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: Write a project proposal abstract for 'PRODUCTIVITY TOOLS: Automated Tools to Measure Primary Productivity in European Seas. A New Autonomous Monitoring Tool to Measure the Primary Production of Major European Seas' to be submitted under Seventh Framework.

assistant: **Abstract**

PROTOOL stands for PROductivity TOOLs: Automated Tools to Measure Primary Productivity in European Seas. The project will develop and adapt sensor technologies to measure primary production of phytoplankton with automated optical techniques, so that they can be placed on ships of opportunity (SOOP, ferries, container ships). The complete PROTOOL Measuring Device will consist of (1) a fluorometer measuring the rate of photosynthesis (using the variable fluorescence approach), (2) an algal absorption meter and (3) a hyperspectral reflectance unit. It will measure key water quality parameters like chlorophyll a, suspended matter concentrations and the light attenuation coefficient. The design will be modular so that each unit can also be used separately. The different versions of the sensors and protocol modules will be tested in the Baltic Sea, the North Sea, the English-Channel and the Gulf of Biscay, as well as in a number of Dutch estuaries. In the first 3 cases, the PROTOOL equipments will be placed next to a ferrybox on ships of opportunity. These field tests will provide the conversion factors required to calibrate the PROTOOL fluorometer. These campaigns will also produce maps of primary production with high temporal and spatial resolutions. The PROTOOL Measuring Device is unique because it is the first sensor technology that can measure autonomously biological process RATES and not only biological quantities (like chlorophyll concentration). It will provide detailed information on primary productivity which is a fundamental parameter in the carrying capacity of any ecosystem. With its technological development, PROTOOL will contribute to  a much better assessment of changing marine ecosystems. PROTOOL partners will further promote the inclusion of primary producti
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 'Planetary-scale indexing of sequencing data' demonstrating excellence, impact and implementation quality for a Horizon Europe call.

assistant: **Abstract**

Nowadays a huge amount of planetary DNA and RNA sequencing data is available and continues to double every two years. However, efficiently analyzing this data is impossible due to its size measured in petabases. Many high-impact biological discoveries could be made but are prevented by the lack of fast search algorithms. I recently demonstrated this potential by discovering an order of magnitude more RNA virus species within all public RNA samples. A global index, i.e. a planetary genomic search engine, would unlock instant and inexpensive search within petabase-scale data.I hypothesize that I can create a searchable index for all of the public DNA and RNA sequencing data. Leveraging my unique expertise across algorithms and data structures for biological sequences, my plan is to design efficient methods to assemble and compress all available sequencing data, and then construct an external-memory index that will support versatile biological queries.A planetary sequencing data index will enable a myriad of bioinformatics analyses that are currently out of reach. I will demonstrate the utility of the index by constructing a database of human transcripts with novel diseases associations, discovering novel microbial species, and providing a search engine for environmental metagenomes. The resulting unprecedented collection of assembled genomes and compressed reads will lift a major challenge in data accessibility, improving its efficiency by several orders of magnitude, revolutionizing the scale of future bioinformatics analyses.


**Keywords:** bioinformatics, sequencing data, algorithms, indexing, k-mers, compression, genome assembly
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: Explain how 'Novel testing strategies for in vitro assessment of allergens' goes beyond current state-of-the-art under Sixth Framework.

assistant: **Innovation**

Allergies to sensitising agents are steadily increasing. Risk assessment for potential skin- or lung-sensitisers, completely depends on animal testing. The overall objective of Sens-it-iv is to produce in vitro alternatives for these assays, and develop them upto the level of pre-validation. Besides reducing animal experimentation, an increase the accuracy of predicting sensitising potencies is expected. In vitro mechanisms, relevant for in vivo sensitisation, will be identified at the level of human lung or skin epithelial cells (EC), dendritic cells (DC) and T-cells.These efforts imply specific scientific (S) and technologic (T) objectives:a. Existing data on sensitising, irritating and toxic compounds are collected (S).b. In vivo changes induced by selected compounds in the specified cell types are described using functional genomics (S).c. Similarly, the impact of compounds on individual cells, and the interaction between these cells is assessed in vitro (S).d. The physico-chemical properties of chemicals responsible for metabolic activation and hapten-formation are determined (S).e. The data are collected in an Inductive Database allowing queries for data patterns and predictive models (T).f. Mechanisms specifically involved in skin and respiratory sensitisation are identified using bio-informatics (S).g. The information is used to adapt/improve existing techniques, and to develop organotypic models derived from human cells assays (T).h. A proof of principle is established on a set of selected skin and respiratory sensitisers, irritants and toxic compounds (T).Sens-it-iv is innovative primarily by the coordinated and extensive characterisation of the impact of compounds on cell-cell interactions for identification of the key mechanisms of sensitisation. Consistency
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 an impact statement for 'Titin can govern epigenetic remodelling', explaining its relevance to EU policy priorities under Horizon 2020.

assistant: **Impact**

Heart disease is a staggering clinical and public health problem and the leading cause of death for both men and women in Western countries. The underlying pathomechanism of nearly all aetiologies relates to altered contractility and cardiac tissue tension but also gene expression changes and epigenomic remodelling. Within the sarcomere, the fundamental contractile unit in striated muscle, the giant protein titin is the major source of cardiac passive tension. Since sarcomeres are connected to the nucleus, I hypothesise that titin passive tension is transmitted to the nucleus and sensed by the mechano-sensitive nuclear lamina, affecting chromatin structure and gene expression, similar to cytoskeleton passive tension in nonmuscle cells. I will test this hypothesis in human cardiomyocytes derived from induced pluripotent stem cells (hiPSC-CMs) with either a low or high titin-derived passive tension by editing the titin gene locus. I will also investigate whether changes of titin tension affect sarcomere-resident chromatin remodellers: Smyd1, Smyd2, and HP1γ. Combining fluorescence and super-resolution imaging with chromatin-immunoprecipitation sequencing and RNA sequencing, I will delineate a comprehensive map of titin-derived epigenetic remodelling in hiPSC-CMs. The TiGER project will dissect a complex biophysical mechanism leveraging on hiPSC-CMs as they represent an exceptional platform to unveil human cardiac-specific phenomena that require extensive gene editing, culture, and imaging. As titin-derived passive tension changes during development, physiology, and disease, TiGER’s results could have major implications for cardiac pathophysiology and could unlock future compelling research avenues. I will explore this novel role for titin as an epigenetic remodeller under
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 'The evolution of menstruation in primates'.

assistant: **Objectives**

Menstruation is a recent evolutionary innovation in primates: the trait is present in some species (humans, baboons) but not in closely related others (orangutans, vervets). In the latter and in most mammals, the uterine endometrium is reabsorbed at the end of the cycle instead of being shed when fecundation has not occurred. The molecular and genetic underpinnings of this complex process are not fully understood, despite its critical involvement in gynaecological conditions. I propose to discover the molecular mechanisms leading to menstruation by comparing the uterine linings from five primate species at the cellular, functional and genetic levels. The objectives are to identify the gene networks and non-coding regulatory elements that control the advent of menstruation in primates, and to understand how this genetically inherited trait was acquired in primate genomes during the evolution of the human lineage.In Aim 1, I will leverage single-cell transcriptomics to uncover the cellular composition and marker modifications that differentiate the uterine linings of menstruating and non-menstruating primates. In Aim 2, I will use deep transcriptomics and accessible chromatin assays on sorted endometrial cell populations to identify genes and non-coding regulatory regions differentially activated in menstruating species. This analysis will reveal the molecular pathways, regulation networks and cellular interplay involved in uterine tissue shedding vs. reabsorption.In Aim 3, I will replace these modifications within the context of primate genome evolution: I will elucidate the mutational dynamics by which genetic novelty has emerged during the adoption of menstruation, and how the functional divergence of the endometrium compares to other reproductive and somatic tissues.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: Describe the novelty, innovation potential and advance beyond the state of the art for 'Scalability, Robustness and Fundamental Limits in Large Scale Heterogeneous Networks' (ScaleHetNet).

assistant: **Innovation**

The proposed research will make a contribution towards the analysis and synthesis of large scale complex networks: fundamental theory will be developed and important applications will be addressed, by extending tools from control theory. Networks are present throughout the physical and biological world, but nowadays they also pervade our societies and everyday lives. Major challenges that will be addressed are:1. The engineering of large scale heterogeneous networks that are guaranteed to be robust and scalable.2. The reverse engineering of biological networks.A distinctive feature of the networks we would like to engineer, which falls outside more traditional domains in systems and control, is that of scalability, i.e. the ability to guarantee robust stability for an arbitrary interconnection by conditions on only local interactions. The methodologies that will be developed will have a significant impact in various applications where scalability is important, such as data network protocols, group coordination problems and power distribution networks, as they can lead to network designs with guaranteed robustness, thus avoiding conservative schemes with poor performance.The proposed project will also make a contribution towards the reverse engineering of biological networks at the molecular level. Life in the cell is dictated by chance; noise is ubiquitous with its sources ranging from fluctuating environments to intrinsic fluctuations due to the random births and deaths of molecules. The fact that a substantial part of the noise is intrinsic provides a major challenge in control theoretic methodologies. How can feedback be used to suppress these fluctuations, what are the associated tradeoffs and limitations, and how does nature manage to handle these so efficiently? 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 the 'Expected Impact' section for the project 'Identification of pathogenicity and virulence genes of the necrotrophic fungus Ascochyta spp. by genome-wide transcriptome analyses coupled to high-throughput next-generation sequencing' (AscoTransSeq), addressing dissemination and exploitation.

assistant: **Impact**

This project aims at identifying genes involved in pathogenicity and virulence of Ascochyta spp., the causal agents of ascochyta blight in legumes. Legumes are economically and agronomically important crops for sustainable agriculture in the European community, that have a very high potential for human and animal nutrition and the potential to fix atmospheric nitrogen. However, diseases, and especially ascochyta blight, strongly limit stable yield and quality. All major legume crops suffer from an ascochyta blight as a major constraint. The genomes of four different pathotypes of Ascochyta rabiei differing in virulence and of an isolate each of A. pinodes and A. lentis have been sequenced. This information coupled with state-of-the-art transcriptomic technologies will be applied to unravel the pathogenicity and virulence of these fungi at the molecular level. The genomes of the four pathotypes of A. rabiei will be compared to identify the genes underlying virulence. In addition, using deepSuperSAGE technology, the transcripts expressed by the pathogen during different steps of the infection process in the ascochyta-legume interaction will be compared to each other and to the transcriptome of the fungus growing in the absence of the host. This approach will identify genes specifically involved in pathogenicity. Another outcome of the project will be the construction of a global transcript map of the different genomes depicting the location of transcribed genes. During the project the applicant will learn up-to-date next-generation sequencing and gene expression techniques, and different bioinformatics software. This should substantially extend the applicant’s range of expertise beyond her existing experience in plant pathology, traditional breeding and molecular marker 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 a project proposal abstract for 'Mechanisms of cell dysfunction by aggregation dynamics of polyQ-containing proteins' to be submitted under Seventh Framework.

assistant: **Abstract**

Protein aggregation is a hallmark of several ageing-related neurodegenerative diseases, such as Huntington’s disease (HD), Alzheimer’s disease and prion-mediated diseases. Different cellular pathways influence the rate of aggregation, and clearance of intermediate protein species and aggregates in the cell (for example, autophagy or proteasomal degradation). Many signalling pathways regulate these processes. These signalling events, and the molecular pathways downstream are not completely understood. In HD there is an inverse correlation between the number of CAG triplets found in mutated huntingtin (htt) and the age-of-onset of the symptoms. However, there is a wide variation in the age-at-onset of the disease among carriers of short mutant glutamine tracts, suggesting that the genetic background strongly influences the severity of the disease. Hence the broad objective of this proposal is to find molecules that modulate protein aggregation.We will use in vivo (C. elegans) and in vitro (mammalian cells) models of HD to find new molecules and pathways that modulate aggregation and toxicity induced by polyglutamines. The second objective of this proposal is to understand the mechanism by which mHtt toxic species alter cellular processes, with special focus on pre-synaptic function.
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 'Expected Impact' section for the project 'Combined operando spectroscopy with model-based experimental design to study the mechanism of catalytic surface reactions' (OpeSpeKin), addressing dissemination and exploitation.

assistant: **Impact**

Global warming from CO2 emissions is one of the greatest challenges facing mankind. Catalysis offers the potential to utilize CO2 as a carbon source, however improved catalysts are required. To unlock the potential of catalytic CO2 conversion, it is neccessary to observe catalysts in-action ‘in-operando’ to design improved active sites and more active/selective and energy efficient processes. Operando spectroscopy is an effective technique in investigating the reactions that take place on catalyst surface. Combining operando spectroscopy with kinetics (spectrokinetics) offers a powerful approach for studying the underlying mechanism of the reaction. This approach can enhance our understanding of the surface reactions and further elucidate the role of surface intermediates in real time of reaction. In this work, the evolution of the concentration of reactants, surface species and products will be used jointly in kinetic modelling to understand the mechanism of the reaction. In most kinetic studies, the procedure leading to a possible reaction mechanism is experiment- and time-intensive. Therefore, in this research, model-based design of experiment (MBDoE) techniques will be employed in designing a set of experiments to obtain the most informative data for development of kinetic model.Overall, this research project intends to integrate operando spectroscopy with microkinetic modelling to rational design and optimization of new efcient catalytic systems for conversion of CO2.The project aims at:1.Optimizing operando spectroscopy set-up2.Developing alternative kinetic models from microkinetic analysis3.Employing MBDoE techniques to operando spectroscopy system4.Identification of reaction mechanism and precise estimation of kinetic parameters5.Investigating the correlation o
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 Europe proposal on 'The development of a full scale plant for the production of sustainable medium chain fatty acids'.

assistant: **Concept**

To meet the value-chain-wide need for a viable circular economic model that facilitates the achievement of the EUs sustainabilitygoals, ChainCraft has developed an economically-viable process that converts organic residues into valuable biobased mediumchain fatty acids (MCFA) for the agrifood and material industries. Our unique and patented solution is based on a three-stepprocess using open culture fermentation and downstream processing to create mixed MCFA and their downstream fractionatedpure products. We take organic residues from municipalities, supermarkets and food production industries and convert them intoMCFA. These MCFA are supplied to industries producing a.o. animal feed, food, herbicides, plasticizers, and detergents. In return,some of these companies supply industries of which their waste stream will again be used as feedstock in our process, making ittruly circular.Our next target in making the chemical industry more sustainable, is the construction of a full scale plant using our circular technology. The first milestone in achieving this target is the final investment decision (FID). To reach this milestone we need the are several major steps with significant challenges we need to make: a contract for feedstock and location; validate our product with our potential customers; arrange agreements with these customers; and then design our plant based on this acquired knowledge. As these steps involve significant risk the support of EIC is key in achieving our target and will help us making the necessary steps to execute our sustainable plan.


**Keywords:** fatty acids,  waste,  sustainable,  MCFA,  circular