maintained their independence throughout this timeframe (Venice, Genoa, Lucca), the Republic of Ragusa (today in southernmost Croatia) and the Dutch Republic. A multidisciplinary corpus of sources is taken into account, including: praising texts celebrating Republican values; paintings and engravings displaying civic rituals, or portraying mythological prosopopoeias of the Republic; and written accounts of public ceremonies, such as the election of the Doge or the triumph performed after a victorious campaign.RISK provides the first comprehensive overview of these Republican displays of state power in an era - the so-called Ancien Régime - that is generally perceived to have been marked by the rise of a unique political model, i.e. the absolute monarchy. By comparing the representation of kingship and the staging of the Republican state, RISK analyses to what extent the absolutist framework influences the display of ideals such as freedom, equality, and the common good. The goal is to comprehend how the rhetorical devices of Baroque culture extoll a power that does not apply to someone (the King), but rather to something (the Republic and Republican virtues).RISK is expected to lead to a paradigm shift in our understanding of early modern cultural policy and propaganda. Indeed, Ancien Régime republicanism offers a repertoire of images and concepts that embodies an alternative mode of thinking about the state. This legacy allows us to challenge the perceived idea of a Janus-faced early modern Europe, where a series of binary oppositions would supposedly herald the transition towards modern democracy (monarchy versus r
system: You are an expert grant writer specializing in European Union research funding proposals. You write compelling, well-structured proposal sections that demonstrate excellence, impact, and implementation quality, using precise EU terminology and following best practices for Horizon Europe, Horizon 2020, and earlier framework programmes.

user: Draft the 'Objectives and Scope' section of a Horizon 2020 proposal for the project 'Revitalizing the clinical potential of type I IFNs in fighting influenza A virus infections with AcTaferon.'.

assistant: **Objectives**

Based on their antiviral and antitumor effect, type I interferons (IFNs) were believed to be the miracle drug to tackle viruses and cancer. However, clinical IFN applications remained limited due to severe side effects resulting from widespread cellular sensitivity to IFN, which limits the administrable doses. Hence, the drug concentration at the desired infection or tumor site is often too low to be fully therapeutic efficient. AcTaferon (Activated-by-Targeting interferon), co-developed by Prof. Uzé, circumvents these obstacles. By fusing an IFN mutant with strongly reduced receptor binding affinity to a targeting moiety that recognizes a surface marker on specific cells, AcTaferon remains inactive “en route” through the body and unveils its biological activity only on specific target cells. Robust tumor regression without side effects and preliminary antiviral effects underscore the huge clinical potential of AcTaferon to fight cancer and viral diseases. By combining the AcTaferon and influenza expertise of Prof. Uzé and Prof. Saelens, respectively, this interdisciplinary project offers the opportunity to broaden the innovative AcTaferon therapeutic strategy from the cancer to the viral infection field. Influenza A was selected as a pilot target as seasonal influenza A epidemics and occasional pandemics remain a serious health threat causing substantial morbidity and mortality. Influenza A-targeted AcTaferons will be developed and analyzed in relevant in vitro and in vivo models. Eventually, all knowledge will be transferred to Orionis, a company that will implement the AcTaferon technology to develop novel drugs. My background on the intracellular processes that negatively regulate cytokine receptors and hence influence the cellular sensitivity to a (therapeutic) cyt
system: You are an expert grant writer specializing in European Union research funding proposals. You write compelling, well-structured proposal sections that demonstrate excellence, impact, and implementation quality, using precise EU terminology and following best practices for Horizon Europe, Horizon 2020, and earlier framework programmes.

user: Compose a compelling abstract for 'Global Amyloid Mapping: Solving Amyloid Nucleation by Deep Mutagenesis' demonstrating excellence, impact and implementation quality for a Horizon Europe call.

assistant: **Abstract**

Amyloid fibrils form and precipitate in more than 50 incurable human diseases, including Alzheimer’s and Parkinson’s disease. All proteins may be able to form amyloids, at least under certain circumstances. However, aggregation is actually rare as the process of amyloid formation is controlled by a high kinetic barrier: protein sequences have to cross a free energy barrier to nucleate transition states which then seed irreversible fibril formation. Short-lived transition states are extremely challenging to study using biophysical methods. We have recently developed a massively parallel genomics approach to quantify the rate of aggregation of thousands of protein sequences. We also have evidence that, by quantifying the interactions between mutations, we can capture the key interactions between residues in the transition state. Here, we will unleash the potential of this approach by targeting the following aims:1) Map the impact on amyloid nucleation of all possible mutations in >60 human and functional amyloids - generating reference atlases for clinical variant interpretation2) Build an energetic and structural model of the transition state of disease-associated amyloids3) Uncover sequences across the genome that nucleate amyloids in response to environmental stressThis project will uncover the rules required to understand, predict and engineer amyloid formation. By identifying the mutations that do and do not lead to amyloid formation, we will reveal which variants accelerate aggregation and cause disease. We will also address one of the most important questions in the field, i.e. identifying the interactions established in the transition states of amyloid nucleation, guiding the development of therapeutic approaches in amyloid diseases, including the worst kinds of d
system: You are an expert grant writer specializing in European Union research funding proposals. You write compelling, well-structured proposal sections that demonstrate excellence, impact, and implementation quality, using precise EU terminology and following best practices for Horizon Europe, Horizon 2020, and earlier framework programmes.

user: Compose the 'State of the Art and Innovation' section for a Seventh Framework proposal on 'A Systems Biology Approach to Elucidate the Yeast Metabolic Network'.

assistant: **Innovation**

The ultimate goal of systems biology is to generate mathematical models to comprehensively describe the dynamics of a biological system. Among all biochemical and informational systems that operate in cells, metabolism is unique because the composition and topology of the network of metabolic reactions is almost completely known. What is currently poorly understood, is how this system operates, how it is controlled and how it adapts to changing conditions of supply and demand. Most current models of metabolism and of biological processes in general are limited by the incompleteness and the restricted diversity of the data they are based on.  In this project I propose to generate, for the first time, quantitative data sets of all metabolic proteins and their regulatory phosphorylation sites in the model organism yeast Saccharomyces cerevisiae, under a defined set of conditions. Such a comprehensive proteomic analysis will be achieved by means of a novel targeted proteomics approach, pioneered in the host group and which I preliminarily developed in the first months of my work. In the context of a well-established collaboration with metabolomics and computational systems biology groups at ETH Zurich, the generated proteomic and phosphoproteomics data on metabolic enzymes will be coupled to quantitative data of the associated mRNA transcripts, metabolites and metabolic fluxes. Integration of these different quantitative data types will be done with a genome-scale mathematical model of the whole yeast metabolism. The data generated will be unprecedented and the research will set us on a path towards the understanding of the control structure of S. cerevisiae metabolism and the identification of key regulation sites that actively control metabolic processes, advancing both t
system: You are an expert grant writer specializing in European Union research funding proposals. You write compelling, well-structured proposal sections that demonstrate excellence, impact, and implementation quality, using precise EU terminology and following best practices for Horizon Europe, Horizon 2020, and earlier framework programmes.

user: Write clear, measurable objectives and define the scope for the project 'Artificial Motor Proteins: toward a designed, autonomous protein motor built from non-motor parts' (ArtMotor) under Horizon 2020.

assistant: **Objectives**

Molecular motors and machines are essential for all cellular processes that together enable life. Built from proteins, with a wide range of properties, functionalities and performance characteristics, biological motors perform complex tasks and can transduce chemical energy into mechanical work more efficiently than human-made combustion engines. Sophisticated studies of biological protein motors have led to much structural and biophysical information and the development of models for motor function. However, from the study of highly evolved, biological motors it remains difficult to discern detailed mechanisms, for example about the relative role of different force generation mechanisms, or how information is communicated across a protein to achieve the necessary coordination. A promising, complementary approach to answering these questions is to build synthetic protein motors from the bottom up. Indeed, much effort has been invested in functional protein design, but so far, the ‘holy grail’ of designing and building a functional synthetic protein motor has not been realized. The purpose of ArtMotor is to design and build functional, synthetic protein motors capable of moving and transducing energy, based on existing, non-motor protein modules of known molecular function. Harnessing the synergy of expertise in computational protein design, structural and molecular biology, and single-molecule detection, we will use a two-pronged approach to (a) construct relatively simple protein motors that will require external control, while (b) construct, step by step, an autonomous protein motor capable of moving along a track. Such a functional, synthetic protein will constitute a ground-breaking advance in synthetic biology, physics and engineering. In addition to gaining new in