0799175D-EB70-4F8A-87FA-0054F2B2D7D5Grey Milk and Lost Kin: Re-sounding, Re-visioning, and Re-membering Trauma in the Scottish Gypsy Traveller ArchivesClosed2775728Studentship&quot;We have no right to any form of writing, that is our curse,&quot; proclaimed a 1950s Gypsy Queen (Lecouteux 2016, p.6). This research transforms the curse of &quot;internalised oppression&quot; (Davis 1981) as my ancestors incite an uprising by way of the archives. My practice-based research aims to retrieve and revalue &quot;subjugated knowledge&quot; (Foucault 1980) through critical archival interventions, place-based approaches, experimental filmmaking and literary practices. I will interrogate the absence and rupture of 'knowing' caused by forced assimilation and cultural dispossession, exploring the sociocultural impacts of knowledge suppression and its far reaching mechanisms of denial. Grounded in lived experience, this study adds to urgent scholarly work seeking to transform the cultural ramifications of colonial legacies which actively erase Indigenous and Local knowledge systems, their cultural heritage, and collective identity. My family avoided persecution by keeping our genealogy secret and disavowing our Scottish Gypsy Traveller ancestry.From the mid twentieth century onwards, vast institutional archives were amassed in Scotland of the travelling peoples' oral traditions. Newly accessible online since the pandemic, I will subvert these archives to activate the affective, cultural and experiential injuries of &quot;racial capitalism&quot;, drawing out the traumatic traces of invisibility and exclusion (Gordon 2008). I will then reframe and valorise the Gypsy Travellers' knowledge system, building power relations through &quot;re-citation&quot; with other subjugated cosmologies. Finally, I will undertake an intersectional exploration emphasising the feminist and decolonising interventions of re-sounding, re-visioning and re-remembering, mobilising solidarity and liberatory consciousness to counteract &quot;epistemic violence&quot; (Galv&aacute;n-&Aacute;lvarez 2010).Thus, I will create a body of work, including film, art and audio works, that act as &quot;a counter-archive of knowledge&quot;-underpinned by Indigenous narrative and listening strategies (Horavoka 2017). In this way, my research will contribute to experimental sonic and cinematic techniques and methodologies, whilst generating critical pathways that pluralise knowledge systems more widely.2025-03-301291772D-DFCE-493A-AEE7-24F7EEAFE0E9AHRC2022-09-30INCOME_ACTUAL027757286CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified07BECE74-80E1-4CA9-9643-012F35B2F636Medical diagnosis through the application of Artificial IntelligenceClosed2642845StudentshipThis project will look at some aspect of medical diagnosis through the application of Artificial Intelligence which will be determined in more detail by the end of year one2025-09-29B71128B2-1767-4204-9D19-EEB1383C2D1EOther NPIF2021-09-30INCOME_ACTUAL026428456CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified07D6E9EA-F096-44BF-BAF6-01F2D3DE4489DNA methylation age acceleration: examining the role of socioeconomic position and dietClosed1907672StudentshipThis project proposes to investigate whether socioeconomic position is associated with DNA methylation in the MRC National Survey of Health and Development (1946 birth cohort), and whether indicators of diet might mediate any associations found.2025-09-29924BE15C-91F2-4AAD-941A-3F338324B6AEESRC2017-09-30INCOME_ACTUAL0The first stage of analysis found an association between individuals' life course socioeconomic position (that is, parental occupation, educational attainment, adult occupation and household income) and epigenetic markers of biological ageing at age 53 in a sample of individuals from the MRC National Survey of Health and Development, a British birth cohort of individuals born in 1946. Epigenetic ageing biomarkers are one of a set of novel ageing biomarkers based on molecular biology. Other biomarkers in this group included telomere length and biomarkers based on transcriptomics, metabolomics and proteomics. Epigenetic ageing biomarkers have been found to be better at quantifying biological ageing than the other novel ageing biomarkers in this group. Greater epigenetic ageing has been associated with increased risk of mortality, increased risk of cancer and cardiovascular disease, and worse ageing outcomes such as poorer physical function and frailty. The analysis examined first and second generation epigenetic ageing biomarkers. The research makes use of second generation epigenetic ageing biomarkers which have not been examined in UK data to date. The results show that early life disadvantage is associated with greater midlife biological ageing. There is also evidence that disadvantage across the life course is associated with greater biological ageing in midlife depending on the epigenetic ageing biomarker examined. The results indicate that social disadvantage is associated with worse biological ageing.Greater epigenetic biological ageing has been associated with increased mortality risk, increased risk of cancer and cardiovascular disease and worse physical functioning in old age. The results show the importance of preventative measure for later life health and ageing that focus on reducing societal inequalities, and also suggest that these measures should be applied from early childhood and beyond.D6838300-CC30-4745-921F-D53221105FBC5e5f9863ab6364.01330492Communities and Social Services/PolicyHealthcare5C80154F-FC85-45E3-A673-DE515281D5B8Life course socioeconomic position and body composition in adulthood: a systematic review and narrative synthesis.International journal of obesity (2005)efb0009ac942206954268ce9341f9093Bridger Staatz C2021-01-010307-05656213685d5315c4.374962014E986B9C-1997-43ED-8AD8-9C22DA08F199Socioeconomic position and body composition in childhood in high- and middle-income countries: a systematic review and narrative synthesis.International journal of obesity (2005)efb0009ac942206954268ce9341f9093Bridger Staatz C2021-01-010307-05656213685d898d33.163929041F6E3275-F596-4BD4-9B3A-1017C9AB0491Life course socioeconomic position and DNA methylation age acceleration in mid-life.Journal of epidemiology and community healthcf4482a475dc1df134493fab62407a61George A2021-01-010143-005X6213685d1b6cf4.7104483519076726CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified00C808C1-2360-4DF3-9CC0-008A1DA7F5D6A modular sea lice removal system utilising electro-anaesthesia, low-pressure pumping and waterjets to gently remove lice without inducing stress and compromising fish welfare.Closed10057221EU-FundedElectrolicer will be the first system that can combine sea lice removal with fish welfare during treatment. The system has been designed by Ace, a company with extensive experience in electro-anaesthesia. Water is inserted into the pipeline to create suction that draws fish calmly from the cage into the tube. Electrolicer then holds the fish in a calming low-voltage electric field that relaxes the muscles, and low-pressure water gently removes lice and eggs. Electrolicer also reduces expenses associated with adopting this technology. The solution can be used on an existing, generalised work boat, instead of requiring the purchase of a dedicated sealice removal vessel. By avoiding chemicals and favouring multi-modal treatments within the system, Electrolicer also addresses treatment resistance in lice. Ace is backed by sustainable investment group Aqua-Spark, whose mission is to invest in companies using technology to improve sustainability in aquaculture2025-10-31240CEBFD-1052-4EAC-88DF-D88A163D61C8Horizon Europe Guarantee2023-01-01INCOME_ACTUAL1092637100572216CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified114DBE51-0DC8-4E2A-AA8F-00801DFBF3C0Social and Economic Implications of Transport Sharing and AutomationClosedES/S001875/1FellowshipThis study will link the changing nature of jobs due to automation and the platform economy to regional infrastructure planning and transport operations, and the role specifically of transport automation within this context. The patterns and forms of jobs are changing due to many different reasons, leading to non-traditional work schedules and differences in commuting patterns, non-standard work travel patterns, and even elimination of certain jobs and creation of new ones, with significant implications for regional infrastructure planning and transport operations. At the same time, there are enormous changes anticipated in infrastructure and operations, due to large-scale automation in the transport sector (eg autonomous and connected vehicles). This project will make estimates of the changing nature of jobs due to these considerations at the regional level towards the goal of deriving the transport and regional infrastructural planning consequences. The project will use labour market survey data as well as privately-held labour market data on jobs, skills and industry to estimate regional variations due to these trends, given regional industry-occupation mix. These changes will be linked to the Spatial Urban Data System (SUDS), which is a UK-wide geospatial data infrastructure under development within UBDC containing transport infrastructural and operational conditions. , and which has been recently used to identify areas of transport poverty throughout the UK and the extent to which and which we will expand through work with the project's industrial partners. Using these data sources, we will identify regional automation risks due to unique industry and skill concentrations and derive transport and infrastructure planning implications. Within this context, we will also evaluate the role of autonomous vehicles given potentially different commuting patterns using specialist transport simulation models. We will further develop specialist transport simulation models to ascertain which packages of &quot;last-mile&quot; transport solutions (low-energy station cars, autonomous vehicles, shared transport, active travel and demand-response services) are likely to bring about high-quality, sustainable and socially-equitable forms of transport accessibility in areas at risk of changing nature of jobs. We will then combine the results of our various model scenarios, using ensemble forecasting methods utilising Bayesian Model Averaging or related techniques to ascertain which packages are more likely to bring about high-quality transport accessibility in the selected areas.With 66% of the world's population estimated to be living in urban areas by 2050, the need to provide new transport infrastructure and to address traffic congestion, road fatalities, air pollution, and associated problems continue to generate debates in policy circles. Impact on local economic development and labour market planning: The work related to estimating the potential impact of automation and AI on jobs given skills required in the occupation-industry mix regionally available is likely to be of immense value to regional infrastructure planners and business owners, as well as for skills-development initiatives and organisations in the local economic development planning. Through UBDC's networks, we will engage local authorities and other stakeholders in co-creating our results on this topic, so as to involve our work in their planning processes. Transport and infrastructure planning and operations impact: Additionally, there is a range of shared technology, automation and use of AI and Machine Learning (ML) being proposed in transport, and a growing business community involved in their development and use. Although the trends surrounding automation and sharing transport are being driven primarily by private companies, governments around the world are increasingly developing policies to support as well as to regulate many of these developments, and the UK government has an active programme on Connected and Autonomous Vehicles (CAV); among the high-value economic infrastructure to be funded through the 2016 National Productivity Investment Fund (NPIF) is &pound;390 million for future transport including ultra-low emission vehicles and CAVs. Additionally, various types of shared mobility services, e.g., car-sharing, dynamic ride-sharing, on-demand personal mobility vans, and express, crowd-sourced urban delivery services, under the banner of Mobility-As- A-Service (MaaS) are now offered by private companies in UK cities. Just as the introduction of the private car in the beginning of the twentieth century transformed the way we live our daily lives and the ways in which cities developed, large-scale automation, connectivity and sharing of mobility resources (sharing economy) are expected to be a step-change changing daily lives in future society and the form and functions in cities.We expect that our results will help highlight significant regional planning and operations impact of such technology, against the backdrop of changing commuting and work-related travel patterns resulting from the changing nature of jobs. Industrial Impacts: The approach will allow us to evaluate spatial and regional effects of varying degrees of automation and sharing mobility, and to identify new markets in smart cities and urban planning. Our industry partner, Peter Brett Associates, views that the risks of emerging technology being left out of the planning agenda are great due to lack of empirical data, leading technology disruption in transport to occur in an ad-hoc way. Having the results of the analysis and the associated data would help them reach new markets and also to reduce uncertainty in their forecasts. Scottish MaaS, has similarly noted that the methods and results being proposed will help them reach new markets both geographically thereby opening up UK companies to a global pipeline of contracts in integrating CAVs into infrastructure planning and construction, and MaaS solutions in addressing expensive last-mile problems facing city managers worldwide.2021-10-11924BE15C-91F2-4AAD-941A-3F338324B6AEESRC2018-01-19INCOME_ACTUAL302343Rutgers UniversityUnited StatesRutgers Urban and Civic Informatics LabIntelligentTraffic Modelling in NYC17D3368C-5B0D-477B-ADCD-0CEB8733C2E0A new dataset is created for predicting the taxi pickups in NYC, which combines a series of factors from heterogeneous sources. This is arguably the first dataset that covers four varying feature set in NYC for the prediction: [A] temporal and real-time features (e.g. time-of-day, day-of-week, and hourly weather conditions from Meteoblue (https://www.meteoblue.com), [B] averages of demographic and socioeconomic features such as income levels and unemployment of census tracks where pick-ups occurred during the time interval, from the American Community Survey 2008-2011 5-year sample (https://www.census.gov/programs-surveys/acs) [C] average travel-to-work characteristics such as the proportion of commuters who walk or take public transit in the census tracks in which the pickups are located during the interval, also from the census data and [D] social and built environment characteristics of the census tract where the pickup occurred during the period, for example of crime levels from the NYC police department (https://www1.nyc.gov/site/nypd/stats/crime-statistics/historical.page), and data on the built environment (e.g. density of transport facilities such as the number of transport stops, stations and other facilities) from the NYC Planning Department \footnote{\url{https://www1.nyc.gov/site/planning/data-maps/open-data/dwn-selfac.page}}.}60495802d28c76.41049741-1Their data scientists are mostly responsible for collecting and cleaning the traffic and social media dataset, conducting some preliminary analysis about the explanatory features, and carrying out a data engineering job to convert it into the format that is recognizable to our program.The biggest contribution that I made was creating a new intelligent traffic system, introducing UBERNET - a deep learning based predictive system, and then help them to set it up on the local NYC data.Academic/University2020-01-01An Evening with UberParticipation in an activity, workshop or similarRegionalA37E8CCC-6C4B-49A1-9E41-E586C1D2DBC9200 people attended this Evening Event with Uber, where we discussed the possibility of predicting Uber demand at local and global level, thereby improving the design of the intelligent traffic system.5e5d91fce9e7a5.86631715falseProfessional Practitioners2020Traffic Scotland EventParticipation in an activity, workshop or similarLocal90930E11-859C-4D43-A2FB-D9DE37EB5EA9Around 80 people attended this event, where I gave a presentation about taxi flow prediction using deep learning based approaches, which could further optimize the current intelligent system. Many audiences are intrigued later on and asked for more detailed information.60491ca5b69e36.00490099falseProfessional Practitioners2020U21 ERC WorkshopParticipation in an activity, workshop or similarInternationalAB52B7F6-BEDB-48B9-A5B8-ACF4375D89C5150 researchers in the transport community attended the workshop, which sparked questions and discussion afterwards, with increased from several cohorts who are interested in using deep learning approach to facilitate transportation system.5c86be8d5c1e47.83133641falseSchools2018Transportation Research BoardA talk or presentationInternational395947E9-7E90-4D83-BC3D-126FD75E4B21I made an oral presentation at the international conference Transportation Research Board 2020, where people from industry such as Uber and Toyota asked questions with respect to the feasibility of applying our traffic prediction approach on their dataset, many people from traffic community also interested in our approach with constructive suggestions.5e5d906de49ad9.97984186falseIndustry/Business2020We developed a multi-level Wavenet framework that take a series of meta-data features into account so as to effectively capture the varying demand patterns. Specifically, the model is a one-dimensional convolutional neural network that includes two sub-networks that aims to encode the source series and decode the predicting series, respectively. The two sub-networks are combined by stacking the decoder on top of the encoder, which in turn, preserves the temporal patterns of the time series. Experiments on large-scale real taxi demand dataset of NYC demonstrate that our model is highly competitive to the existing ones.Traffic demand prediction is at the core of intelligent transportation systems when developing a smart city. Accurately predicting taxi demand can help the city manager/operater to optimize the resources, and thus reducing the drivers' waiting/idle time which waste energy and cause traffic congestion. However, exploiting traffic time series to facilitate the demand prediction is a thorny problem since traffic demand usually unevenly distributed over time and space.1BE9742F-2BDF-4CA3-9759-564E3A9193A15c869a7f289e46.13736350Digital/Communication/Information Technologies (including Software)Transport3B8DAD7B-D64A-43A5-BB54-76FA1343B6AEPredicting Taxi Demand in NYC with Wavenet03310d8b5f9ffeb172b6855fab7fbe11Long Chen2019-01-015c86bb5c429be5.5677080224B3DC51-AF43-4FB5-8CE3-1B4375FBFC45Modelling and Predicting Individual Salaries in United Kingdom with Graph Convolutional Network03310d8b5f9ffeb172b6855fab7fbe11Long Chen2018-01-015c86a7c82fae35.74862917ES/S001875/1D7B3C750-5146-47F0-B10D-145C65C76B3B56Civil eng. & built environmentFA3D6B2E-20C9-4738-A451-89FBB11592A016Electrical engineering1908FDF5-1C61-4F33-B47F-3E91675C88AA8Info. & commun. Technol.184898E4-BFA4-4527-9835-7EB4EC15821916Science and Technology Studies990813BA-F64D-4C20-BF55-5D96210DAA9E8Artificial IntelligenceFD031323-3ED1-42EC-84FE-AF21AA5B607F16Robotics & Autonomy184898E4-BFA4-4527-9835-7EB4EC15821916Science and Technology StudiesF6DFE439-6799-42C8-8C33-ABDFBBE848A056Transport Ops & Management0C15BC4F-A128-4F7E-ADAB-013E262DD5CFMicrobial Interactions Within Denture BiofilmsClosed2119089StudentshipMost microorganisms naturally grow within biofilms in both environmental and industrial systems. Biofilms on denture surfaces are widely acknowledged and arise in cases of poor oral/denture hygiene and where dentures are not removed whilst sleeping. Key microorganisms in denture biofilms include fungi of the genus Candida as well as bacteria that can originate from other oral sites or from exogenous sources. The majority of denture biofilm studies have targeted Candida as these fungi are highly adept at adhering to denture acrylic and can induce the infection, denture associated stomatitis. Denture biofilms are, however, ideal for investigating microbial interactions since they are readily accessible, polymicrobial and variable in their microbial composition and can be modelled in vitro. Furthermore, difference in conditioning of the denture surface may also lead to differential species colonisation and biofilm behaviour. Preliminary studies in our School of Dentistry have highlighted the effect that bacterial species may have on denture biofilm composition and behaviour of Candida albicans. We have found that Candida growth can be inhibited in biofilms by Pseudomonas aeruginosa, whilst other bacteria, such as certain streptococcal species can influence the morphologyof C. albicans. The reasons for these effects remain unclear, but could be due to specific associations between species, or a feature of a wider community effect on the biofilm. Project aims The aims of this PhD are therefore to explore the types and mechanism(s) of microbial interactions that occur in biofilms, using denture biofilms as model systems.2022-12-31198E4A3D-B2DC-45D4-8351-7CCEC4061876BBSRC2018-09-30INCOME_ACTUAL021190896CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0C552636-8921-4940-9DAB-01530F14011ASafe and Sound - secure and sustainable Cloud3D servicesClosed750553VouchersSafe and Sound will enable Hao2.eu to research and develop good practise standards and approaches to deliver secure and sustainable Cloud3D services which proactively anticipate and support the needs of vulnerable groups such as people with autism and learning disabilities.2014-01-3112E03F45-B517-4D83-A182-3D142D1A471AInnovate UK2013-07-31INCOME_ACTUAL50007505536CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0C60F5D3-E107-48CC-B301-001DF513DA5EDoctoral Training Grant (DTG) to provide funding for 3 PhD studentships.ClosedNE/H526886/1Training GrantDoctoral Training Partnerships: a range of postgraduate training is funded by the Research Councils. For information on current funding routes, see the common terminology at https://www.ukri.org/apply-for-funding/how-we-fund-studentships/. Training grants may be to one organisation or to a consortia of research organisations. This portal will show the lead organisation only.2011-03-308A03ED41-E67D-4F4A-B5DD-AAFB272B6471NERC2009-09-30INCOME_ACTUAL71627NE/H526886/16CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0C7B57E9-2B50-4E12-863B-01EFA021D066Undestanding microbial communities through in situ environmental 'omic data synthesisClosedNE/L011956/1FellowshipThe purpose of this research is to integrate different sources of 'omics data in environmental science for microbial community analysis. The computational based comparative analysis of DNA sequences may provide information about genome structure, gene function, metabolic and regulatory pathways and how microbial genomes evolve. However, to fully delineate microbial activity and its response to environmental factors, it is necessary to include all levels of gene products, mRNA, protein, metabolites, as well as their interactions. I propose to use large-scale whole genome metagenomic sequencing for assessment of taxonomic and functional diversity of microbial communities. The data generated by metagenomic experiments are both enormous and inherently noisy, containing fragmented DNA sequences representing as many as thousands of microbial species. After using pre-filtering steps, including removal of redundant, low quality sequences, the short DNA sequences are assembled together into longer contigs of overlapping reads, and these contigs may then be scaffolded into full genomes in a bottom-up approach. Having obtained the assembled contigs, the obvious next step is to use publically available databases to annotate the coding regions in these contigs. This will tell us WHAT functionality is available and provide information on WHO is there, the metagenomic sequences are binned, i.e., by associating a particular sequence with an organism. This can be done by either searching for phylogenetic markers or by looking for similar sequences in existing public databases. The end result is the community profile of different samples in terms of organismal abundances within each sample. Whilst metagenomic analysis gives a profile of the microbial community at a specific place or time, and their potential functional, it does not reveal which genes are actually being transcribed. I thus propose to integrate sequencing-based metatranscriptomics in which total RNA (a proxy for gene activity) is extracted from microbial community, converted to cDNA and sequenced without the need for cloning. This will provide information on the regulation and expression profiles of complex communities by enabling quantitative measurements of dynamic expression of RNA molecules and their variation between different states reflecting the genes that are being actively expressed at any given time. However, the story is still far from complete, as we do not have direct evidence of the metabolism within a cell. To give a more complete picture of living organisms, I will integrate metabolomics which will provide unique chemical fingerprints that are a function of specific cellular activity. In particular, the focus will be on identifying habitat-specific endogenous and exogenous metabolites along distinct geochemical conditions. These metabolites will be detected using two-dimensional gas chromatography coupled with mass spectrometry. They will be related to the expression levels from transcriptomes using information on metabolic pathways readily available from annotating metagenomic sequences. In this way we will integrate all three sources of information, mapping the metatranscriptome onto the assembled annotated metagenomes and reconciling the reconstructed metabolic pathways with observations on metabolite concentrations and fluxes. From this we will be able to predict the metabolic function of the entire community not simply who is there.The removal of complex organic contaminants from soils will be one of the major environmental challenges facing the United Kingdom over the coming decades and recommendations based on this proposal will be of use to stakeholders especially, the remediation consultants, industry regulators i.e. SEPA and local councils. Brownfield development is an important part of the societal shift towards sustainability. Many contaminated brownfield sites sit unused for decades because the cost of cleaning them is more than the land would be worth after redevelopment. This research will impact on our ability to achieve sustainable reclaim of environmental capital and will allow adaptive re-usability. The Earth Microbiome Project has generated an enormous collection of data with the intention of producing a global Gene Atlas describing protein space, environmental metabolic models, and characterizing a global environmental parameter space for microbial communities. This global environmental sample database is an ambitious initiative that is community-driven. The tools developed in this fellowship will exploit this vast amount of information to provide useful insights on the Earth's microbiome and to catalogue all the microbes that live on earth. This will be of great benefit to mankind as whole, these microbes are performing vital functions, and to environmental researchers. Methanogenesis is a key process in the carbon cycle, methane is a more potent greenhouse gas than carbon dioxide, therefore understanding its metabolism at a community level is of fundamental importance if we are to incorporate microbial processes into models of climate change. Methane is an important greenhouse gas yet its production could play a part in the transition to a low carbon economy. Water treatment is the fourth most energy intensive sector in the UK and consumes approximately 1% of the UK's electricity. Reducing the energy required to treat wastewater would therefore have major benefits both by reducing costs and carbon dioxide emissions. Anaerobic digestion (AD) reactors have the potential to provide these benefits. They do not require the same energetically costly aeration as aerobic methods and through the action of methanogens produce biogas. Better understanding of methanogenesis could lead to more efficient AD reactors.2019-10-318A03ED41-E67D-4F4A-B5DD-AAFB272B6471NERC2014-11-01INCOME_ACTUAL425506The analytical tools led to the exploration and in turn development of a CD-TREAT diet for treatment of Crohn's Disease https://www.medpagetoday.com/gastroenterology/inflammatoryboweldisease/76931and was published in Gastroenterology 2019A6F76344-21EB-414E-9D0D-F425844C6746SocietalEconomic56db53d617c9b4.68617352Agriculture, Food and Drink,Education,Environment,Healthcare,Pharmaceuticals and Medical BiotechnologyI established my Environmental'Omics lab in School of Engineering, University of Glasgow in November 2014 which specialises in developing novel pipelines for analysing genomic data in an environmental context. My lab is centered around my fellowship and focuses on microbial ecology at both mesoscopic and macroscopic scales by integrating 'omics data (metagenomics, metatranscriptomics, metabolomics, and metaproteomics) for microbial community analysis. Software (http://userweb.eng.gla.ac.uk/umer.ijaz/#bioinformatics): Under this grant I am developing software tools and methodologies to integrate different sources of omics data, namely, metagenomics, metatranscriptomics, metabolomics, and metaproteomics. Here are the list of major software I have contributed to during my fellowship: RvLab (R virtual Laboratory for ecological community analysis) Software:https://portal.lifewatchgreece.eu/ Reference: A. Oulas et al. Biodiversity Data Journal, 4, e8357, 2016.(doi:10.3897/BDJ.4.e8357) CONCOCT (A software for binning metagenomic contigs with coverage and composition) Software: https://github.com/BinPro/CONCOCT Reference:J. Alneberg et al. Nature Methods, 11(11):144-1146, 2014. (doi:10.1038/NMETH.3103) (PMID:25218180) TAXAassign (A bash based pipeline for generating taxonomic profiles using NCBI's Taxonomy) Software: http://www.github.com/umerijaz/taxaassign Reference: J. Alneberg et al. Nature Methods, 11(11):144-1146, 2014. (doi:10.1038/NMETH.3103) (PMID:25218180) NMGS (A software for fitting the Unified Neutral Theory of Biodiversity with Hierarchical Dirichlet Proces) Software: https://github.com/microbiome/NMGS Reference: K. Harris et al. Proceedings of the IEEE, 105(3):516-529, 2017 (doi:10.1109/JPROC.2015.2428213) seqenv (A pipeline capable of annotating genetic sequences with Environmental Ontology) Software: https://bitbucket.org/seqenv/seqenv/src Reference: L. Sinclair &amp; U. Z. Ijaz et al. PeerJ, e2690, 2016. (doi: 10.7717/peerj.2690) microbiomeSeq (An R package for microbial community analysis in an environmental context) Software: https://github.com/umerijaz/microbiomeSeq Tutorial/Demo: http://userweb.eng.gla.ac.uk/umer.ijaz/projects/microbiomeSeq_Tutorial.html SeqEnv-Ext (A taxa-centric extension to seqenv pipeline, which consisted of two parts, each providing environmental annotations under different context, with first part providing taxon abundance on a per term basis while the second part lists environmental term abundance under a per taxon context. A separately developed program that required the use of the original seqenv pipeline, this enabled two different methods of viewing environmental annotations, which significantly augments the analysis capability of the pipeline. Software: http://hie-pub.westernsydney.edu.au/0610b020-39fb-11e7-b55d-525400daae48/ Reference: A. Z. Ijaz, T. Jeffries, U. Z. Ijaz et al. PeerJ, 5:e3827, 2017. (doi:10.7717/peerj.3827) pyTag (A tool for identification and analyses of ontological terms in application area specific literature surveys) Software: https://github.com/KociOrges/pytag NanoAmpli-Seq (A workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform) Code: https://github.com/umerijaz/nanopore Reference: S. T. Calus, U. Z. Ijaz, and A. Pinto. bioRxiv 244517, 2018 (doi: 10.1101/244517) Orion Cluster: Without any institutional or dedicated technical support, I have single-handedly built and managed an HPC facility in Engineering called Orion Cluster (http://userweb.eng.gla.ac.uk/umer.ijaz/#orion). I bought first server in 2012 through the Unilever grant and since then I have religiously pursued my collaborators for in-kind contributions, as well as allocating small equipment budget on every grant I am applying. Five years later, I have spent ~&pound;114K on 13 servers with more equipment to be purchased in two months time through recently allocated &pound;22K (on SAIC) grant. Orion Cluster stands at an operational capacity of 368 cores, ~450TB disk space, and will serve &gt;70 PGR/T and staff (60 existing and regular users and hence the reason why I have an increasing supervision workload). This facility now sits at the heart of all major research groups I am involved with and is envy of many others. One of the reason why I have managed to attract funding and collaborators is through development of bespoke workflows (originating from my research) that I regularly updates and share on my website (http://userweb.eng.gla.ac.uk/umer.ijaz/#bioinformatics; http://www.tinyurl.com/JCBioinformatics; and http://www.tinyurl.com/JCBioinformatics2) as well as providing a single place for &gt;400 bioinformatics tools. My cluster and bioinformatics tutorials are of strategic importance Expansion to other technologies/hardware and award generation (http://userweb.eng.gla.ac.uk/umer.ijaz/#research_Grants): The developed tools/software methodologies and the research being conducted under my NERC fellowship was instrumental in getting further funding from numerous research councils. This includes recent expansion to population genomics and epidemiology (Scottish Infection Research Network/Chief Scientist Office Project entitled &quot;Molecular epidemiology of Clostridium difficile in Scotland: developing novel, clinically applicable research methods to combine genomic analysis with health informatics&quot;). For the past one year, I am trying to put my engineering experience to good use, by expanding my research to include: Raman spectroscopy enabled microfluidics (NERC NE/P003826/1 grant entitled &quot;Stable Isotope Probing with Resonance Raman Cell Sorting to profile influence of ocean acidification on microbial carbon fixation&quot;); hardware system integrating liquid handling, incubation and sensing with an embodied genetic algorithm, which directs evolutionary optimisation of microbial growth (with Professor William T Sloan, University of Glasgow; EPSRC Global Challenges Research Fund EP/P029329/1); and development of artificial intestinal Salmon gut system through bioreactors (BBSRC BB/P001203/1 grant entitled &quot;A microbial basis for Atlantic Salmon energetics&quot;). Supervision (http://userweb.eng.gla.ac.uk/umer.ijaz/#supervisions): I have been directly involved with the supervision of 13 PhD students and 2 PDRAs (with more to be recruited). Two PGR students (Caitlin Jukes, and Asha Rani) have recently defended their viva successfully. All of my supervisions involve utilisation of tools developed under my NERC grant. Repute: I have gained considerable repute at both national and international levels. I am collaborating widely with academics located in Manchester, Warwick, Dundee, Aberdeen, Liverpool, Norwich, Reading, London, Belgium, Finland, Greece, Norway, Ireland, Austria, Thailand, Czech republic, Australia, Germany, France, and Netherlands. As a consequence I have been invited to visit/speak at numerous institutes including: Faculty of Science, Cesk&eacute; Budejovice; Helenic Centre for Marine Research, Greece; Centre for Microbial Ecology and Technology, Ghent, Belgium; Edinburgh Amplicon Sequencing Group; Earhlam Institute (formerly TGAC); Unilever R&amp;D laboratories (Colworth/Port Sunlight); London School of Hygiene and Tropical Medicine; and Health Informatics Centre Dundee. My research leadership potential was recognized by NERC who funded me to attend a &pound;23,100 advanced leadership course in Cambridge.Please see the section on &quot;What have you discovered or developed through the research funded on this grant&quot;EE0A48DE-2BE6-4B51-9050-14E12654B91456db4f3db020b5.66717896Agriculture Food and DrinkDigital/Communication/Information Technologies (including Software)EducationHealthcarehttp://userweb.eng.gla.ac.uk/umer.ijazAmplicon sequencing on Illumina sequencing platforms leverages their deep sequencing and multiplexing capacity, but is limited in genetic resolution due to short read lengths. While Oxford Nanopore or Pacific Biosciences platforms overcome this limitation, their application has been limited due to higher error rates or smaller data output. In this study, we introduce an amplicon sequencing workflow, i.e., NanoAmpli-Seq, that builds on Intramolecular-ligated Nanopore Consensus Sequencing (INC-Seq) approach and demonstrate its application for full-length 16S rRNA gene sequencing. NanoAmpli-Seq includes vital improvements to the aforementioned protocol that reduces sample-processing time while significantly improving sequence accuracy. The developed protocol includes chopSeq software for fragmentation and read orientation correction of INC-Seq consensus reads while nanoClust algorithm was designed for read partitioning-based de novo clustering and within cluster consensus calling to obtain full-length 16S rRNA gene sequences. The datafiles and protocols provided here represent the intermediate files during data processing and associated detailed workflow.1315E9AC-ACB8-42FD-BAE4-97ED50AEAB97B0282B32CAAtrueSupporting data for "NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform."Database/Collection of data2018This article presents metagenomic-assembled genomes (MAGs) of prokaryotic organisms originating from chicken caeca. The samples originate from broiler chickens, one group was infected with Newcastle Disease Virus (NDV) and one uninfected control group. There were four birds per group. Both groups were raised on commercially available antibiotic free feed under a semi-controlled setup. The binning step of the samples identified 130 MAGs with50% completion, and10% contamination. The data presented includes sequences in FASTA format, tables of functional annotation of genes, and data from two different approaches for phylogenetic tree construction using these MAGs. Major geochemical cycles at community level including carbon, sulfur, and nitrogen cycles are also presented.6CF7696B-2C4F-4C62-BE79-D91FF31AEC4665a5a993843e80.18637899true<b>Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan</b>Database/Collection of datahttps://figshare.com/articles/dataset/_b_Dataset_of_130_metagenome-assembled_genomes_of_healthy_and_diseased_broiler_chicken_ceca_from_Pakistan_b_/24901878202445412CC0-DA2D-4487-A8BE-6FA79CF3FDADAdditional file 6 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7ae9e49c6.04991611D3DFA513-565C-4681-B398-2A123A68174CBinning metagenomic contigs by coverage and composition.Nature methodsde8d1caf81e365c3e9ff09579de0a6e2Alneberg J2014-01-011548-70915536c93bf386f3.63361150DA65A765-8A96-4F85-878D-0A1339465FDFAdditional file 8 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526c44a62817.409660709ABD4A7E-7EFF-4C92-8F7E-8FAC3244B681Exploration of marine bacterioplankton community assembly mechanisms during chemical dispersant and surfactant-assisted oil biodegradation.Ecology and evolution61ac1dc6db0e8a5735887de507ea5c31Nikolova C2021-01-012045-7758613fdc53641620EA3510C-5576-455F-AAB5-DEE1F23F6EABA detailed analysis of the gut microbial diversity and metabolic activity in children with obesity of different aetiology and lean controlsProceedings of the Nutrition Society614ab942f7b5ca90143931e5d006b3f2Khan M2015-01-01563c7672ad42b5.341547429B39C482-BA59-4B45-8E9A-AFF575A14936First proof of concept for full-scale, direct, low-temperature anaerobic treatment of municipal wastewater.Bioresource technologya97ab20d06486826771a13be390cc515Trego AC2021-01-010960-852461262c363717bFCFEB1BC-8E26-4003-BB01-85200DEDE230A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiomefb59bfc4867c742b2174168e75d99ebeI. Ab Aziz2023-01-0166a895d347d40F5DEA5BC-DAF8-4E35-90F4-9FF313417875Bioreactor scalability: laboratory-scale bioreactor design influences performance, ecology, and community physiology in expanded granular sludge bed bioreactorsd3511033c1f7a8f7a6513110b6910a5fConnelly S2017-01-0167526bece24221.888066762369D03C-C64B-4104-8DEB-26913B2B5958DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies.Scientific reportsc7d0793e24d86e7d24749f27055186ffFrau A2019-01-012045-23225dae5f02072437.786087275534A66D-53A2-4BEA-B985-CB05C9135E6DAdditional file 3 of Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbationsebf4406f047e3e8937b4f5853015c88dCheaib B2020-01-0165e8e8d02fc818.178959913210A058-E9F6-4407-A723-E1E1D3F5E9D2Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-01602717e100d2f5907B445-C646-419D-A71F-4B26A5BC4E2AMetabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.Molecular ecology0e773a4aff5cfd840a523d8e12ed1231Ray JL2016-01-010962-1083589482ac1a19a2.5661201911C12394-603C-4B3C-AC02-AC894D76DD95Microbial influencers and cotton leaf curl disease (CLCuD) susceptibility: a network perspective.Frontiers in microbiologybc32f3a8cc40351683169581b006a88dAqueel R2024-01-011664-302X675287651a5a43.32030449EA39574E-F5D0-43B1-A301-5844A6350082Machine Learning Approach to Predict Quality Parameters for Bacterial Consortium-Treated Hospital Wastewater and Phytotoxicity Assessment on Radish, Cauliflower, Hot Pepper, Rice and Wheat CropsWater9cd0e0f763e420d6c31437bf6dcd294eRashid A2022-01-0161dbd2f78f06724270782-9336-4AE7-92EC-A141E76DAC00Additional file 8 of Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants61ac1dc6db0e8a5735887de507ea5c31Nikolova C2021-01-0165e8e685b16c57.9276427768B92AE3-BC28-4086-AADC-4FC8D2916D29Additional file 1 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7e0d01024.218808470BBD9FF2-2A1F-47B9-A1D0-93E08934AE39An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insightsPeerJ592e1ddfe7dfc345bf8f35baa0882163Koci O2018-01-012167-83595c5aba0b5ca0e2.27159299FE6FFBF2-5189-4F8F-86E5-7ABA719062D1Gut microbial ecology and exposome of a healthy Pakistani cohortGut Pathogens9cbc0b283c9e45c4998761a66c45ced1Gul F2024-01-011757-474965c3612d005f28.107177550C11ECE3-9818-4972-A055-1310040A3CD7Emerging investigators series: microbial communities in full-scale drinking water distribution systems - a meta-analysisEnvironmental Science: Water Research & Technology3bf3bace9d94ea130939e341c0f5b065Bautista-de los Santos Q2016-01-01589482acd19003.332071675643F78A-EAAF-44F8-8110-3AB86A304B6FSystems biology approach to elucidation of contaminant biodegradation in complex samples - integration of high-resolution analytical and molecular tools.Faraday discussions87a7d9da23bcb0a19d1b3b94c72e535eGauchotte-Lindsay C2019-01-011359-66405dae5d20032888.24392491FD79356B-0B48-4695-81D8-3513C9C1B57FCViewer: A Java-based statistical framework for integration of shotgun metagenomics with other omics datasets592e1ddfe7dfc345bf8f35baa0882163Koci O2023-01-0164846e9a05c414E66AFFD-82AB-4687-9684-3EC32BD9431DInflammation associated ethanolamine facilitates infection by Crohn's disease-linked adherent-invasive Escherichia coli.EBioMedicineb5073faa89c115de97b8d37db046b819Ormsby MJ2019-01-012352-39645dae5cb43322e6.35028523D98DC00D-F91A-498E-B995-3A520A3581BEAdditional file 5 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7af950ce2.77332876F6E487B3-4923-4886-8535-A7B74E9DE587Linking Microbial Community Structure and Function During the Acidified Anaerobic Digestion of Grass.Frontiers in microbiologyf0daad434060fd5eb8027acc38087e5dJoyce A2018-01-011664-302X5c5aba09865ac0.5938498430EB89E0-9A6E-4E81-97E3-D5A9BD51F3E6Additional file 1 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526bab521779.50245342E21CC5A4-7F6C-45DE-B402-02C3CFD07A18Additional file 8 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7a5cb7374.78103932F423A52E-B8A7-446A-8A40-6093A2990765SalmoSim: The Development of a Three-Compartment In Vitro Simulator of the Atlantic Salmon GI tract and Associated Microbial Communitiesbd8899b572ba2cff70a3204d25097102Kazlauskaite R2021-01-0167527d5dd0bcd2.900195627582FBB6-5AF6-4FDC-92CD-87F671BB1F7BGut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn's disease.The American journal of clinical nutrition5ca7b1bb586940a4e6b03c3eb9275dbaNichols B2024-01-010002-9165662262e4ea55a0.7712777785AA591E-EBE5-4CFD-A7BC-625ED2336A5EMOESM1 of The effect of DNA extraction methodology on gut microbiota research applications41592addbe7ed7bd4bb66e0747bf25b4Gerasimidis K2016-01-0167526bea289f92.349073235E8B2D73-3243-4574-8A1A-2242C789E7B2Additional file 11 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526a477e5776.76092575517397CB-3CAF-41DA-91EC-3D969DD06FE5Additional file 7 of Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants61ac1dc6db0e8a5735887de507ea5c31Nikolova C2021-01-0165e8e683ef7d03.21067005208B698E-8F3F-4AD0-A241-EBA1142940D2Response and Oil Degradation Activities of a Northeast Atlantic Bacterial Community to Biogenic and Synthetic Surfactants61ac1dc6db0e8a5735887de507ea5c31Nikolova C2021-01-0165bb8495cadee7.89860557228C1803-7002-4F56-AB29-FF98AF727B23Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations.Microbiomeebf4406f047e3e8937b4f5853015c88dCheaib B2020-01-012049-26186023dea2093c36.82726325B08FE746-516A-4DA7-ACAA-C00277278FE2Galacto-Oligosaccharide has no Effect on Glucose Tolerance, inflammatory Markers or Intestinal Permeability in well-controlled Type 2 DiabetesProceedings of the Nutrition Society687a9ee4731147702ef3139511110ff0Pedersen C2016-01-01589482acef78b4.86729099ACF0EB95-5589-4505-A390-D83713DF4C90Differential utilisation of dissolved organic matter compound fractions by different biofilter microbial communitiesAQUA - Water Infrastructure, Ecosystems and Society50178a5e21b1422b93f5e1d16cf32862Vignola M2023-01-0164fb54bce3a7d4BC12F73-BF24-4B5E-867D-036177D4EF76Differential prevalence and host-association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems.The Science of the total environment2960ae0a582eaf74e334a30518127725Sevillano M2020-01-010048-9697602717ef14fc508DD8FEB-CF09-4AF7-B031-1A64597CF732Additional file 12 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7dd9a92e1.08948650208BF49E-DEA1-42BC-9938-8A367C169FDCAssessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines29f43963559065d949816972cfbe29e9Belén Torondel2016-01-016694c6ea77cd2D90645E7-8D12-40EE-BAAF-0E2CCDABAFE0Temporal changes in the gut microbiota in farmed Atlantic cod ( Gadus morhua ) outweigh the response to diet supplementation with macroalgae17af8dd4a59a944e9d8515761540a353Keating C2020-01-01602717b48c843C95EFE38-5C9A-4D9E-A626-5A5B622D2DBCDisinfection exhibits systematic impacts on the drinking water microbiomeMicrobiome257749f715b398b71deec930dc78d7a3Dai Z2020-01-012049-26185f86fc93b704f2.1268581986A6FCD4-FCB7-4E93-A0C1-98E514B6EBBAEditorial: the reduction of faecal calprotectin during exclusive enteral nutrition is lost rapidly after food reintroduction.Alimentary pharmacology & therapeuticsd94f3e8c8618eed592325c8d1a6dfc7aWall CL2019-01-010269-281365bb84a7ed5886.69771355A01D8DBA-ACBB-49C1-9280-60BA0C843E06Intestinal fatty acid binding protein is a disease biomarker in paediatric coeliac disease and Crohn's disease.BMC gastroenterology4146c13ab42c36eb8f95381540ba3073Logan M2022-01-011471-230X628b5831e421dA068640E-E4AD-4BE4-BCF9-83F2BC055ADBThe active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool.Microbiome39207eeeb3e0ec22ec112980ea9a6788De Vrieze J2018-01-012049-26185b6577ba918815.405320763E7DE24D-F0C6-43BD-9DCA-74474D8367F1Additional file 6 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526c86e64267.20236877AE5E3666-7CF7-47A7-923A-2CCD0F74D9A0Ecological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method88c82403c77579dd7f204f2c5d7c2d77Cholet F2022-01-016214a7a42d534AFCFC148-43D2-48C7-9A8B-FF5E5AEACF9BComparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use.PLoS pathogens3c4e16cbb7c88f019e8c81e723a76c35Parsons BN2017-01-011553-73665a2fc818ce9a19.4609630633DC4278-0D86-461C-B5E7-0FFA611B785DAdditional file 2 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526b0aa52a76.77767089BEDEF63B-AD48-4123-A98B-D5CB9799E03EBacterial diversity along a 2600 km river continuum12c967eac14a8bb6c3d9f72489cc9e57Savio D2014-01-0156db4d982a3dc1.873105711997619C-0D66-45C6-B2E4-E04ED5AF4CB6Biokinetics of microbial consortia using biogenic sulfur as a novel electron donor for sustainable denitrification.Bioresource technologyb91a2fa6376f0483f0630b0f6dd7e966Kostrytsia A2018-01-010960-85245c5aba37e300b6.203216444A79C6AB-E03C-4504-ADB1-95651000CB8BResponse and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactantsMicrobiome61ac1dc6db0e8a5735887de507ea5c31Nikolova C2021-01-012049-2618614c29f75296b8A7A5F14-757C-4254-9A63-EF240639B5A3Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate4b41deb51497fa0019816de7ecbb0828Umer Zeeshan Ijaz2022-01-016752824651a7a3.56476454BD03A1D5-AC23-401A-B2B9-6903F56BBCB2Additional file 6 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526be6b5c1e5.575729743FCBA2AC-20C0-4A97-A486-088464DCAC4FPotential nitrification activity reflects ammonia oxidizing bacteria but not archaea activity across a soil-sediment gradientEstuarine, Coastal and Shelf Science94a7d94359ad19a4909c2392e00962b1Tatti E2022-01-0161997be89ba52C5728043-BC6C-457F-9F94-07701F0A0D99NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platformc13fb48b46703eefa2a6268f92ad215fCalus S2018-01-01602718b6a1474FEF5F04B-9CA8-4BF7-86CC-CB6AB466D4BDComprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter45bd288f291517f9c4ab0972a477cb2fIjaz U2018-01-01602718baea831A851A14B-E1C2-401D-A1A5-A24B25A7D8EBLinking microbial community structure and function during the acidified anaerobic digestion of grassf0daad434060fd5eb8027acc38087e5dJoyce A2018-01-0167526bc84797c7.5036992839395BA7-5384-4B53-99D7-E0E763807C3CAdditional file 4 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7b6e474e6.821156224C9C9ED1-DCB6-4978-B343-B51D25FE40D0Differential ratio amplicons (Ramp ) for the evaluation of RNA integrity extracted from complex environmental samples.Environmental microbiology88c82403c77579dd7f204f2c5d7c2d77Cholet F2019-01-011462-29125c65632b064f35.379732413D1DE705-9E36-4060-883A-9723BE6AEB1ADeploying an In Vitro Gut Model to Assay the Impact of the Mannan-Oligosaccharide Prebiotic Bio-Mos on the Atlantic Salmon ( Salmo salar ) Gut MicrobiomeMicrobiology Spectrumbd8899b572ba2cff70a3204d25097102Kazlauskaite R2022-01-012165-0497627971bf1d0948.47561513E2AB9F33-4469-4371-9406-E80AC827B7D5Genome erosion and evidence for an intracellular niche - exploring the biology of mycoplasmas in Atlantic salmon.Aquaculture (Amsterdam, Netherlands)ebf4406f047e3e8937b4f5853015c88dCheaib B2021-01-010044-8486609f7d6c39a6f251B0C2F-462D-4B22-B83E-163445671C6FA Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078.mBio384f794748bc85c2fc08a066092b27a1Dingle KE2019-01-015e3c332ac7e903.81398015F07A7F63-56BA-4908-A0C1-EA70CCE9480DSeqenv: linking sequences to environments through text mininge506342dcf52c1c6e1b4a7839ce2ca75Sinclair L2016-01-0167526c3a23fc37.29508971DF57D54F-95AF-4C98-807E-539AA5CEA837A droplet-based microfluidic approach to isolating functional bacteria from gut microbiota.Frontiers in cellular and infection microbiologyfb99189ffe4fbb37f9241e6a384c7342Yin J2022-01-012235-298862ffab9c2ba43D5D1CAE9-48AD-4B22-9F88-0CB559AB8368Autotrophic denitrification of nitrate rich wastewater in fluidized bed reactors using pyrite and elemental sulfur as electron donorsEnvironmental Technology & Innovation16e22ff86c1e7a58715f7a6a9c9ac73fCarboni M2022-01-01630824beefd2447F047D3-C5F5-40C7-A303-5654D3ABCC6AAdditional file 12 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526c3b4a4bf7.82874084DBE4D5B1-6283-4D6B-A5B1-6A7974CF51F1Treatment of Active Crohn's Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition.Gastroenterologyd7345234614416bb9bd579b4d96b81e4Svolos V2019-01-010016-50855c5aba428eb1f6.02481456ECA56E73-5B98-47EF-8B03-222BB309C365Safe and robust data-driven cooperative control policy for mixed vehicle platoonsInternational Journal of Robust and Nonlinear Control742abcf3b2792406abecfc75e7768e48Lan J2022-01-0163dcfb2847f370.37126138951B190A-2340-40FF-B11F-05332C5A776EThe reduction of faecal calprotectin during exclusive enteral nutrition is lost rapidly after food re-introduction.Alimentary pharmacology & therapeutics4146c13ab42c36eb8f95381540ba3073Logan M2019-01-010269-28135dae5e46b11c40.833439540AFFF5AD-516B-4A21-978D-2CA3DBE4992EAdditional file 1 of Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbationsebf4406f047e3e8937b4f5853015c88dCheaib B2020-01-0165e8e8d08709d4.21693673161B9BB5-CC79-4269-831F-851181FC12A6The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their 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ecology17af8dd4a59a944e9d8515761540a353Keating C2018-01-010168-64965c5aba304aabd0.37868232E1A39D2C-1792-4C2E-8FCB-FC944B1901B8Dietary triggers of gut inflammation following exclusive enteral nutrition in children with Crohn's disease: a pilot study.BMC gastroenterology7d782475214c1e77b1f4c44845973befGkikas K2021-01-011471-230X61ac3c19c8aacB1BE0015-F96E-4D5C-9D13-7C63590BFDF6Terminal restriction fragment length polymorphism is an &quot;old school&quot; reliable technique for swift microbial community screening in anaerobic digestion.Scientific reports39207eeeb3e0ec22ec112980ea9a6788De Vrieze J2018-01-012045-23225c5aba21094629.97187037BEF581B7-DACE-4EE9-B828-DE16E0633C2FEcological Observations Based on Functional Gene Sequencing Are Sensitive to the Amplicon Processing Method.mSphere88c82403c77579dd7f204f2c5d7c2d77Cholet F2022-01-012379-504262f888525abfe0.874926823A162681-7163-422D-9C6E-C29982817C32Additional file 2 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526b92c9b128.02593249C9DB22B3-8550-4994-AF77-C93A96932F83The skin microbiome in psoriatic arthritis: methodology development and pilot data.Lancet (London, England)c2685702858b443ca26a149471b7062eCastelino M2015-01-010140-67365536c93c812a37.50704969B1025571-A232-4480-BEBE-9FC502D5EC5EBacterial diversity along a 2600 km river continuum.Environmental microbiology12c967eac14a8bb6c3d9f72489cc9e57Savio D2015-01-011462-29125536cbb9caefd1.584438503B4F661A-49AB-4098-9360-DAE9C6C31C55Additional file 10 of Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants61ac1dc6db0e8a5735887de507ea5c31Nikolova C2021-01-0165e8e693566d36.73975761BED78508-19D4-4726-906B-C705B8289734A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesisnpj Biofilms and Microbiomesebcb32334e2f74144f1d0934387a51abMills S2022-01-012055-5008632d3dd1028682E0623C6-AC71-4211-A20D-685A83DF3581Host-microbiome interactions in human type 2 diabetes following prebiotic fibre (galacto-oligosaccharide) intakeBritish Journal of Nutrition687a9ee4731147702ef3139511110ff0Pedersen C2016-01-010007-1145589482ad1b3518.812181642EC6E823-29DA-4A51-94A7-4E60A341C66COptimized R functions for analysis of ecological community data using the R virtual laboratory (RvLab).Biodiversity data journalbe2a94fc825354e834eb05a8745e7180Varsos C2016-01-011314-2828589482abecdb27.7871443914E7D8FA-AF57-4AF6-ADE6-F229148A9912Analysis of 61 exclusive enteral nutrition formulas used in the&nbsp;management of active Crohn's disease-new insights into dietary disease triggers.Alimentary pharmacology & therapeutics4146c13ab42c36eb8f95381540ba3073Logan M2020-01-010269-28136023de9f43a1e5.73852882674AA891-A24B-4A8C-8BF1-4D11CA95ECE4Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants61ac1dc6db0e8a5735887de507ea5c31Nikolova C2020-01-0160271928aa8fc0216B4FB-03C8-47CC-8D28-A5134320463ADrivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet.NPJ biofilms and microbiomes17af8dd4a59a944e9d8515761540a353Keating C2022-01-012055-500862725f597bbd4FC10A0C3-71D9-44B1-8596-02FDF39B3387Comprehensive Longitudinal Microbiome Analysis of the Chicken Cecum Reveals a Shift From Competitive to Environmental Drivers and a Window of Opportunity for Campylobacter.Frontiers in microbiology3c5d0b2967e8b09d545e2deb131e89f6Ijaz UZ2018-01-011664-302X5e3c33e923f158.723148745986C038-B6DB-4245-A014-5AAFF91EAA8EAdditional file 3 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7b56c5da7.49970909C1E1A929-843D-43E8-8428-1066567BE737DOP52 The faecal bacterial and fungal microbiome of newly-diagnosed, treatment na&iuml;ve children with Crohn's disease and the modifying effects of exclusive enteral nutrition and re-introduction of habitual dietJournal of Crohn's and Colitis41592addbe7ed7bd4bb66e0747bf25b4Gerasimidis K2023-01-0163dc07a405964C34198CC-3D99-49D6-B88B-1EAD0CA10282Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines.Microbial biotechnology8703ad164021168fbb518a8586736317Torondel B2016-01-011751-791556db4d97b6de43.1871191835F8A469-FCC5-4A6D-9EDC-C52CB9D1E2D6DOP68 CD-TREAT diet induces remission and improves quality of life in an open label trial in children and adults with active Crohn's DiseaseJournal of Crohn's and Colitisd7345234614416bb9bd579b4d96b81e4Svolos V2022-01-0162fff11d339faFDD9AD33-1093-40D4-81D0-50B895C9AC52First evidence for temperature's influence on the enrichment, assembly, and activity of polyhydroxyalkanoate-synthesizing mixed microbial communitiesFrontiers in Systems Biologyc49c8e05d15160edb97d85e408c9fd1bTrego A2024-01-01675288f39dd0a2.783881071E37E449-12F0-47FE-868B-17E74B241A10CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets.Microbiome592e1ddfe7dfc345bf8f35baa0882163Koci O2024-01-012049-26186688583f0c4b88E34CA2B-4186-4199-BA95-E5DA738B4B47P380 Changes in faecal microbiome and metabolome are more pronounced in Crohn's disease patients who adhered to the CD-TREAT diet and responded by calprotectin.Journal of Crohn's and Colitisd7345234614416bb9bd579b4d96b81e4Svolos V2023-01-0163dc07a5a370f6D53CB12-ACE1-4B4E-B07C-25DA621FAB75An automated identification and analysis of ontological terms in gastrointestinal diseases and nutrition-related literature provides useful insights592e1ddfe7dfc345bf8f35baa0882163Koci O2018-01-0165bb8400272764.464188138D155B57-F431-482B-A9E1-D4B8C851B525Bacterial community analysis in upflow multilayer anaerobic reactor treating high-solids organic wastes.Biotechnology progresse522e04b2610fcd4de23fe86debd7daeCho SK2017-01-011520-60335a6617ee112e26.22023362AF0DC81D-AA54-4868-8B39-CE8E8B37B87116S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus.Scientific reports53b66e3fe5923aa8e9a27654748caecbReich I2018-01-012045-23225c5aba19c52272.6258524207A08800-7871-4B32-9FA3-253979583875Additional file 1 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526b0586b757.3654552775523BFD-594F-49C2-89B7-DDA747C40392Bioreactor scalability: laboratory-scale bioreactor design influences performance, ecology, and community physiology in expanded granular sludge bed bioreactorsd3511033c1f7a8f7a6513110b6910a5fConnelly S2017-01-0167526b0fcff079.562802549B4834B7-3FAB-42A2-B859-369F2093EB3FCotton Microbiome Profiling and Cotton Leaf Curl Disease (CLCuD) Suppression through Microbial Consortia associated with Gossypium arboreumbc32f3a8cc40351683169581b006a88dAqueel R2023-01-0164aff45b5b260855A0A53-E9E7-4571-BD5B-CBD7C3DA8B0FNext-Generation Sequencing to Identify Lacustrine Haptophytes in the Canadian Prairies: Significance for Temperature Proxy ApplicationsJournal of Geophysical Research: Biogeosciencesaf90ef024c20ae95dd703cacc61c2274Plancq J2019-01-015dae5e37695384.7848167652B46768-DF0D-4399-A7DE-3FAA45CC1D7ANeutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar.Applied and environmental microbiology04325d9feab8d669c8595336fc064408Heys C2020-01-010099-22406023de96cd0869.92599135CB50B9B2-7671-42E3-AFD8-FD12AF0304B4A Cross-Sectional Study of Potential Antimicrobial Resistance and Ecology in Gastrointestinal and Oral Microbial Communities of Young Normoweight Pakistani IndividualsMicroorganisms1b0d7de3cdb5cdafe93e976ef200cc41Batool M2023-01-012076-260763d1054493c273F66200F-CACA-4929-A7BF-04E9B37A7B56Additional file 2 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7db951022.202435978EC53871-8802-4E99-8DCF-FA20EF241854Carboxylic acids production and electrosynthetic microbial community evolution under different CO2 feeding regimens.Bioelectrochemistry (Amsterdam, Netherlands)1651a8c8389e19c3747e331370f69a76Dessì P2021-01-011567-5394602717ddc1078C781F7FC-7C6E-4958-9D40-F045EAA4AB94Additional file 7 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526bea501058.32880019514E596B-5287-441A-B905-A3576F80E13FAdditional file 1 of Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbationsebf4406f047e3e8937b4f5853015c88dCheaib B2020-01-0165e8e89361f5d4.462614729A84AF6F-BCD6-4440-8E6A-C2FC1028EC93Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage17af8dd4a59a944e9d8515761540a353Keating C2018-01-0167526bf9d3c0c9.33316560CE3B134A-FFF7-44B9-878B-674EE056A814Molecular insights informing factors affecting low temperature anaerobic applications: Diversity, collated core microbiomes and complexity stability relationships in LCFA-fed systems.The Science of the total environmentfade14a3384de22ad83e51433c35ef62Singh S2023-01-010048-96976433070855aef8DC50847-CD07-4FEF-820E-8F98CCDDE218Additional file 11 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526c90bf34b3.71562962B07FBA9D-C717-480C-9711-A728387B3FF6De Novo Growth of Methanogenic Granules Indicates a Biofilm Life-Cycle with Complex Ecologyc49c8e05d15160edb97d85e408c9fd1bTrego A2019-01-0160271919ece93F9DB43BD-92A9-471D-918F-5D0000CEABCAComparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori -induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor useee380db2dd0572ff1f27c88b0e07f243Parsons B2017-01-01602718da27d47308BDBE9-50E9-4080-866C-8899E92F335BSalmoSim: the development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communitiesbd8899b572ba2cff70a3204d25097102Kazlauskaite R2021-01-01602ae84ba620a8E4FCB7E-85DD-4419-B2F4-F9EE1E006056Additional file 12 of A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling8e1eeaf0112eb212b235f054c78094ffDâ??Amore R2016-01-0167526bebaab2e8.8349225906540403-2E46-4A41-9C7E-92403851FD8ECotton microbiome profiling and Cotton Leaf Curl Disease (CLCuD) suppression through microbial consortia associated with Gossypium arboreum.NPJ biofilms and microbiomesbc32f3a8cc40351683169581b006a88dAqueel R2023-01-012055-5008657a9809e9483FCCD5595-EB27-4C8E-9FA7-EBBF60C2B7A8Microbial community assembly and dynamics in Granular, Fixed-Biofilm and planktonic microbiomes valorizing Long-Chain fatty acids at 20&nbsp;&deg;C.Bioresource technologyfade14a3384de22ad83e51433c35ef62Singh S2022-01-010960-852461607e0a471f18CF36FD8-1FF9-4191-A90B-05E42F7FF326Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate.Frontiers in microbiology3c5d0b2967e8b09d545e2deb131e89f6Ijaz UZ2022-01-011664-302X63332f6f2d9e8CD86B706-9A48-4BAE-AB55-0EE6F98FD6EBDietary Triggers of Gut Inflammation Following Exclusive Enteral Nutrition in Children with Crohn's Disease: A Pilot Study7d782475214c1e77b1f4c44845973befGkikas K2021-01-0160fecb64cbf18874BAAAD-A8CE-40D4-B43A-A75BAFCE4FECAdditional file 10 of Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-0165e8e7dc04b709.63263041B47FD49E-2BFF-4001-931C-BA7258DF93B0Analysis of pit latrine microbiota reveals depth-related variation in composition, and key parameters and taxa associated with latrine fill-up rate4b41deb51497fa0019816de7ecbb0828Umer Zeeshan Ijaz2022-01-01675285dc1de7b5.018281969BCC9346-888D-402B-8250-2ED7684D28C0Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data.BMC bioinformatics596d9dfa2eaaf473b1e4dc87210b939dSchirmer M2016-01-011471-2105589482aca6c1d9.53711314F5C927A9-DA48-48BA-B743-0F9ADC3DFA1AExtending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences.PeerJc0f9ba30f44a7628926730baa7902901Ijaz AZ2017-01-012167-83595a6618fa1f8241.303509447B7A36D9-AF3C-44A9-9DF6-2CE372908E07Size Shapes the Active Microbiome of Methanogenic Granules, Corroborating a Biofilm Life Cycle.mSystemsa97ab20d06486826771a13be390cc515Trego AC2020-01-012379-50776023df49e1b5f3.1400825550C69F0A-A7BF-4BAB-BAC7-51BF8DCBA91AAdditional file 9 of Response and oil degradation activities of a northeast Atlantic bacterial community to biogenic and synthetic surfactants61ac1dc6db0e8a5735887de507ea5c31Nikolova C2021-01-0165e8e684c02465.94748729C00871CB-2036-4C24-BE2F-626362854651Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter.Microbiome33ac40eabdbbe3c78670b76114ce3d1aMcKenna A2020-01-012049-26185f852f9dd975d3.65617109NE/L011956/1F673FD2B-013B-47E5-9E62-03BAB1E7348E10Environmental engineering4CCA4C04-0C28-41BE-8869-FA6391A7F00520Microbial sciences29F3DF16-3094-4F79-BC69-8D05FB55182670Omic sciences & technologies513702B4-7C48-41F2-A1A0-8B4E8BEDCABC10Assess/Remediate ContaminationC6A85141-ED79-4266-86E5-F6D25217C97F40Environmental GenomicsAF3F5E7C-7FB6-4588-9174-6018BA2A231B20Environmental Microbiology7E61B40B-93E5-4D69-8C89-426ED7E0D2B420Metabolomics / Metabonomics937A9F23-021A-4604-8979-A28E0E04F82510Transcriptomics0C8BB41D-B4B5-4A91-B6AA-00D48582C5AEReal-time prediction of cellular states in 3D lattice light sheet microscopyClosed2430216StudentshipProgramme overview: This MRC-funded doctoral training partnership (DTP) brings together cutting-edge molecular and analytical sciences with innovative computational approaches in data analysis to enable students to address hypothesis-led biomedical research questions. This is a 4-year programme whose first year involves a series of taught modules and two laboratory-based research projects that lead to an MSc in Interdisciplinary Biomedical Research. The first two terms consist of a selection of taught modules that allow students to gain a solid grounding in multidisciplinary science. Students also attend a series of masterclasses led by academic and industry experts in areas of molecular, cellular and tissue dynamics, microbiology and infection, applied biomedical technologies and artificial intelligence and data science. During the third and summer terms students conduct two eleven-week research projects in labs of their choice. Project overview: Lattice light sheet microscopy (LLSM) is a new technology to visualise fast cellular processes at the time scale of 1 second, in 3D. LLSM is very low through-put however, limiting its use for studying rare events, such as cell divisions. In close collaboration with industrial partner Intelligent Imaging Innovations Ltd. (3i), suppliers of LLSM, we will develop an integrated imaging pipeline to classify and anticipate physiologically meaningful events during the cell cycle using state of the art machine learning. The main goal is to 1) enable automated control of the image acquisition and increase its throughput, and 2) make it possible to analyse statistically significant numbers of well-defined cellular events and their progression from an early stage, which often go unnoticed by even the most expert human experimenter. Enabling detailed spatio-temporal analysis of the 3D imaging data will help to better understand the timing and control of different stages of cell division and recognise more subtle defects in cell division which can affect development or diseases such as cancer where divisions occur uncontrolled. This is an interdisciplinary project at the interface of cell biology, computer science and engineering, enabling fundamental science to improve human health through world-class biomedical research. Health focus is enabling biological research into genetic risk and disease mechanisms, aiming at new strategies for early diagnosis and treatment. The specific training the student will receive is geared towards quantitative and interdisciplinary skills and understanding of whole organism physiology in addition to that of single cells in the main project. The training in advanced machine learning and computing addresses the demand for team scientists and technology specialists and will help to build new software technologies and imaging instruments that will become available to the biomedical community in the future.2024-12-30C008C651-F5B0-4859-A334-5F574AB6B57CMRC2020-10-04INCOME_ACTUAL024302166CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0511D9D6-93E0-4C3E-83EE-0182527AFDADNewton's CradleClosed10117189Department for Science, Innovation & TechnologyA novel organisational model that addresses gaps in how we deploy, evaluate and leverage medical AI at scale, with a research-led methodology and an industrial focus.2024-10-3112E03F45-B517-4D83-A182-3D142D1A471AInnovate UK2024-03-01INCOME_ACTUAL70000101171896CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0519C4B0-EC16-4A83-8E7E-0074D0CD7A94The University of Nottingham and Siemens Energy Industrial Turbomachinery Limited KTP 23_24 R1Closed10074740Knowledge Transfer PartnershipTo develop and implement a novel methodology, for rapidly analysing the heat transfer and flow performance of additively manufactured porous lattice structures within high temperature gas turbine applications.2024-10-3112E03F45-B517-4D83-A182-3D142D1A471AInnovate UK2023-11-01INCOME_ACTUAL45000100747406CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified07EA8DEB-ED66-4495-944A-01F7A59DFFB6REPOXYBLE: Depolymerizable bio-based multifunctional closed loop recyclable epoxy systems for energy efficient structuresActive10067645EU-FundedMaterials, especially advanced materials, are the backbone and source of prosperity of an industrial society” (Materials 2030 Manifesto). The Green Deal and the Digital Decade establish high-priority policies for Europe, where 70% of all technical innovations are directly or indirectly attributed to advanced materials. Lightweight and high-strength materials have consistently played a key role in the construction of fuel-efficient and high-performing transportation structures. Lightweight materials such as glass and carbon fibres composites are commonly used due to their intrinsic properties such as high mechanical performance. However, the poor recyclability and recovery aspect poses a significant challenge. The end-of-life aspect of these materials is crucial, as when landfilled they release toxic substances into the environment. Moreover, minimising resource use, energy of manufacturing processes and optimising waste disposal of future advanced materials can help mitigate cost and product’s end-to-end footprint acrossits global lifecycle, thereby significantly improving its overall environmental performance. REPOXYBLE will create a new class of high-performance materials -bio-based epoxy composites targeting cost and energy effectiveness, recyclability and sustainability. REPOXYBLE assumes an upstream approach more efficient and effective than having to address deficiencies at the end of the product development process. This approach integrates product performance, multifunctionality, sustainability, safety and potential legal concerns, while there is still time to act, on the monomers’ synthesis, the resin formulation and the future composite design. REPOXYBLE is driven by two complementary market applications in the aerospace and automotive sectors.2026-11-30240CEBFD-1052-4EAC-88DF-D88A163D61C8Horizon Europe Guarantee2022-12-01INCOME_ACTUAL410973100676456CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified08985353-1E14-4F3D-9480-0020ACFD7CC2The Multimodal Translation of Intangible Cultural HeritageActive2930848StudentshipMotivation Intangible Cultural Heritage (ICH) represents the dynamic tapestry of human civilization, encapsulating our collective traditions and cultures. As highlighted by the 2003 UNESCO Convention on the Safeguarding of the ICH, preserving these diverse cultural manifestations is crucial. In the digital era, technological advancements such as transmedia, VR, AR, and 3D modeling allowed diverse forms of information to be digitally transformed and presented in increasingly vivid and comprehensive digital formats (Alivizatou-Baeakou, 2017; Rossau et al., 2019). While these innovations offer unique opportunities to enhance the representation of ICH, they also pose challenges in representing its dynamic, multimodal nature. Furthermore, current digitalisation methods tend to be technocentric and often overlook the cultural contexts and holistic nature of ICH, potentially leading to a loss of its evolving, living character (Carboni &amp; de Luca, 2016). Addressing these challenges necessitates interdisciplinary solutions. There is increasing recognition of the need for a comprehensive digitalisation theory that integrates semiotics with new media technologies (Nantke, 2017), aiming to enrich the digital representation of ICH (Berlanga-Fern&aacute;ndez, 2022). As Olteanu &amp; Ciula(2022) argue, &quot;digitalisation-when dealing with conversion across media-are forms of intermedial translation, hence of relevance to translation studies that found its theoretical grounding in semiotics&quot;. Building upon this, this research aims to contribute to bridging these gaps by developing a theoretical and practical framework based on multimodal translation theory. This framework, tailored for cross-contextual applications, will bridge traditional understandings with the digital realm. It will focus on digitally preserving and representing the intangible attributes, living nature, and multimodal characteristics of ICH. Aim and Objectives: The overarching research aim of this project is to craft a viable digitalisation pathway for the digital preservation and representation of multimodal ICH content that addresses both challenges and opportunities. The focus is on ensuring long-term development while respecting diverse and multivocal cultural contexts. The objectives are as follows: 1: Apply interdisciplinary multimodal analysis to decode the diverse characteristics of ICH, reflecting its multifaceted nature and significance in socio-cultural contexts. 2: Explore translation strategies for transferring ICH from traditional to digital formats, ensuring the preservation of its intrinsic meaning across different modalities and contexts. 3: Develop a flexible theoretically informed and practically-oriented framework for multimodal translation of ICH, enhancing its digital access and relevance in a rapidly evolving digital world. Contribution: This research introduces multimodal translation from an interdisciplinary viewpoint and aims to provide a theoretically-informed and practically-oriented framework for effectively preserving ICH in today's digital landscape. Academically, it forges a link between systemic functional linguistics and design theory, developing an innovative digital translation system that offers a richer and more culturally attuned representation of ICH. On the application level, the research enhances preservation and dissemination processes, employing advanced digital techniques for efficient data management and broader accessibility. This approach enriches ICH propagation, supports its systematic inheritance, and promotes cultural exchange through a shift towards more dynamic ICH engagement.2027-09-291291772D-DFCE-493A-AEE7-24F7EEAFE0E9AHRC2024-09-30INCOME_ACTUAL029308486CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified00CDCA79-8C71-453A-AA24-0181FDBB9BC6How do cells shape and interpret PIP3 signals?ClosedBB/I003916/1Research GrantMulti-cellular organisms rely on a large array of different transmitter substances to allow certain cells to control the behavior of others. The more sophisticated the organism the more complex the cell to cell communication. In mammals this language probably involves hundreds of fundamentally different types of transmitter. Clearly such systems need a large collection of specialized receptor molecules that can detect the individual presence of any particular transmitter. Further, these receptors, typically found on the outer surface of the cell's limiting membrane, have to signal their specific stimulation by passing a molecular message into the cells interior, effectively informing the cell that the receptor has been activated. Clearly, if a cell has many different types of receptors on its surface the molecular signal generated inside the cell by each different receptor (often called an intracellular message) must identify and distinguish which specific receptor has been stimulated. Otherwise the cell could not discriminate between the transmitters present on the outside of the cell and could not respond correctly. Hence, mammalian cells have vastly complex intracellular signalling mechanisms continuously informing the cell of what is happening in other parts of the organism or its environment. One such intracellular signalling molecule or 'message' is PIP3. It is a phospholipid molecule found on the inside surface of the cell's limiting membrane. Levels of PIP3 rise rapidly on activation of a large number of receptors. This is surprising given the problems the cell faces in knowing precisely which receptor has been activated when it detects an intracellular signal. This grant application is to understand how it is possible that rises in PIP3 can encode specific messages from so many different receptors. We have performed some experiments that have, in fact, shown that PIP3 in cells is not a single type of molecule. At least four tiny variants of PIP3 can be detected, called molecular species of PIP3. Interestingly, we find that these different molecular species of PIP3 do not respond equivalently to different ways of activating the cells we work with. We and others have also found that the different receptors can make the levels of PIP3 rise for different times and to different maximum levels. We propose that these small differences are very important inside the cell for discriminating whether a certain receptor has been stimulated. This is a 'clever' economy or efficiency on the part of the cell and allows it to use similar mechanisms to perform many different jobs. Although on the surface these might appear trivial details in the business of understanding biology, it has recently been discovered that many different cancers are caused by mutations in genes that regulate PIP3 levels in cells. Mutations that by chance cause the production of PIP3 to be increased without any need for receptor stimulation make cancers much more likely to occur. Mutations that by chance stop the enzymes that normally break down PIP3 from working also make cancer more likely to occur. As a result it is clear that understanding how PIP3 is made and then interpreted by cells is crucial for us to better understand how cancer occurs and how to treat it. Many companies are already trying to design drugs that will reduce PIP3 levels to fight cancer. This work will help us understand how to make better drugs of that type.This proposal is a collaboration between biochemistry groups at BI and mathematical biologists at the EBI to achieve a detailed and quantitative understanding of a major mammalian signal transduction pathway, the PI3K network. Several PI3K isoforms exist in cells that can be selectively engaged by a variety of cell surface receptors to generate the membrane phospholipid PIP3. PIP3 is the initial signal, which is then transduced by 10-50 effector proteins into the regulation of complex cell responses, such as cell growth and movement. Our strategy is to focus on collecting robust, high quality data sets in a panel of isogenic, non-transformed breast cell lines (MCF10a) in which key endogenous components of the pathway can be manipulated and to embed iteration between experiment and modelling to arrive at a more satisfactory explanation of: 1) the key factors which shape the magnitude and spatiotemporal properties of PIP3 signals in response to hormonal stimulation (EGF, insulin, LPA) and oncogenic mutation; 2) The way in which different PIP3 effectors interpret these PIP3 signals and 3) the relative importance of individual PIP3 effectors in delivering regulation of chemokinesis, growth and global transcription. We plan to use homologous gene targetting, siRNA suppression and pharmacological inhibition of pathway components and measure the impact of these perturbations, in several relevant cellular contexts, on i) the levels of PIP3 and other phosphoinositides measured by a novel, quantitative mass spectrometry assay that allows systematic analysis of fatty acid composition; ii) the activity and spatial distribution of several PIP3 effectors (in some cases via knock-in of endogenous GFP-fusion proteins); iii) chemokinesis, markers of growth and global transcription (using next generation sequencing). Models will be built at several levels in the pathway and integrated to allow a deeper understanding of this network and guide more effective therapeutic intervention1) Identify the beneficiaries of this work. See the section 'the beneficiaries'. To restate, ignoring our proximal research community, they would include, within the life-time of the grant; (a) an international and broad group of commercial and academic researchers, (b) the BBSRC, our host Institutions (Babraham and EBI), (c) the post-doc researchers on the grant through the training they receive and (d) our IPA partner Astra Zeneca. In addition, in the longer term, (e) the health care sector, patients and the UK's economic competitiveness. 2) How would they benefit? a) From the technologies and approaches we propose to apply in this application. Most signficantly the lipidomics strategies we have developed to enable sensitive, medium through-put analyses of the different molecular species of PIP3. This advance enables the development of potentially direct read-outs of the effectiveness of PI3K inhibitors in a clinical setting, through the opportunity to take frozen cell or tissue samples and sensitively and quantitatively analyse their PIP3 content. Until now companies have relied on surrogate read-outs of PI3K activity that have a variety of technical and intellectual weaknesses. This approach will also change the phosphoinositide research community, historically there has ben a huge pausity of data in the field through the technical or financial challenges in capturing this type of data. This has severly limited attempts to model this pathway. b) See beneficiaries section. The BBSRC would gain from delivery of their objectives in their recently formulated strategic plan, specifically in the Bioscience for Health priority. As an IPA application, this project has evidence of its commercial relevance as 'basic research underpinning the pharmaceutical sector'. Its use of modelling is in line with the BBSRCs drive to change the culture of modern biology towards being more mathematically based. c) Both the EBI and BI have internationally competitive research environments where the post-docs would learn within a project that has both direct commercial relevance, substantial contact time with a major pharmaceutical company and a multi-disciplinary approach. d) Will benefit from accelerated access to a internationally competitive grouping working in a field in which AZ have direct interest in their inflammation and oncology programmes and from having first option on any IP that might emerge from the project. More specifically they will gain direct leverage from results with the cell lines and inhibitors we have chosen to focus upon; both are used within their own, internal, research programmes. They will also gain early insights into the lipidomics approach we have developed and how they might use it to solve long-standing problems with bio-markers of activity in the PI3K pathway in whole animal or clinical studies. e) These could be longer terms outcomes resulting from improved focus on the most appropriate PI3K targets and hence the best PI3K-selectivity profile of potential drugs in specific therapeutic setting and the development of more relevant and useful bio-markers. As our IPA partners oncology programme is based in the UK (Alderly Edge, Macclesfield) the above should give competitive advantage to UK business. 3) How would we ensure the above potential benefits are realised a) Presentations at international science meetings, publications, good data sharing practice, seminars at companies b) Through the projects funding and execution c) Regular meetings between EBI and BI labs and with AZ researchers (see work plan) d) Through (c) and see Case for support e) The IPA status of this application and the success of past research collaborations (&pound;300K) with AZ are based on our approach to, and conduct within, collaborations with industry. AZ have confidence we will put effort into transferring knowledge and skill and that it will give them competitive advantage in getting good therapeutics into the market-place.2015-10-04198E4A3D-B2DC-45D4-8351-7CCEC4061876BBSRC2011-05-30INCOME_ACTUAL1086512AstraZenecaUnited KingdomAZ/Cosulich040F1A62-2672-48FC-8EA3-5CD936A68AD9Papers and models (still in development), much work is currently being written-up.546485a40f8d63.36861866-1Insights in to commercial directions and interests in this area.We are measuring and modelling agonist and onco-mutant driven changes in PIP3 signalling and then using selective inhibitors and RNAi to understand how the PIP3 signalling network operatesPrivate2009-01-01University College LondonUnited KingdomDivision of BiosciencesNick Luscombe83956FB2-0BEB-48BE-83AB-E2EC7B41CDB2Publications, a number are on-going. Multi-disciplinary, biochemistry, computer modelling, bioinformatics, biological chemistry/mass spec development.546373be5e37e1.52808872-1Training in bioinformatic techniquesWe provided data, knowledge and experienceAcademic/University2012-01-01Akita UniversityJapanSasaki_ mass spec and prostateFB91242C-4135-4103-9385-30D02A045768Norton et al (2016) Adv Biol Regul. 60:36-45. doi: 10.1016/j.jbior.2015.10.005 Ferguson et al (2007) Nat Cell Biol. 9(1):86-91. Malek M, Kielkowska A, Chessa T, Anderson KE, Barneda D, Pir P..... Stephens LR, (2017). PTEN Regulates PI(3,4)PSignaling Downstream of Class I PI3K.. Molecular cell, 68 (3), pp. 566-580.e1058b5b5498fbad4.10061619-1Intellectual input, reagents, mass spectrometric methods, personnelIntellectual input, reagents, mass spectrometric methods, personnelAcademic/UniversityUniversity of TorontoCanadaSergio_Grinstein_SopBDA4EDD2F-4FA4-45E7-9F14-D35A4F8D136DManuscript currently in Press at Nature Cell Biology622209a4e34a73.10799339-1They lead the project, providing the intellectual framework and the vast majority of the data.We used our mass spectrometry methods to define a new phosphoinositide reaction mechanism for the Salmonella effector protein SopBAcademic/University2021-01-01University of TorontoCanadaSergio_Grinstein_SopBC6905A81-EAB0-4C83-8D0A-BD62F5A5C6F2Manuscript currently in Press at Nature Cell Biology622209a4e34a73.10799339-2They lead the project, providing the intellectual framework and the vast majority of the data.We used our mass spectrometry methods to define a new phosphoinositide reaction mechanism for the Salmonella effector protein SopBAcademic/University2021-01-01Work experience for year 12 school studentsParticipation in an activity, workshop or similarLocal12E7E021-450D-4EC1-8CA2-7960F3D4EE51Work shadowing for a yr 12 school student to understand biomedical research Student applied and got an offer on a biomedical degree course54624afb870e31.83032049falseSchools2014Training other researchers in use of lipidomics techniques.Participation in an activity, workshop or similarInternational1DE862B4-A98C-479A-928D-4A0165332C14Researchers visit BI for 1-5days typically to observe, discuss or trouble shoot lipidomics techniques. PhD students, PIs, technicians and commercial staff have been involved. Researchers from Japan, France and UK.56c1b05185e4f0.04081206falseProfessional Practitioners2012,2013,2014,2015Public engagement ageing meetingParticipation in an activity, workshop or similarRegionalA95CB5EC-BBB2-4538-8F44-F02AE3C67739A meeting held at Cambridge Guildhall with brief presentations from a panel of mixed scientific backgrounds followed by Q&amp;A and group discussions; also practical demonstrations of how reaction times, hearing, etc changes with age56d8cee11d7279.62768293falsePublic/other audiences2012Cambridge Science FestivalParticipation in an activity, workshop or similarRegional77551C1B-EB73-4091-99CC-0CFA0DC9624EExhibit at Cambridge Science Festival was attended by all age groups with extensive interaction and discussion56d8ce6350d1e8.87454856falsePublic/other audiences2015Invited lecturer to international meetings (average 2-3 per year)A talk or presentationInternationalC3ADBA4B-017F-44BB-B20E-6348B7EDAB95promoted discussions, collaborations scientific collaborations, joint grants and publications546215ce564be0.43637759falseProfessional PractitionersPre-2006,2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019To determine the isoform of PI3Ks that are best targetted in different forms of cancer. Previous dogma and much pharmaceutical investment had being based on the concept that in tumours lacking the tumour suppressor PTEN PI3Kbeta was selectively augmented and the primary therapeutic target. Part of our study showed this is untrue. This has changed biotech PI3K targetting strategy and funding. We have shown that a well known tumour suppressor (an inhibitor of tumour progression) is a PI(3,4)P2 phosphatase in addtion to its other known roles, this has important implications for cancer progression and understanding how different mutations in cancer interact and can influence therapeutic strategy. Further work flowing from this award went to show that PTEN, a human tumour suppressor and PIP3-3-phosphatase is also a PI(3,4)P2 3-phosphatase and this is important for its cellular functions and this has led to new strategies to inhibit and modulate PI3K pathway activity.20147D2304F0-DBC0-4353-A179-C05D5DEC2FB1Economic56bb02289579c5.29857628Healthcare,Pharmaceuticals and Medical BiotechnologyWe have developed a new method to measure PI(3,4)P2 a critical intracellualr signal. We have shown PI(3,4)P2 is degraded by an enzyme that is a key inhibitor of tumour progression and when the tumour suppressor is removed, and a potentially affected person becomes much likely to get cancer, this is in part because the levels of PI(3,4)P2 signal in cells becomes dangerously high. We have developed tools to analyse large complex changes in mRNA accumulation in response to genetic and pharmacological manipulation of PI3K activity. We have clarified mechanisms of PI3K regulation that are relevant to therapeutic strategy in cancer trails and treatment.Our basic-biology results have already changed companies strategies in targeting specific cancer types with specific PI3K inhibitors.4D52A5B3-C6DB-4FE9-A6A8-121A9D7642B95463702eb55f51.13006653HealthcareTo accompany article published in Molecular cellFCAC02C2-83FF-4A93-90F9-C7F2F0B77D5A65dde63762b4a4.87758778truePTEN regulates PI(3,4)P2 signalling downstream of Class I PI3KDatabase/Collection of datahttps://data.mendeley.com/datasets/tnj6m88k6w/12017In collaboration with Jonathan Clark in the Biological Chemistry Facility at the Babraham Institute we have developed novel mass spectrometry approaches for measuring different molecular species of phosphoinositides in cells and tissues. This work has utilised chemical derivatisation coupled to LC-MS and involved the synthesis of several isotope-enriched internal standards.2F8A1BEF-59A2-4A4C-8CBB-0D798C754392The main impacts have been numerous publications (&gt;30 as of 2021), collaborations and clinical trials of PI3K inhibitors.622203963dc4b7.38742910trueMass_spectrometry_analysis_of_phosphoinositidesTechnology assay or reagenthttps://www.babraham.ac.uk/science-services/biological-chemistry/jonathan-clark20111BCCE0A5-4219-4EBB-BC74-A356BBB56178Signaling via class IA Phosphoinositide 3-kinases (PI3K) in human, breast-derived cell lines.PloS one335ea1a5172fc6d0d647e3c40642d987Juvin V2013-01-011932-62035463715fc2e9c6.1324974251C1B0A3-003D-4A00-B75E-F3E14DEEC964Gß? is a direct regulator of endogenous p101/p110? and p84/p110? PI3K? complexes in mouse neutrophils.Science signalingae569daa6ccaf41d0010a7fe61afd363Rynkiewicz NK2020-01-011945-08775fb8f7363be6f0.5824395810E53A94-0FDB-4B39-8B77-2A5021CFA648Lysophosphatidylinositol-acyltransferase-1 (LPIAT1) is required to maintain physiological levels of PtdIns and PtdInsP(2) in the mouse.PloS oneb69f958d0a381f3030849518250d3521Anderson KE2013-01-011932-62035463715eed0fc3.363209955A0059D5-B1D8-4D30-8987-827AFFF8F1F0PIP-ing Lipids on Membranes: PTEN Takes the Cake.Molecular cell3f910d0addbd5b7d25d64a230f01a74cRavi A2017-01-011097-276567520f44d96161.58607893BEE9337E-7861-4C71-BF4A-6E2E2EAC1F0FPTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K.Molecular cell32166a1af7e300ccef30545562aeb163Malek M2017-01-011097-27655a8af658dee1a5.01603718E6EBDC5C-BE0E-4AE6-88B5-AF9F7EE13069BMX acts downstream of PI3K to promote colorectal cancer cell survival and pathway inhibition sensitizes to the BH3 mimetic ABT-737.Neoplasia (New York, N.Y.)15b2aa803b28c58fa133b58ee608eaaePotter DS2014-01-011476-558656bb048eb1ca51.75181505555C0D8A-E699-4D8C-A779-5330CDBBE111Emerging evidence of signalling roles for PI(3,4)P2 in Class I and II PI3K-regulated pathways.Biochemical Society transactions9d3df4506683f973bcc340d59b4b4a5eHawkins PT2016-01-010300-512758b439901d0341.870016286C7D9796-1B70-4B5C-80B6-8377D49DA2D4A new approach to measuring phosphoinositides in cells by mass spectrometry.Advances in biological regulationbc631ac334819daffd5622aa3c7c24a6Kielkowska A2014-01-012212-49265463715f8e64a2.18675920552B0D31-2ED1-4D94-AB5B-515822552F9FProfiling of phosphoinositide molecular species in human and mouse platelets identifies new species increasing following stimulation.Biochimica et biophysica acta. Molecular and cell biology of lipids81f01c0fef8f0f705aa63e4abb959f27Mujalli A2018-01-011388-19815c7d421b71a352.746719251207BB2C-F8F4-4A21-B62B-7191D932914APerturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop.Nucleic acids research51585f72da0559dba579b0473aa0f917Kiselev VY2015-01-010305-104856b0cdd91ead15.0921803513AC9610-6CCC-42A6-B012-37245A6F714AQuantification of PtdInsP3 molecular species in cells and tissues by mass spectrometry.Nature methodsedc5f7c0e58dfe61e7f81d9f8d2b7544Clark J2011-01-011548-70915463715d78f491.68822835F7611F0A-7B46-40EA-B1A9-46C810A3F84AInvestigating the effect of arachidonate supplementation on the phosphoinositide content of MCF10a breast epithelial cells.Advances in biological regulationb69f958d0a381f3030849518250d3521Anderson KE2016-01-012212-492656b0cdd9b2d104.684859687C40895B-8C27-40EF-B5C4-B5CAAFA102E8Frontline Science: TNF-a and GM-CSF1 priming augments the role of SOS1/2 in driving activation of Ras, PI3K-?, and neutrophil proinflammatory responses.Journal of leukocyte biology7f84660b423d6c09271cb9f398505849Suire S2019-01-010741-54005c7d43ac1cf6e4.11278104AA3EB8F0-EBE8-4937-BB12-07647D1F9BF7Quantitation of class IA PI3Ks in mice reveals p110-free-p85s and isoform-selective subunit associations and recruitment to receptorsProceedings of the National Academy of Sciences2c1b247a4f72aa031fc0966736f27c27Tsolakos N2018-01-010027-84245c470237728630.886656964385722E-6091-49D7-8A3F-8CA563EFAC5EInactivation of the Class II PI3K-C2ß Potentiates Insulin Signaling and Sensitivity.Cell reports83ed02408872fd806a388ba2a32fb91cAlliouachene S2015-01-0156b0cdd8ca10e9.80705522BB/I003916/12D9083F0-05FA-4726-9EB2-3FCC293CAAF925Biomolecules & biochemistry999F0B31-F127-410A-A520-963B336BECE725Cell biology29F3DF16-3094-4F79-BC69-8D05FB55182613Omic sciences & technologies945E0A55-10CB-4E91-BCCB-7CB22CFE223212Tools, technologies & methodsEF22E4A7-F12A-4859-8A95-E0179E3570EC12Biological membranes6D0F40FF-D03E-4429-A764-185BC521A84013Catalysis & enzymology2A0F6391-E88A-4396-9D63-25A68EEDA63513Communication & signallingCA10DA58-174F-4FE6-B61B-8EEBFB8192E212Receptors812BD191-6D4F-4F72-852D-0F63AD58ABD812Research approaches937A9F23-021A-4604-8979-A28E0E04F82513Transcriptomics018ACD8A-DE0F-4F6C-82FF-00EFDE30F246Characterising the performance of low loading electrodes for hydrogen technologiesActive2928626StudentshipThis project is associated with deep understanding of the operation and performance of electrodes for electrochemical devices used in electrolysers, flow batteries, and fuel cells. These devices will allow the efficient capture of renewable electricity and storage/interconversion as hydrogen (see Royal Society report &quot;Large-scale electricity storage&quot;). Deployment of electrochemical hydrogen systems is growing at a tremendous pace, but in order to achieve the well defined KPIs we need: a 10-fold reduction in catalyst requirements; significant improvements in performance; and increased longevity. The purpose of this experimental iCASE is the improved performance of these electrodes whilst reducing the catalyst requirements (and thus cost), coupled to improved understanding and ability to model the performance of these systems. Such improvements can only be achieved through a deeper understanding of performance of the electrochemical interface at which reactants, electrons and ions must be efficiently transported to the catalytic interface. These systems are crucial for the UK and world to reach their net-zero aspirations by 2050. The topic cuts across a number of themes in the UKRI including the Energy and decarbonisation theme (Solutions to reach net zero), the Manufacturing the future theme and the Physical Sciences theme. The project is extremely well aligned with the UK's 2022 NMS strategy for which 'the measurement infrastructure needed to support the hydrogen economy as it develops' is a government priority2028-09-29798CB33D-C79E-4578-83F2-72606407192CEPSRC2024-09-30INCOME_ACTUAL029286266CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified01E6F588-13F6-461E-AEB0-00B2FCEAAFD5MUSHFORM: Transforming Spent Mushroom Substrate into High-Performance, Chemical-Free Pulp Moulded PackagingClosed10181283Collaborative R&DImagine if the containers holding your supermarket mushrooms were made from the waste generated growing those same mushrooms. That circular vision is exactly what MUSHFORM aims to prove. **The Double Problem We're Solving** UK mushroom farms produce over 100,000 tonnes of delicious mushrooms annually---but create over 500,000 cubic metres of &quot;spent substrate&quot; waste, costing growers &pound;3-15M annually to manage. Meanwhile, food packaging manufacturers import wood pulp, blast it with harsh chemicals (caustic soda, chlorine bleach), consume massive energy (3,500-4,500 kWh per tonne), then add plastic coatings to create containers that never truly biodegrade. Two industries. Two problems. One circular UK solution. **Nature's Hidden Gift** Here's the breakthrough: mushrooms are nature's master decomposers. As they grow, their fungi release powerful enzymes that break down tough plant materials---essentially doing 70% of the pulping work that paper mills achieve with toxic chemicals. After harvest, the spent substrate has already been biologically &quot;pre-processed.&quot; Think of mushrooms as unpaid factory workers, preparing packaging material while producing food. **The Technology** Led by Yr Ardd Fadarch Eryri Cyf. t/a Madarch Cymru, working with Bangor University's pilot facility (managed by professional project specialists), we'll test whether three types of spent mushroom substrate can be transformed into sturdy food packaging using only mechanical processing---no chemicals, no bleaching, no plastic coatings. Just steam, pressure, and precision engineering. **The Products** Picture supermarket eggs in trays made from mushroom waste. Takeaway containers that started life supporting shiitake cultivation. Protective packaging that could literally return to mushroom farms as compost. Products---egg cartons, food trays, corner protectors---are home-compostable in 12 weeks, cost less than imports, eliminate chemicals, and convert growers' disposal costs into revenue, closing the perfect loop: waste from food production becomes food packaging. **Why This Matters---Supporting UK Communities** Mushroom growers transform &pound;3-15M annual disposal costs into revenue. Packaging manufacturers access over 500,000m&sup3; of pre-processed, domestic feedstock. By Year 5:35 rural jobs created across UK mushroom-producing regions, &pound;1.2M tax revenue generated, supporting economic development in agricultural communities. Consumers get packaging with genuine environmental credentials---not &quot;industrially compostable&quot; but actually biodegradable in your garden or back in mushroom production. This is the circular economy in its purest form: one food sector's waste becomes another's feedstock, processed domestically, used domestically, composted domestically, then returned to UK farms. No imports. No chemicals. No waste. Welcome to packaging that completes the cycle it began in from soil, through mushrooms, carrying food, then back to soil---or back to mushrooms.2026-03-3012E03F45-B517-4D83-A182-3D142D1A471AInnovate UK2026-02-01INCOME_ACTUAL25000101812836CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified02103DD9-A889-4067-B44E-006A617A8BDFEye in the SkyClosed10037439Collaborative R&DAbstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.2023-01-3112E03F45-B517-4D83-A182-3D142D1A471AInnovate UK2022-07-31INCOME_ACTUAL0100374396CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified0248EF3F-DD65-4561-BD94-020C64D6F13DVANTAGE - An intelligent payload that enables UAVs to autonomously land on maritime vessels, ultimately addressing Urban Air Mobility requirements.Closed10008315BEIS-Funded ProgrammesAbstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.2023-09-29B51DB087-2804-4E46-8896-F5FC40D5A4FDATI2022-03-31INCOME_ACTUAL210000100083156CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified02563003-C0B6-42B2-BBC9-01F8D289E65EDevelopment of molecular imprinting with liquid chromatographt-massClosed1677978StudentshipDevelopment of molecular imprinting with liquid chromatography-mass spectrometry HD-SRM for the sensitive and selective detection of proteins2019-09-29198E4A3D-B2DC-45D4-8351-7CCEC4061876BBSRC2015-09-30INCOME_ACTUAL0250United KingdomGBPUnited Kingdomen_GBJohn Beynon Travel and Conference Fund2016-09-01British Mass Spectrometry SocietyCAAED9F7-7B7D-4C93-ADF6-3C38F3E219135c8292ea5aa071.04432429Charity/Non Profit2016-08-31500CanadaUSDEcuadores_ECHuman Proteome Organisation (HUPO) World Congress 2018 Travel Stipend2018-09-01Human Proteome OrganizationD114D887-0FDB-43B1-9B65-98AC335782085c829082a9f756.50057518Charity/Non Profit2018-08-31300United KingdomGBPUnited Kingdomen_GBJohn Beynon Travel and Conference Fund2018-09-01British Mass Spectrometry Society4D0A58E0-F162-4E86-A3D9-984E434914E15c8291ab41ea67.63563298Charity/Non Profit2018-08-31250United KingdomGBPUnited Kingdomen_GBJohn Beynon Travel and Conference Fund2017-09-01British Mass Spectrometry SocietyDB708D8C-4796-4822-AE4B-472EFACF66525c829276b4fe16.71008967Charity/Non Profit2017-08-31E0C227D0-0DB6-4F13-A229-E732ED4CD2D7The measurement of KRAS G12 mutants using multiplexed selected reaction monitoring and ion mobility mass spectrometry.Rapid communications in mass spectrometry : RCMf0b853c384b19d76e8c09068e63f8af3Norman RL2020-01-010951-41985e45186db0b557.4718198016779786CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified027CDB72-517A-4A0D-AE08-00FDFAE8F76CEstablishing a test methodology for PFAS-free barrier materials for the hydrogen economyClosed10158010Grant for R&DThis project addresses the technical challenges associated with accurately measuring hydrogen permeation in rubber materials used in key industries such as energy and automotive. As the UK government advances ambitious hydrogen production goals and global hydrogen demand continues to rise, the establishment of reliable, standardised testing methodologies for hydrogen permeation is critical to ensuring safety, performance, and long-term durability in hydrogen applications. Currently, rubber components in hydrogen systems are evaluated using testing standards from the oil &amp; gas sector, predominantly suited for high-pressure conditions. However, there remains a substantial gap in measurement methodologies where variations in temperature and pressure significantly affect the behaviour of hydrogen permeation and diffusion. The primary focus of this project is therefore the development of robust and standardised test methods capable of quantifying hydrogen permeation under diverse temperature and pressure gradients. These methods will specifically target existing PFAS-free rubber materials, such as EPDM, HNBR, VMQ, and fluoropolymers developed using non-fluoro surfactant technologies and reinforced with graphene and other 2D nanomaterials. This methodology development will leverage the extensive expertise and experience of The University of Manchester. Additionally, the collaborative framework provided by the A4I program will facilitate industry-wide adoption and impact, aligning closely with the UK's hydrogen strategy and broader decarbonisation objectives. Ultimately, the project aims to deliver a reliable, standardised permeation testing protocol, significantly enhancing material selection processes and contributing to the advancement of sustainable, high-performance rubber solutions in the transition to a low-carbon economy.2026-01-3112E03F45-B517-4D83-A182-3D142D1A471AInnovate UK2025-06-30INCOME_ACTUAL10084101580106CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified027FCA23-6711-407E-A392-020B8329DDABThe role of commensal organisms as pro-infectious agents in Staphylococcus aureus infection dynamics.ClosedMR/R001111/1Research GrantStaphylococcus aureus is an important human pathogen that causes significant death and disease around the world. The problem is exacerbated by the spread of antibiotic resistant strains such as Methicillin Resistant S. aureus (MRSA). MRSA is generally a hospital-associated infection but recently community acquired MRSA has increased in the apparent absence of antibiotic selection. Thus there is a constant need to develop new control regimes for S. aureus, as this organism has begun to show resistance even to new antibiotics such as linezolid and no vaccine is available. To win this battle we must not only produce new treatments and preventative measures but also to understand the complexities of how S. aureus causes disease and thus how interventions can be best utilised, to reduce the disease burden and to minimise the development and spread of resistance to antibiotics. How do humans get infected with S. aureus? We have made the astonishing discovery that relatively harmless skin organisms and even their component cell walls are able to cause significant exacerbation of S. aureus infection, allowing disease to occur with a hugely reduced infectious dose. The most common route of human infection is via a wound and of course this will occur with whatever material gets in, including S. aureus. We have named the material that can augment S. aureus infection as &quot;pro-infectious agents&quot;. We have opened a window on natural infection and in doing so provide novel avenues for trying to understand disease and how we may prevent it. The current application takes an interdisciplinary approach to understand how infection is initiated, the nature of material and organisms that can act as pro-infectious agents, how infection progresses and how such knowledge may be utilized to prevent and/or cure disease. Our background work and that proposed necessitates an integrated team led by a microbiologist and a clinician with research expertise in innate immunity. This combined expertise, coupled with important partners around the world, provides a proven network to underpin our ambitious proposal. Our work is underpinned by the use of animal models of infection, as this complex process cannot be recapitulated in vitro without understanding of what happens in vivo. We have uniquely developed the vertebrate zebrafish embryo as a model of S. aureus systemic disease. This provides a high-throughput, genetically tractable system where host:pathogen interaction can be observed in a living host. The importance of this model is that it has not only provided important insights into pathogenesis but has also informed our use of a mammalian system thus replacing many mouse experiments directly, reducing the numbers of mammals used and refining our approach. We will use a combination of animal models, together with in vitro analysis to determine the breadth of material that can augment S. aureus infection and the cellular and molecular mechanisms underlying this effect. Infection will then be mapped from initiation to endpoint in order to identify bottlenecks as sites for the development on novel intervention strategies. We will use a variety of approaches including state-of-the-art intravital microscopy in all models to determine the pathway of infection. The application provides an integrated package that will further our understanding of disease mechanisms and how this information may be used to inform clinical practice.S. aureus is able to cause a wide range of diseases, with no vaccine available and antibiotic resistance common. It is therefore crucial to understand how S. aureus infection is initiated and progresses in order to identify novel clinical interventions. We have made the exciting discovery that skin commensal organisms, and even their isolated cell walls, can augment S. aureus infection. We have called the augmenting material &quot;pro-infectious agents&quot; and have shown its addition to result in a massive decrease in the inoculum of S. aureus required to cause serious disease. These findings are extremely pertinent to human infection, as this will always occur from within a polymicrobial milieu. It is important now to capitalize on our initial results to understand the breadth and basis of the augmentation phenomenon and how this might be exploited in the development of new approaches to tackle S. aureus. The project will take an interdisciplinary approach, with global partners, using a combination of in vivo and in vitro analyses. We will investigate the molecular basis of pro-infectious agents in terms of those organisms and components able to augment S. aureus disease, coupled with an elucidation of the host response to pro-infectious agents from the molecular, through cellular to the whole host level. This will be set within a determination of the progression of S. aureus infection to understand how disease is established as a complex interaction between host and pathogen and how this dynamic is altered by the presence of pro-infectious agents. Finally, we will examine how our discovery of pro-infectious agents can be utilized in the design of a vaccine and other immunological interventions. Such ambitious goals, from fundamental understanding to translation, can only be achieved via an integrated team of investigators and partners, providing molecular understanding of host:pathogen interaction with important ramifications for human disease.The proposed project will develop an integrated, interdisciplinary platform to study S. aureus disease and the effect of prophylactic and treatment regimes. There will be a variety of impacts over a range of timescales and arenas. - Academia (expected timescale year 1 onwards): will benefit from the information gained during the project, communicated both orally and via publication. Also given the unique use of the zebrafish embryo model of S. aureus pathogenesis, Sheffield will become a hub for collaboration and training. Transgenic zebrafish lines generated in this project will have diverse utility for other applications. The innovative multidisciplinary approaches we are taking will be a model for others working on related problems. - Industry (expected timescale year 2 onwards): will benefit as potential users of the data concerning the use of antibiotics and the establishment of pathogen population dynamics during infection to test existing or develop new control regimes, such as vaccination. Direct links to Biotech companies such as Absynth and pharmaceutical companies such as GSK are in place to facilitate direct translation of key findings. - National Health Service (expected timescale year 2 onwards): The cost to the NHS of healthcare associated infections (of which MRSA is the most significant) has been estimated by the HPA to be &pound;1billion a year in England alone. This is predominantly in terms of delayed discharge, with associated knock-on effects of full hospitals, cancelled operations and lack of beds for non-emergency admissions. If we were able to identify new ways to treat or prevent MRSA, this would have a major impact on the NHS. - Government bodies (expected timescale year 2 onwards): will benefit from the information on the role of microflora in disease augmentation as it will inform decisions as to decontamination of wound sites. - Local communities (expected timescale year 2 onwards): via outreach activities will benefit from greater knowledge of this scientific area and engagement with scientific advances made locally. - Society more broadly (expected timescale year 2 onwards): will benefit if the findings of this project translate to a reduction in the spread of antibiotic resistant bacteria, or new strategies for the treatment of infectious disease. - UK PLC (expected timescale year 2 onwards): will benefit through the development of commercial activities, and added value to both biotechnology and pharmaceutical companies. In addition, the economic burden of MRSA infection in the UK can be counted in the billions of pounds, from missed work and additional costs following hospital discharge. Small reductions in spread of antibiotic resistance could have large impacts on the productivity of the UK workforce. - Undergraduate/postgraduate/post docs (expected timescale year 1 onwards): will benefit through development of skills in cell biology, microscopy, in vivo studies etc. cascaded down through teaching interactions within the lab. - Media (expected timescale year 1 onwards): will benefit through the applicants' participation in radio and newspapers interviews.2021-06-29C008C651-F5B0-4859-A334-5F574AB6B57CMRC2018-01-01INCOME_ACTUAL703187University of CalgaryCanadaThe Calgary Stroke ProgramCalgary Partnership6296F3BA-9D2F-46E5-A775-889413E16840Boldock, E., Surewaard, B.G.J., Shamarina, D., Na, M., Fei, Y., Ali, A., Williams, A., Pollitt, E.J.G., Szkuta, P., Morris, P., Prajsnar, T.K., McCoy, K.D., Jin, T., Dockrell, D.H., van Strijp, J.A.G., Kubes, P., Renshaw, S.A. &amp; Foster, S.J. (2018) Human skin commensals augment Staphylococcus aureus pathogenesis. Nature Microbiology doi: 10.1038/s41564-018-0198-3.5c618136179588.97817984-1Testing of novel approaches to understand bacterial pathogenesis. In particular, the use of intravital microscopyWe developed the background data and hypothesesAcademic/University2016-01-01Cheltenham Science Festival 2018Participation in an activity, workshop or similarNationalB4466806-2E1F-4C00-909F-E3F25840D33AHands on exhibit and stand in the area of microbiology, microscopy and antimicrobial resistance5c61827fc48641.99105787falseSchools2018Staphylococcus aureus is a human commensal organism and opportunist pathogen, causing potentially fatal disease. The presence of non-pathogenic microflora or their components, at the point of infection, dramatically increases S. aureus pathogenicity, a process termed augmentation. Augmentation is associated with macrophage interaction but by a hitherto unknown mechanism. Here, we demonstrate a breadth of cross-kingdom microorganisms can augment S. aureus disease and that pathogenesis of Enterococcus faecalis can also be augmented. Co-administration of augmenting material also forms an efficacious vaccine model for S. aureus. In vitro, augmenting material protects S. aureus directly from reactive oxygen species (ROS), which correlates with in vivo studies where augmentation restores full virulence to the ROS-susceptible, attenuated mutant katA ahpC. At the cellular level, augmentation increases bacterial survival within macrophages via amelioration of ROS, leading to proliferation and escape. We have defined the molecular basis for augmentation that represents an important aspect of the initiation of infection. Animal work in the UK was performed in accordance with the Animal (Scientific Procedures) Act 1986. At the University of Sheffield, work was completed under project licences P3BFD6DB9 and PPL 40/3699 for murine work, or P1A4A7A5E for zebrafish work, with ethical approval from the University of Sheffield Local Ethical Review Panel. At Imperial College London, work was conducted under licence P4C824899 with approval from the Imperial ethical review board. At INRAE, animal work was approved by the local ethics committee (COMETHEA or &quot;Comit&eacute; d'Ethique en Exp&eacute;rimentation Animale&quot;, Centre de Recherche Ile de France - Jouy en Josas - Antony) under the registration numbers 15_08, and by the French Ministry of Higher Education and Research APAFIS #480-2015041518048149v1, where all animal experiments were performed in accordance with European directive 2010/63/EU. Animal experiments in Calgary were approved by the University of Calgary Animal Care Committee and were in compliance with the Canadian Council for Animal Care Guidelines (protocol nr. AC16-0148). MDMs were derived, with informed consent, from the blood of healthy volunteers, in accordance with guidelines from the South Sheffield Research Ethics Committee (07/Q2305/7).6D69CAA0-15C4-4B57-A380-404E066ECA8E65dfa4072f7e27.63532206trueCommensal bacteria augment Staphylococcus aureus infection by inactivation of phagocyte-derived reactive oxygen speciesDatabase/Collection of datahttps://figshare.shef.ac.uk/articles/dataset/Commensal_bacteria_augment_Staphylococcus_aureus_infection_by_inactivation_of_phagocyte-derived_reactive_oxygen_species/151347092021Macroautophagy/autophagy functions to degrade cellular components and intracellular pathogens. Autophagy receptors, including SQSTM1/p62, target intracellular pathogens. Staphylococcus aureus is a significant pathogen of humans, especially in immunocompromise. S. aureus may use neutrophils as a proliferative niche, but their intracellular fate following phagocytosis has not been analyzed in vivo. In vitro, SQSTM1 can colocalize with intracellular Staphylococcus aureus, but whether SQSTM1 is beneficial or detrimental in host defense against S. aureus in vivo is unknown. Here we determine the fate and location of S. aureus within neutrophils throughout zebrafish infection. We show Lc3 and Sqstm1 recruitment to phagocytosed S. aureus is altered depending on the bacterial location within the neutrophil and that Lc3 marking of bacterial phagosomes within neutrophils may precede bacterial degradation. Finally, we show Sqstm1 is important for controlling cytosolic bacteria, demonstrating for the first time a key role of Sqstm1 in autophagic control of S. aureus in neutrophils. AR: autophagy receptor; CFU: colony-forming unit; CHT: caudal hematopoietic tissue; GFP: green fluorescent protein; hpf: hours post-fertilization; hpi: hours post-infection; LWT: london wild-type: lyz: lysozyme; Map1lc3/Lc3: microtubule-associated protein 1 light chain 3; RFP: red fluorescent protein; Sqstm1/p62: sequestosome 1; Tg: transgenic; TSA: tyramide signal amplification; UBD: ubiquitin binding domain.28103330-A604-4692-89FA-6D117DE38C8D65df9f8c939100.44019563trueNeutrophils use selective autophagy receptor Sqstm1/p62 to target <i>Staphylococcus aureus</i> for degradation <i>in vivo</i> in zebrafishDatabase/Collection of datahttps://tandf.figshare.com/articles/dataset/Neutrophils_use_selective_autophagy_receptor_Sqstm1_p62_to_target_i_Staphylococcus_aureus_i_for_degradation_i_in_vivo_i_in_zebrafish/128513602020Macroautophagy/autophagy functions to degrade cellular components and intracellular pathogens. Autophagy receptors, including SQSTM1/p62, target intracellular pathogens. Staphylococcus aureus is a significant pathogen of humans, especially in immunocompromise. S. aureus may use neutrophils as a proliferative niche, but their intracellular fate following phagocytosis has not been analyzed in vivo. In vitro, SQSTM1 can colocalize with intracellular Staphylococcus aureus, but whether SQSTM1 is beneficial or detrimental in host defense against S. aureus in vivo is unknown. Here we determine the fate and location of S. aureus within neutrophils throughout zebrafish infection. We show Lc3 and Sqstm1 recruitment to phagocytosed S. aureus is altered depending on the bacterial location within the neutrophil and that Lc3 marking of bacterial phagosomes within neutrophils may precede bacterial degradation. Finally, we show Sqstm1 is important for controlling cytosolic bacteria, demonstrating for the first time a key role of Sqstm1 in autophagic control of S. aureus in neutrophils. AR: autophagy receptor; CFU: colony-forming unit; CHT: caudal hematopoietic tissue; GFP: green fluorescent protein; hpf: hours post-fertilization; hpi: hours post-infection; LWT: london wild-type: lyz: lysozyme; Map1lc3/Lc3: microtubule-associated protein 1 light chain 3; RFP: red fluorescent protein; Sqstm1/p62: sequestosome 1; Tg: transgenic; TSA: tyramide signal amplification; UBD: ubiquitin binding domain.DBCADAFF-90FC-4BBD-892C-07C9555089AE65df9f8d414d01.60695457trueNeutrophils use selective autophagy receptor Sqstm1/p62 to target <i>Staphylococcus aureus</i> for degradation <i>in vivo</i> in zebrafishDatabase/Collection of datahttps://tandf.figshare.com/articles/dataset/Neutrophils_use_selective_autophagy_receptor_Sqstm1_p62_to_target_i_Staphylococcus_aureus_i_for_degradation_i_in_vivo_i_in_zebrafish/12851360/12020This is the raw data supporting the findings (both main text and supplementary) for our manuscript &quot;Clonal population expansion of Staphylococcus aureus during infection can occur due to escape from a finite number of intraphagocyte niches&quot;. Each excel file contains the raw data for each figure.93D5D4B4-2C1D-478F-A0DA-F77EDCDB77D565f4c13803ad76.53378984trueClonal population expansion of Staphylococcus aureus during infection can occur due to escape from a finite number of intraphagocyte nichesDatabase/Collection of datahttps://figshare.shef.ac.uk/articles/dataset/Clonal_population_expansion_of_Staphylococcus_aureus_during_infection_can_occur_due_to_escape_from_a_finite_number_of_intraphagocyte_niches/18551081/12023Staphylococcus aureus is a human commensal organism and opportunist pathogen, causing potentially fatal disease. The presence of non-pathogenic microflora or their components, at the point of infection, dramatically increases S. aureus pathogenicity, a process termed augmentation. Augmentation is associated with macrophage interaction but by a hitherto unknown mechanism. Here, we demonstrate a breadth of cross-kingdom microorganisms can augment S. aureus disease and that pathogenesis of Enterococcus faecalis can also be augmented. Co-administration of augmenting material also forms an efficacious vaccine model for S. aureus. In vitro, augmenting material protects S. aureus directly from reactive oxygen species (ROS), which correlates with in vivo studies where augmentation restores full virulence to the ROS-susceptible, attenuated mutant katA ahpC. At the cellular level, augmentation increases bacterial survival within macrophages via amelioration of ROS, leading to proliferation and escape. We have defined the molecular basis for augmentation that represents an important aspect of the initiation of infection. Animal work in the UK was performed in accordance with the Animal (Scientific Procedures) Act 1986. At the University of Sheffield, work was completed under project licences P3BFD6DB9 and PPL 40/3699 for murine work, or P1A4A7A5E for zebrafish work, with ethical approval from the University of Sheffield Local Ethical Review Panel. At Imperial College London, work was conducted under licence P4C824899 with approval from the Imperial ethical review board. At INRAE, animal work was approved by the local ethics committee (COMETHEA or &quot;Comit&eacute; d'Ethique en Exp&eacute;rimentation Animale&quot;, Centre de Recherche Ile de France - Jouy en Josas - Antony) under the registration numbers 15_08, and by the French Ministry of Higher Education and Research APAFIS #480-2015041518048149v1, where all animal experiments were performed in accordance with European directive 2010/63/EU. Animal experiments in Calgary were approved by the University of Calgary Animal Care Committee and were in compliance with the Canadian Council for Animal Care Guidelines (protocol nr. AC16-0148). MDMs were derived, with informed consent, from the blood of healthy volunteers, in accordance with guidelines from the South Sheffield Research Ethics Committee (07/Q2305/7).4354DDFF-70F6-4211-9F1C-30263BCEAC0D65dfa43a09d050.62768875trueCommensal bacteria augment Staphylococcus aureus infection by inactivation of phagocyte-derived reactive oxygen speciesDatabase/Collection of datahttps://figshare.shef.ac.uk/articles/dataset/Commensal_bacteria_augment_Staphylococcus_aureus_infection_by_inactivation_of_phagocyte-derived_reactive_oxygen_species/15134709/12021This is the raw data supporting the findings (both main text and supplementary) for our manuscript &quot;Staphylococcus aureus cell wall structure and dynamics during host-pathogen interaction&quot;. Each excel file contains the raw data for each figure. Murine work was carried out according to UK law in the Animals (Scientific Procedures) Act 1986, under Project License P3BFD6DB9 (Staphylococcus aureus and other pathogens, pathogenesis to therapy, University of Sheffield Review Board).25BDC124-0DAF-48E9-81D9-A62F2330E48861ebee16a0c0c4.40755595trueStaphylococcus aureus cell wall structure and dynamics during host-pathogen interactionDatabase/Collection of datahttps://figshare.shef.ac.uk/articles/dataset/Staphylococcus_aureus_cell_wall_structure_and_dynamics_during_host-pathogen_interaction/137464692021This is the raw data supporting the findings (both main text and supplementary) for our manuscript &quot;Clonal population expansion of Staphylococcus aureus during infection can occur due to escape from a finite number of intraphagocyte niches&quot;. Each excel file contains the raw data for each figure.CD3DED59-0EC1-4407-95B2-D84A27B3440063ed5140093da4.56260141trueClonal population expansion of Staphylococcus aureus during infection can occur due to escape from a finite number of intraphagocyte nichesDatabase/Collection of datahttps://figshare.shef.ac.uk/articles/dataset/Clonal_population_expansion_of_Staphylococcus_aureus_during_infection_can_occur_due_to_escape_from_a_finite_number_of_intraphagocyte_niches/18551081202328529CE0-45E3-46D1-AC71-53BD6D358F45Clonal population expansion of Staphylococcus aureus occurs due to escape from a finite number of intraphagocyte niches.Scientific reportse5e5a2af2acfd4bf9bff68ccf2d49f88Pidwill GR2023-01-012045-232263ec2738764249.30577067E4CB2EBF-6C44-49D7-ABAE-618EA8FA6EA6Commensal bacteria augment Staphylococcus aureus infection by inactivation of phagocyte-derived reactive oxygen species.PLoS pathogense8b8b70d41204ef67f5afc08219a57f4Gibson JF2021-01-011553-736661f97c61515d71.43034643DB2A2B9A-45E3-4570-8AE1-43DAC9E749832601. Identification of Staphylococcus aureus Genetic Factors Associatiated with the Subversion of Macrophage Phagosomal AcidificationOpen Forum Infectious Diseases9819be6ab36d0e3a67623b97cea4fd62Morris P2019-01-0167ab6c79159f02.250346754E7110D4-955F-45EC-A6F3-B04AAF8799D0Human skin commensals augment Staphylococcus aureus pathogenesis.Nature microbiologya489d56a05ef53914f775cf3ad41cfc6Boldock E2018-01-012058-52765b9bc2dfed7633.7854140652048584-D621-4FDC-BEE3-2EF0D198EBF7The Role of Macrophages in Staphylococcus aureus Infection.Frontiers in immunologye5e5a2af2acfd4bf9bff68ccf2d49f88Pidwill GR2020-01-011664-32246014f227b3f057.9099284419440650-3C1E-418D-95EE-A6E3ABDBF9CCResident risks.Nature microbiology5e2d45794933216b91d672e9e397b613Spoto M2018-01-012058-5276675243265a45a3.4766911881C5E4CC-F1BC-4D97-8007-B308477804A0Demonstration of the role of cell wall homeostasis in Staphylococcus aureus growth and the action of bactericidal antibiotics.Proceedings of the National Academy of Sciences of the United States of America9289d41c2d59bb76d0611b6cfef2d9d0Salamaga B2021-01-010027-842461fc6f31da42b2.99125838CA618115-BDE5-44F2-8B82-477925519ADANeutrophils use selective autophagy receptor p62/SQSTM1 to target Staphylococcus aureus for degradation in vivo in zebrafish6d0058b9873c2884fe0fb044f03c6b70Gibson J2019-01-0165bb8296101831.56601605B66496DD-78A2-4D59-8E97-E3370C9619BEStaphylococcus aureus cell wall structure and dynamics during host-pathogen interaction.PLoS pathogens71f47816609b3b09ea897307e94ac64fSutton JAF2021-01-011553-736661f7056098a6f1.7218466560D8B67F-F524-4DBB-937A-5897836DAE6CNeutrophils use selective autophagy receptor Sqstm1/p62 to target Staphylococcus aureus for degradation in vivo in zebrafish.Autophagye8b8b70d41204ef67f5afc08219a57f4Gibson JF2021-01-011554-86275f8a0df426a5f2.03078697F68D3DE0-5DDC-4667-BE48-F5F8AACB5208Tetracycline and Oxacillin Act Synergistically on Biofilms and Display Increased Efficacy In Vivo Against Staphylococcus aureus.Current microbiology7a94b2ff9076a8fa3e596e8da25091dbTooke AK2024-01-010343-865167400206739663.40553289MR/R001111/16CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified02D113B2-C9DC-486E-953C-016B03A07CB9Evaluation and Demonstration of Gravity GradiometersClosedEP/R020353/1Research GrantQinetiQ Ltd, Imperial College and the University of Oxford will jointly investigate the use of novel gravity gradiometers to detect buried objects such as pipes, tunnels and sinkholes. We will model the gravitational field of a range of buried targets, and investigate methods to mitigate noise and clutter. We will determine what type of objects are detectable, at what range, and develop some outline Concepts of Operation. We will investigate the applicability of a range of sensors, both high performance &quot;cold atom fountains&quot; and lower-cost MEMS-based devices, configured as gravity gradiometers, and compare them to the performance of commercially available sensors. We will build a single-axis gravity gradiometer based on two existing gravimeters, and use this to validate our models with through short field trials to demonstrate the detection of a buried object.Economic benefits: Four million holes are dug in British roads every year, 300,000 of them in London alone. 36% of London traffic delays caused by roadworks, with a total cost to London business is not far short of &pound;1 billion. This is likely to be replicated in cities across the country. According to some estimates, half the holes dug by the water industry are in the wrong place. The ability to sense a buried pipe before starting to dig would greatly reduce unnecessary disruption. A major benefit of this research will be to inform the National Quantum Programme of expected targets and detection ranges using gravity gradiometers based on the published performance of a range of gravity sensors, including ones being developed by the National Quantum Programme. This information is likely to help guide the parties involved in the development of their devices. Social impacts: The UK does not have a sovereign capability in full-tensor gravity gradiometry. The classical-technology Lockheed Martin FTG instrument is ITAR-controlled, and can only be used for a very strictly controlled set of applications. This work would pave the way towards a sovereign capability which could be used for both commercial and military applications without ITAR restrictions. Environmental impacts: Stand-off detection of buried objects will have a positive environmental impact, as it will allow remote sensing as opposed to physical investigation and inspection. Earth and planetary science: though deployment of gradiometers in Earth orbit is being pursued separately with Thales-Alenia UK, some of the technical challenges will require similar approaches. We would therefore anticipate cross benefits from this project to Earth and planetary gravity measurements using compact gradiometers. Such measurements aim to quantify on Earth the effects of climate change through ice-sheet loss and aquifer degradation. Regional impacts: Remote detection of dense smuggled material at borders/ports would potentially not only increase security but also reduce delays, supporting the freer movement of goods.2019-02-28798CB33D-C79E-4578-83F2-72606407192CEPSRC2017-11-01INCOME_ACTUAL40242Imperial College LondonUnited KingdomDepartment of ComputingDevelopment of Terrestrial Gradiometer4E21519D-4BEC-4016-8DBA-15DB6AA68855Proposals still in preparation58c52f6fe00229.64575348-1Development of MEMs device (Imperial) Development of Gradiometer System (Qintetiq)Development of gradiometer based upon Imperial MEMs device Development of support electronicsAcademic/University2017-01-01QinetiqUnited KingdomDevelopment of Terrestrial Gradiometer9FD73ECE-E68A-48B3-8D30-8CC8D3DE3673Proposals still in preparation58c52f6fe00229.64575348-2Development of MEMs device (Imperial) Development of Gradiometer System (Qintetiq)Development of gradiometer based upon Imperial MEMs device Development of support electronicsPrivate2017-01-0127537628United KingdomGBPUnited Kingdomen_GBUK National Quantum Technology Hub in Sensing and Timing2024-11-02Engineering and Physical Sciences Research Council (EPSRC)EP/T001046/1CD6D77A9-2D6B-4B82-A7E1-C64F90F5CDC565eefed3d4a838.70323518Public2019-12-016E383D82-A56C-4EA1-BBC4-2FFE28A4C11BStanding on Apollo's Shoulders: A Microseismometer for the MoonThe Planetary Science Journal0e5a2727438c34889f549446115c5ae3Nunn C2021-01-016409c4a647cec8.00525017EP/R020353/16CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified02F3633C-D09A-40F6-A13C-008DE4798432PATT Linked Grant for observational astrophysics at QUB: 2016 - 2018ClosedST/P001041/1Research GrantOur proposal seeks to renew the PATT Linked Grant at Queen's University Belfast. This award will cover our travel and subsistence costs to both STFC and non-STFC observing facilities. The major topics of observational astrophysics research to be covered by the PATT Linked Grant include: - investigations of supernovae and the end stages of stellar evolution; - high temporal, spatial and spectral resolution observations of the solar atmosphere and those of other cool stars; - studies of solar system bodies, including comets and asteroids; - astrochemistry, including that of interstellar and circumstellar clouds; - detection and characterisation of exoplanets.2018-09-29522546B4-4798-4E89-9B88-39938E261897STFC2016-09-30INCOME_ACTUAL47572ST/P001041/17CF2A56C-7A5D-4BF9-A57C-4B95903A836340Astronomy - observationF30322EE-FC8D-4040-BD0E-75A7AB75414E45Planetary scienceFEA1C96C-8692-4C1A-91A4-515CE66B437E15Solar & terrestrial physicsF414E2BD-8FD0-4FA8-8583-A35DA204B04730Extra Solar Planets27700A7F-8AB6-49A6-A1CB-1FCF7CFDD4BE10Galactic & Interstellar Astron244B5D88-3080-4492-BF67-FE7A88CB600715Solar BodiesEB8AD421-C36C-4F6B-939E-FA3750345E6D15Solar StudiesEDE79CED-440A-4CF9-94CD-D1CA1DD49BF830Stellar Astronomy031FB79F-1911-4B17-B82C-014F3A875912Does temperature drive enhanced carbon cycling in Holocene lake sediments?Active2922995StudentshipThis project will use annually laminated (varved) lake sediments to reconstruct Holocene sub-decadal summer temperature and carbon cycling. These records can evaluate: (a) different driver-response mechanisms at different timescales; (b) new temperature (including seasonal bias) and carbon cycling proxies; (c) whether past warmer periods enhanced carbon cycling in lakes.2028-03-308A03ED41-E67D-4F4A-B5DD-AAFB272B6471NERC2024-09-30INCOME_ACTUAL029229956CFA1E1F-F25C-4C23-8FE1-C47AE53E333EUnclassified