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Research Updates December & January 2022

Research Updates December & January 2022

Jan 05 2023 Posted: 12:49 GMT
Funding:
  • Andrew is co-PI on a €4.6m Disruptive Technologies Innovation Fund (DTIF) project, together with Feeltect, Armour Interactive and Odyssey Validation Consultants. This project will develop data-driven improvements to products and protocols associated with measuring and monitoring compression therapy and wound care. The University will receive approximately €1.25m to deliver the statistical and clinical aspects of the project.
  • Pilib is a collaborator on an SFI Frontiers for the Future Programme project led by Derek Morris (Biochemistry) and Dara Canon (Anatomy). This project was awarded €478k in direct costs over a period of 48 months.
     
  • Pilib became a funded investigator at the SFI ADAPT Centre, receiving €68k to support the recruitment of a PhD student to work on graph-based machine learning for biomedical data.
     
  • Bharat's application under the National Challenge Fund – Future Digital Challenge call has been approved for funding by SFI at a value of €198,859.60 direct costs over a period of 18 months with €45,550 in overheads to the university. This project will support two postdoctoral positions. Here is the advertisement, please circulate it as widely as possible.
 
 
News:
  • Niall's list of international collaborators of the school keeps growing, please send more info about your links to foreign institutions. According to SciVal, we're the school of maths with the most international collaborations in Ireland!
     

     
  • Jim was an external examiner for a PhD viva at Lancaster University, UK.
     
  • Andrew worked with local students from Coláiste Iognáid on their BT Young Scientist of the Year project to see if a deposit return scheme (DRS) for plastic bottles and aluminium cans could be monetised in a school setting (using chocolate instead of cash!).
  • Giuseppe is spending two weeks in Israel at Ben-Gurion University of the Negev, to collaborate with Reuven Segev on the connections between differential geometry and biological growth. He is also giving invited talks at the Department of Mechanical Engineering,  Ben-Gurion University, and at the Racah Institute of Physics, University of Jerusalem.
  • Last month, Giuseppe gave an invited talk at the Department of Mathematics, Mechanics and Management, Politecnico di Bari, Italy, on "The origin of residual stress in additive manufacturing".
  • Pilib was an external examiner in December for the viva of Dr. Alexandre Pelletier, a PhD candidate at the European Genomic Institute for Diabetes, Institut Pasteur de Lille, France.
     
  • Pilib participated in the SFI 'Spéirscéalta' (Stories of the Air) project which links researchers with writers to produce scientifically-informed short stories.
     
  • Three members of Pilib's group presented posters at the Irish Computational Biology and Genomics Symposium, which took place in the Aula Maxima here on campus on 1-2 December 2022. Karen Guerrero Vázquez and Kevin Ryan were also on the organising committee for this Symposium (photo).
     
     
     
  • Anna Großbach and several other CRT in Genomics Data Science PhD students from the School (sorry I don't have all the names, see photo for all the cohorts) also attended the Irish Computational Biology and Genomics Symposium. Lydia King (and others) presented a poster. Anna gave a talk about a scoping review and simulation studies on "Modelling Epigenetic Age over Time" in the 'reproducibility in bioinformatics' session.



  • Karen Guerrero Vázquez and Kevin Ryan from Pilib's group took part in the VitaDAO Hackathon (https://longhack.org/). Both were on winning teams, with Karen’s team AdStella coming in 2nd Place and Kevin’s team AGen-iNET coming in 3rd place. Their projects involved a machine learning model to predict the muscle state given future conditions and an end-to-end pipeline for RNA-seq and network analysis.
  • The SIAM Student Chapter at the University of Galway organised the 9th Annual Irish SIAM Student Chapter Conference on 9th December 2022. More than 40 people registered and there were over 35 attendees. The conference had 2 keynote speakers, 7 contributed talks, and 5 poster presentations. 
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  • Victoria (PhD student with Michael McG) won the 2022 Graham Hoare Prize last month. Her article now published in Mathematics Today and is available here. 
     
Papers:
 
McNicholas, B.A., Rezoagli, E., Simpkin, A.J., Khanna, S., Suen, J.Y., Yeung, P., Brodie, D., Li Bassi, G., Pham, T., Bellani, G. and Fraser, J.F., 2023. Epidemiology and outcomes of early-onset AKI in COVID-19-related ARDS in comparison with non-COVID-19-related ARDS: insights from two prospective global cohort studies. Critical Care, 27(1), pp.1-14.
 
Talkar, T., Low, D.M., Simpkin, A.J., Ghosh, S., O’Keeffe, D.T. and Quatieri, T.F., 2023. Dissociating COVID-19 from other respiratory infections based on acoustic, motor coordination, and phonemic patterns. Scientific Reports, 13(1), p.1567.
 
de Freitas, S.M., Hinde, J.P., Demétrio, C.G.B. and Fallah, Lida (2022) Overdispersion models for clustered toxicological data in a bioassay of entomopathogenic fungus. Brazilian Journal of Biometrics, 40, 490–509, doi:10.28951/bjb.v40i4.647
 
Morrissey E, Murphy A, Murphy P, Newell J,  et al. Supporting GPs and people with hypertension to maximise medication use to control blood pressure: Protocol for a pilot cluster RCT of the MIAMI intervention [version 1; peer review: awaiting peer review]. HRB Open Res 2023, 6:6.
 
Davey, M; McGuire, A; Casey, MC; Waldron, RM; Paganga, M; Holian, E; Newell, J; et al. Evaluating the Role of Circulating MicroRNAs in Predicting Long-Term Survival Outcomes in Breast Cancer: A Prospective, Multicenter Clinical Trial. Journal of the American College of Surgeons 236(2):p 317-327, February 2023.
 
McCabe, G. P., & Newell, J. (2022). The art of translational statistics.Stat,11(1), e519. https://doi.org/10.1002/sta4.5198of8MCCABEANDNEWELL
 
Kirwan, C., Hynes, L., Hart, N., Newell .J, Roshan, D. et al. The multimorbidity collaborative medication review and decision making (MyComrade) study: a pilot cluster randomised trial in two healthcare systems. Pilot Feasibility Stud 8, 225 (2022). https://doi.org/10.1186/s40814-022-01107-y
 
Moloney, S., Fitzgerald, D., Roshan, D. and Gethin, G., 2022. Impact of hidradenitis suppurativa-specific wound dressing system on patient quality of life and dressing-related pain: pilot study. Journal of Wound Care, 31(11), pp.898-906.
 
Krieger, N., Chen, J., Testa, C., Roux, A.V.D., Tilling, K.M., Watkins, S.H., Simpkin, A.J., Suderman, M.J., Smith, G.D., De Vivo, I. and Waterman, P., 2022. Use of incorrect and correct methods to account for age in studies on epigenetic accelerated aging: implications and recommendations for best practices. American Journal of Epidemiology.
 
Digby, B., Finn, S.P. & Ó Broin, P. nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs. BMC Bioinformatics 24, 27 (2023). https://doi.org/10.1186/s12859-022-05125-8
 
Q Zhang, AV Cherkasov, N Arora, G Hu, S Rudykh. Magnetic field-induced asymmetric mechanical metamaterials. Extreme Mechanics Letters 59, 101957 (2023) https://www.sciencedirect.com/science/article/pii/S2352431623000032
 
V. Chen, N. Arora, A. Goshkoderia,  C. Willey, Z. Turgut, P. Buskohl, S. Rudykh, A. Juhl, Mechanical instability tuning of a magnetorheological elastomer composite laminate. Composites B 251, 110472 (2023) link
 
S Harmansa, A Erlich, C Eloy, G Zurlo and Thomas Lecuit. Growth anisotropy of the extracellular matrix shapes a developing organ, Nature Communications (to appear).
 
 
Posters:
 
Characterisation of patient-derived cancer-associated fibroblast subpopulations and prediction of neoantigens within the breast tumour microenvironment.
K. Ryan, D. O’Connor, L. Barkley, P. Ó Broin
 
Strategies for the selection of miRNA candidates for the treatment of Sarcopenia using network-based analysis and differential expression scoring.
Karen Guerrero Vazquez, Pilib Ó Broin, Katarzyna Whysall
 
Single-cell characterisation of the hematopoietic bone marrow interactome in health and disease
Sarah Ennis, Alessandra Conforte, Eimear O'Reilly, Tatiana Cichocka, Sukhraj Pal Dhami, Philippe Krebs, Pamela Nicholson, Pilib Ó Broin, Eva Szegezdi
Sarah's poster also received an honourable mention.
 

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