Dragon09/odtu_chatbot huggingface dataset:
molecular mechanisms underlying zika virus transmission by aedes aegypti mosquitoes

the public health response to emerging mosquitoborne viral diseases is often inefficient because the causative agents are recognized and the prevention measures are deployed only after the disease has spread to predict which viruses and mosquitoes have the highest potential to cause future outbreaks understanding the mechanisms determining the virus susceptibility of mosquitoes and the mosquito transmissibility of viruses is needed in this study i propose a twopronged approach to identify both the viral and mosquito factors involved in molecular compatibility between the human pathogenic zika virus and its main vector aedes aegypti by combining my skills in molecular virology with the host labs expertise in mosquito experimental infections in vivo first i will examine the mosquitovirus protein interactome by a proteomics strategy based on crosslinking immunoaffinity purification and mass spectrometry mosquito factors regulating virus susceptibility will be identified by subtractive comparison of virusbinding mosquito proteins between two mosquito strains displaying different levels of zika virus susceptibility the correlation between virus susceptibility and the identified proteins will be validated by geneknockdown assays and expression surveys using a collection of mosquito strains second i will use an innovative reverse genetics system to create chimeric zika viruses from two parental virus strains with different levels of mosquito transmissibility the viral genes required for efficient transmission by mosquitoes will be identified by comparing transmissibility between chimeric constructs together this project will provide important new insights into vectorvirus specificity and significantly improve our understanding of mosquitoborne virus emergence
synbee expanding synthetic biology entrepreneurial ecosystems

synthetic biology is a disruptive technology that enables completely new processes and products for industry medical applications and food production it makes the processes and products cheaper and more sustainable synbio will renew and challenge many major industries the estimated overall market to be affected by synbio exceeds 13 trillion the global synbio market is expected to grow from 53 billion in 2019 to 189 billion by 2024 with a cagr of 288 leading european research organizations have a proven scientific record of excellence in the field however european science remains largely underexploited commercially one impact factor is difficulty to quickly consolidate transdisciplinary teams indeed there is a need for clearer vision on the necessary current and future skills required by the industry synbio is a relatively young discipline made up of multiple subdivisions thus searching for a right profile kol researcher intern is timeconsuming for industrial companies and can be even longer for startups while the boom of accelerators and incubators and entrepreneurial training have driven startup creation the lack of specific thematic approaches can hinder the creation andor maturation of synbio startups the synbee project will address these challenges by iswot analysis matrix of best practices mapping of academic profiles and industry in synbio iigeneral and synbiospecific entrepreneurial training in close interaction with the industryiiinetworking matchmaking between candidates and hosting and mentoring industrial partners hackathons pitch contests ivcreation of a path from talented student to startup creation and investor workshopsvpolicy making and mentoring between ecosystemsvispecific focus will be brought to women in synbio synbee will be implemented by key synbio academia industry accelerators investors from 25 eu countries including 7 emerging and 6 moderate ecosystems
scalable multichip quantum architectures enabled by cryogenic wireless quantum coherent networkin package

todays tremendous interdisciplinary effort towards building a quantum computer promises to tackle problems beyond reach of any classical computer although intermediatescale quantum computers have been recently demonstrated to exceed the capability of the most powerful supercomputers it is widely recognized that addressing any realworld problem will require upscaling quantum computers to thousands or even millions of qubits this proposal focuses on the grand challenge of scalability in quantum computers from a fullstack architectural standpoint and enabled by communication networks operating within the quantum computing package at cryogenic temperatures the quadrature project hence aims to pioneer a new generation of scalable quantum computing architectures featuring distributed quantum cores qcores interconnected via quantumcoherent qubit state transfer links and orchestrated via an integrated wireless interconnect this novel architecture supports reconfigurability to serve massive flows of heterogeneous quantum algorithmic demands the main objectives are i to experimentally prove the first microintegrated allrf qubitstate transfer link within a cryogenic tunable superconducting cavity waveguide in the microwave and thz frequency region for quantumcoherent frequencymultiplex and routing ii to achieve experimentally the transfer of classical data through wireless inpackage links by integrated cryoantennas and tranceivers iii to build protocols for a quantumcoherent integrated network enabling the exchange of qubits through the coordination of the quantumcoherent data plane and the wireless control plane iv to develop appropriate scalable architectural methods such as mapping scheduling and coordination approaches across multiple qcores and v to demonstrate the scalability of the approach via multiscale design space optimization and for a set of quantum algorithm benchmarks with at least 10x improvement in overall performance
climateaware resilience for sustainable critical and interdependent infrastructure systems enhanced by emerging digital technologies

recharged is a transformative project that has the vision to develop a new integrated framework toward a practical visualisation platform in order to optimise and streamline climate resilience and wholelife carbon emission assessments for interdependent transport and energy systems lifelines and assets itesla to achieve this recharged harnesses the power of digital technologies and data to quantify the functionality and recovery of itesla after hazards this is in response to the lack of methods of assessment and communicable visualisations of consolidated climate resilience and wholelife carbon emission metrics for itesla recharged will account for interdependencies that lead to failure propagation in transport and energy systems to accelerate posthazard recovery mitigate losses and societal ramifications due to climate change in doing so recharged underpins synergies and participatory decisionmaking to combat siloed thinking in infrastructure management this project will lead to 50 faster decisionmaking in itesla management 50 reduction of carbon emissions for the two case studies analysed create new jobs and make europeans fit for the digital age recharged is a synergy that combines the exchange of interdisciplinary knowledge and tailored training of staff through an alliance between leading academic institutions industrial partners smes and a research and technology center all beneficiaries are committed to exploiting and transferring their skills and knowledge to incentivise datadriven resilience toward climate adaptation and reduce emissions in critical infrastructure recharged will augment researchers skills and career perspectives create a community of practitioners improve critical infrastructure and ultimately make people feel safer
pseudopin

pseudouridine is abundant in major classes of noncoding rna ncrna including ribosomal rna transfer rna and spliceosomal rnas the watsoncrick base pairing potential of is identical to that of uridine but may stabilize rna structures and engage in rna interactions distinct from those of uridine probably explaining its requirement for cellular viability in addition to the many constitutive sites in major ncrnas recent reports have uncovered induced by specific stimuli or present in specific cell types in rare cases with demonstrated importance for cellular translation and splicing patterns nonetheless the full extent of occurrence and regulatory consequences of induced pseudouridylation remain unknown highlighting the outstanding potential for discovery on this topic pseudopin builds on my observation that the gene encoding pseudouridine synthase pus5 in the plant arabidopsis thaliana exhibits mrna isoform switching upon immune receptor activation in growing seedlings pus5 encodes an organellar enzyme but immune receptor activation induces transcription initiation at a downstream site to exclude the organellar target peptide from the pus5 protein thus giving rise to a nucleocytoplasmic enzyme two questions are being investigated here i can we identify pus5dependent sites upon immune receptor activation and ii can we define functions of selected induced sites in the growthtodefense genetic reprogramming pseudopin uses stateoftheart sequencing methods including direct rna sequencing technology to systematically map in major rna classes after immune receptor stimulation it also lays out strategies to select and study particularly interesting cases the topic remains completely uninvestigated in plants so the project promises to break open a new research field within plant gene expression and thereby provide material to start an independent research career following successful completion of the fellowship
probing the role of mirnas in cluster root development in white lupin

phosphorus p is an essential macronutrient for the production of food crops and the demand for p fertilizer is increasing worldwide earths p is being depleted at an alarming rate urging the need for alternative strategies in order to maximize the availability of agronomic resources optimize crop yields and guarantee food security with less impact on our environment white lupin is the only crop that can form specific organs constituted by numerous short lateral roots the socalled cluster roots crs as an adaptation to low p availability in the soil allowing an efficient acquisition of this nutrient which is fundamental for plant growth and development remarkable advances have been made over the last years in identifying numerous genes involved in different facets of root adaptation to the environment and is known that micrornas play a pivotal role in regulating gene expression during development and in response to environmental cues the main objective of lumiroot is to elucidate the mirnadependent mechanisms regulating the formation of crs in white lupin contributing to optimize plant resource acquisition based on the already proven role of mirnas in root developmental processes i will focus on these networks based not only on their functional importance but also on the broader interest of regulatory pathways controlling the development crs i will in deep functionally analyze the role mir396target genes modules in cr development and reveal novel mirna regulatory networks acting in cr formation and function i also aim to develop mirnabased nanoparticles to modulate in vivo mir396 action as well as other regulatory mirnatarget networks to assess its potential to improve relevant agronomic traits such as crs formationlumiroot project will allow opening the way to crop improvement reducing the need for p fertilizers and will help to select regulatory networks with potential use in the improvement of relevant agronomic traits
synchrony in caregiverchild interactions across neurodiversity

this project aims to boost sustainable collaboration in a crossnational and crossdisciplinary network with the university of warsaw as the widening partner the university of heidelberg university of milano copenhagen university and the university of trento to facilitate knowledge transfer and exchange of best practices in the research on biobehavioral synchrony research exploring how different synchrony measures are related to each other in diverse populations seems highly important as biobehavioral synchrony is known to support health and psychological wellbeing the main goal of the synccin project is to strengthen the university of warsaws scientific and organizational capacity and to make the university of warsaw a leading player in biobehavioral synchrony research the synccin project is formed by five universities carefully selected for their complementary expertise in biobehavioral synchrony it will establish a virtual laboratory for biobehavioral synchrony led by the university of warsaw leading researchers in the field with complementary expertise and experience in strategic areas will collaborate on this project the group will develop a protocol to study different levels of synchronization in parallel behavioral physiological neural subsequently this protocol will be applied in a multicenter research project the transfer of knowledge between partners is vital to this project work packages include sustaining changes at the university of warsaw conceptual framework building for parentchild synchrony methodology transfer and integration joint study dissemination and outreach and management and coordination twinning funds will help make the widening countrys university of warsaw an important research center within the designated field strengthening its research and innovation potential within the european research area its international reputation visibility and its capacity to compete for research funds as a project leader
unravelling the evolutionary origin architecture development and regulation of neuromuscular systems

muscles and neurons are a major hallmark of animals and given their impact on the organisms motility the emergence of an interacting neuromuscular system has tremendously shaped the evolution of animal body plans and behavioral repertoire neurons and muscle cells closely interact and likely have coevolved yet the evolutionary origin of different neuronal and muscular cell types remains elusive mainly due to a lack of thorough studies in basal metazoans in this project i aim to unravel the evolutionary origin architecture regulation and systemic properties of the neuromuscular system by a broad comparative approach among nonbilaterians and by a deeper functional dissection in two model cnidarians the sea anemone nematostella vectensis and the hydrozoan clytia hemisphaerica by comparing single cell transcriptomes we will reveal common or distinct molecular profiles of neurons and muscles in early branching nonbilaterian species ie porifera ctenophora cnidaria and bilaterians ie all other animals allowing us to identify ancestral versus independently evolved neuromuscular modules comprised of specifically interacting cells we will then use genome editing transgenics and newly developed functional tools to unravel the architecture of the cnidarian neuromuscular system on single cell resolution the function of specific neuronal and muscle populations their plasticity and regenerative capacity we hypothesize to identify common cellular network modules allowing for fast and slow neuromuscular regulation in bilaterians and nonbilaterians which may be ancestral or convergently evolved in different animal lineages the expected outcome will impact our understanding of the evolution of organisms with complex body plans
human mobility and climate change in the european context

despite the increase in climateinduced migration studies research on the topic seems to be a prerogative of researchers from the global north focusing on case studies in the global south in particular research on climate change environment and human mobility is underrepresented in european cases despite the increasing number of small scale disasters that displace communities in europe every year european countries are far from being immune to the effects of climate change and natural disasters and just in the recent years extreme weather events have displaced hundreds of thousands of people across europe nonetheless stories of environmentalinduced mobility often remain undetected in the european context home will contribute to address this geographical bias and it will adopt a political ecology approach to focus both on local experiences and practices of environmental changes and mobility in the european context and on how they are nested in power dynamics that produce unequal distribution of climate change effects and shape immobility decisionmaking responses on a societal level this can better inform public policies and strengthening disaster risk and climate change adaptation governance portugal has been identified as an exploratory casestudy with a focus on the effects of slowonset events eg sea level rise slr and suddenonset events eg wildfires on human immobility the action will be conducted by the fellow dr michele dalla fontana at the environmental policy group at the wageningen university the netherlands under the supervision of dr ingrid boas a renowned expert in the field of climate changehuman mobility nexus a secondment period of eight months is foreseen at the institute of social sciences at the university of lisbon portugal under the supervision of prof dr luisa schmidt who combines expertise in climate change adaptation and risks with a profound knowledge of the portuguese context
mutation rate determinants across cellular and evolutionary scales

as individuals age mutations accumulate inexorably in their cells playing a key role in evolution ageing and disease despite their importance we still have a poor understanding of how mutations originate or why some cells accumulate more mutations than others this proposal aims to address these fundamental questions by examining two axes of mutation rate variation among cell types and across speciesin aim 1 we will decode the rules of germline mutation during mammalian spermatogenesis cells in the germline exhibit mutation rates significantly lower than those in the soma through mechanisms that remain unknown leveraging recent breakthroughs in longread dna sequencing we will track the accumulation of mutations from spermatogonial stem cells to mature spermatozoa in mice by integrating this data with existing cell typespecific profiles of gene expression epigenetic marks and chromatin architecture we will delineate how cellular processes influence mutation rates in the germline aiming to reveal differences with patterns in the somain aim 2 we will characterise the dna damage response across primates recent findings suggest that longerlived mammals have lower somatic mutation rates but the underlying mechanisms remain elusive to tackle this question we will experimentally expose primary fibroblasts of ten primates to uv radiation and a promoter of oxidative stress quantifying the impacts on cell viability gene expression genome accessibility and mutation rates and spectra with this comprehensive approach we will disentangle the pathways leading to damageinduced mutations as well as uncover molecular mechanisms that evolution has wielded to select for healthier longerlived primatesin summary this proposal aims to learn about how mutations occurthat is how they originate mechanisticallyas well as why their rate of appearance differs across cell types and speciesnamely what selective pressures drive mutation rate evolution
superresolved stochastic inference learning the dynamics of soft biological matter

the dynamics of biological systems from proteins to cells to organisms is complex and stochastic to decipher their physical laws we need to bridge between experimental observations and theoretical modeling thanks to progress in microscopy and tracking there is today an abundance of experimental trajectories reflecting these dynamical laws inferring physical models from noisy and imperfect experimental data however is challenging because there are no inference methods that are robust and efficient model reconstruction from experimental trajectories is a bottleneck to datadriven biophysicsi will bridge this gap by developing practical algorithms that permit robust and universal inference of stochastic dynamical models from experimental trajectories to this aim i will build dataefficient tools to learn stochastic differential equations and discover physical models employing methods from statistical physics and machine learning the main focus of superstoc will be in resolving models with high precision from limited trajectories to assess the efficiency of the methods i develop i will design informationtheoretical frameworks to quantify how much can be inferred from trajectories that are short partial and noisy the convergence of the resulting algorithms will be backed by mathematical proofs and numerical simulations in realistic conditionsi will apply these new tools to several key open biophysical problems where existing methods are failing condensatemediated interactions between genomic loci cellular mechanosensing in confined environments pattern formation in embryo development and visual interaction between fish leading to collective motionthe resulting algorithms will be implemented into a software designed to be useful for the broad soft biological matter community by proving that one can do more with the same data and providing tools to do so superstoc will help bridge the inference gap towards datadriven biophysics
genomic insights into the heteroplasmy in the invasive species hydroides elegans

hydroides elegans is a significant biofouling invasive species in tropical and subtropical seas causing damages to manmade structures in harbors and incurring economic costs despite its importance the taxonomy and evolution of this organism remain poorly understood hindering conservation efforts and predictions of its future distribution recent phylogenetic reconstructions suggest two cryptic species with one showing higher invasiveness additionally h elegans exhibits heteroplasmy with more than one mtdna type observed due to paternal leakagedriven genomic introgression polygene aims to provide novel insights into this widespread species from genomic morphologic and ecologic perspectives the projects objectives are threefold 1 investigating the origin maintenance and evolution of heteroplasmy in h elegans 2 conducting an integrative taxonomic revision to understand population dynamics and hybridization events 3 modeling the species distribution and climate adaptation potentialpolygene represents a pioneering integrative study focusing on heteroplasmy in annelida that will utilize largescale genomic data morphologic data and distribution modeling to bring a significant step forward in our understanding of mitochondrial evolution and a scientificbased approach for effective management of an important marine invasive species the project fosters collaboration between three research groups at the natural history museum of oslo nhmo and a secondment to the senckenberg research institute sgn nurturing my growth as an independent researcher in evolutionary biology of marine organisms the project allows me to gain and deepen scientific expertise and transferable skills needed to pursue a career either in academia or in policymaking