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Research Biographies

  • Damien Mac Namara

    Principal Investigator

    damian.mcnamara@lit.ie

    Qualifications

    PhD

    Current Research

    ​To date, my research and subsequent publications have spanned across:

       Information Systems Design and Evaluation. My research is centred on the design, implementation and evaluation of a novel user interface (UI) for eVoting systems termed ‘Dual Vote’. This UI consists of a novel optical sensor grid and hybrid ink/electronic pen which allow a voter to vote electronically using a pen and paper. During my research work I was responsible for the requirements gathering, high-level architecture design, composition of an interface taxonomy, and evaluation (incorporating user experience evaluation). 

    User Experience Design.  For the evaluation phase of my research, I used the System’s Usability Scale (SUS) to evaluate the subjective satisfaction of our prototype system. I employed large scale usability tests at LIT during actual student-body elections to facilitate this evaluation, the results of which fed back into the UI design where appropriate.

    Interplay of People, Technology and Social Structures.  Electronic Voting is a social-science where usability is crucial to the success or failure of a project. My work was focused on the removal of usability barriers from eVoting systems since voting electronically is an art which cannot be practiced frequently by the people who are using it. My work was very ‘people focused’ and during the feasibility stage of the project I employed over one-thousand person-to-person surveys in order to  gauge which UI technologies were most preferred among the electorate.  I have also presented at international conferences which are themed on social science and citizen participation in e-governance.​

    Publications

    • Dual Vote: A Novel User Interface For E-voting Systems, Damien MacNamara, Francis Carmody, Ted Scully, Ken Oakley, Elizabeth Quane and J. Paul Gibson. Published in IHCI10 conference proceedings (IADIS International Conference Interfaces and Human Computer Interaction 2010),Freiburg, Germany, 28 - 30 July 2010. ISBN = 978-972-8939-18-2, pages 129-138. Citations: 2

    • DualVote: Addressing Usability and Verifiability Issues in Electronic Voting Systems, Damien MacNamara, Ted Scully, J. Paul Gibson, Francis Carmody, Ken Oakley and Elizabeth Quane. Published (Edition Donau-Universität Krems) in the proceedings of the 2011 Conference for E-Democracy and Open Government (CeDEM11), Danube University Krems, Austria, May 2011, pages 313-322, editors Peter Parycek and Manuel Kripp and Noella Edelmann, ISBN =978-3-90250520-1.

    • Just Like Paper and the 3-colour protocol: a voting interface requirements engineering case study, J. Paul Gibson, Damien MacNamara, Ken Oakley. Presentation at RE-Vote 2011. Published by the IEEE, in the Proceedings of 2011 International Workshop on Requirements Engineering for Electronic (RE-Vote 2011), pages = 66--75, isbn = 978-1-4577-0951-7.

    • A Preliminary Study On A DualVote and Prêt à Voter Hybrid System, Damien MacNamara, J. Paul Gibson and Ken Oakley. Published in proceedings of CeDEM 2012 (International Conference for E-Democracy and Open Government 2012 ), Danube University Krems, Austria, 3-4 May 2012, pages 77-89, editors Peter Parycek and Noella Edelmann, ISBN =978-3-90250520-1. 

    •  UK Patent Number wo2011131355: A system for identifying the location of a paper form. Status: Granted.

    Supervisor

    Dr Ken Oakley and Prof J Paul Gibson

  • John Cosgrove

    Principal Investigator

    john.cosgrove@lit.ie

    Qualifications

    Chartered Engineer DipEE BScEng MTech(AMT) MIEI MA

    Professional Affiliation

    Engineers Ireland

  • Martin Hayes

    Postgraduate Researcher

    martin.hayes@lit.ie

    Qualifications

    B. A. Sc. Bionalysis & Biotechnology

    Current Research

    Post graduate research: Using controlled environmental growth chambers and hydroponics to conduct novel research into beneficial plant microbe interactions aimed at increasing the yield of ecologically important crops. The predicted rise in population, poor soils, the cost of fertiliser’s, climate change and competition for agricultural land show that agriculturally important crops need to be produced with lower cost, increased yield and enhanced resistance to abiotic and biotic stresses. This research is aimed at improving the knowledge of beneficial plant microbe interactions, producing greater yields of leguminous crops. Legumes are an important bio fertiliser crop due to their symbiotic relationship with Rhizobia whereby they release excess Nitrogen from their roots into their surrounding soil and are also responsible for 20% of the protein in our diets consumed directly or indirectly. However the growth of forage legumes is highly restricted due poor climate/ soil (drought). The endophytic fungus Piriformospora indica conveys a wide variety of beneficial effects to its host i.e. increased biomass and stress tolerance. The mutualistic relationship between P.indica and leguminous plants could allow for the transfer of legumes into poor climates/soils where it will act as a bio fertiliser/ forage crop, reducing the need for expensive Nitrogen fertilisers.

    Supervisor

    Dr. Patrick Murray, Dr. Gary Stutte

  • Patrick Murray

    Principal Investigator

    patrick.murray@lit.ie

    Qualifications

    PhD.

    Current Research

    Develop natural products for novel bioactive substances of value to the Healthcare, Forensic, Pharmaceutical, Food, Cosmetics, Agricultural, Environmental, Diagnostic and Bio-Energy Industries. Natural products embraces a diversity of under-explored and under-exploited materials derived from waste streams, marine, plant, animal, mammalian and microbial sources.

    Environmentally sustainable organic processes for the enclosed production of omega-3 polyunsaturated fatty acids (PUFA’s) and carotenoids (e.g. astaxanthin) from microalgae

    Project title: BAMMBO-Biologically active molecules of marine based origin. Funding body: European Union FP7 Cooperation-Biotechnology-KBBE

    Novel high value bioactivities from extremophilic fungi

    Publications

    A Review of Thermophilic Filamentous Fungal Enzyme Systems: Applications in the ‘Agri-Food’ Industries. (2011) The Natural Products Journal. Volume 1, Number 1, pp 2-19 Deborah M. Waters, Patrick G. Murray, Maria G. Tuohy and John Donlon.

    Characterisation of a Talaromyces emersonii Thermostable Enzyme Cocktail with Applications in Wheat Dough Rheology. Enzyme and Microbial Technology doi:10.1016/j.enzmictec.2011.04.006 (2011) Deborah M. Waters Liam A.M. Ryan, Patrick G. Murray, Elke K. Arendt and Maria G. Tuohy.

    Cloning and Expression of a Thermostable α-Galactosidase from the Thermophilic Fungus Talaromyces emersonii in the Methylotrophic Yeast Pichia pastoris. J. Microbiol. Biotechnol. (2010), 20(12), 1653–1663. Similä, Janika, Anita Gernig, Patrick Murray, Sara Fernandes, and Maria G. Tuohy

    Characterization of a multimeric, eukaryotic prolyl aminopeptidase: an inducible and highly specific intracellular peptidase from the non-pathogenic fungus Talaromyces emersonii. Microbiology. 2010 Nov;155(Pt 11):3673-82. Epub 2010 Jun 25.Mahon CS, O'Donoghue AJ, Goetz DH, Murray PG, Craik CS, Tuohy MG.

    Metabolic engineering for improved microbial pentose fermentation. Bioengineered Bugs 1:6, 1-6; November/December 2010. Sara Fernandes and Patrick G. Murray.

    Induction of enzyme cocktails by low cost carbon sources for production of monosaccharide-rich syrups from plant materials. BioResources 2010 Vol 5 (2) 634-649 Caroline T. Gilleran, Alan T. Hernon, Patrick G. Murray, Maria G. Tuohy

    Cloning, heterologous expression, and characterization of the xylitol and L-arabitol dehydrogenase genes, Texdh and Telad, from the thermophilic fungus Talaromyces emersonii, Biochemical Genetics (2010)Vol 48, (5) Page 480. Sara Fernandes, Maria G. Tuohy, and Patrick G. Murray

    Expression of Talaromyces emersonii cellobiohydrolase Cel7A in Saccharomyces cerevisiae and rational mutagenesis to improve its thermostability and activity. Protein Engineering, Design & Selection 23(2):2010 69-79. Sanni P. Voutilainen1, Patrick G. Murray, Maria G. Tuohy and Anu Koivula

    Xylose reductase from the thermophilic fungus Talaromyces emersonii: cloning and heterologous expression of the native gene (Texr) and a double mutant (TexrK271R + N273D) with altered coenzyme specificity. Journal of Biosciences 34(6) 2009 881-890.Sara Fernandes, Maria G Tuohy and Patrick G Murray

    Inhibition of a Secreted Glutamic Peptidase Prevents Growth of the Fungus Talaromyces emersonii. Journal of Biological Chemistry 283 2008 29186-29195. Anthony J. O’Donoghue, Cathal S. Mahon, David H. Goetz, James M. O’Malley, Denise M. Gallagher, Min Zhou, Patrick G. Murray, Charles S. Craik and Maria G. Tuohy

    Purification and characterisation of a N-acetylglucosamiinidase produced by Talaromyces during growth on algal fucoidan. Journal Applied Phycology 20: 2008 557-565. Elaine O’ Connell, Patrick Murray, Charles Piggott, Franck Hennequart and Maria Tuohy

    Enzyme Systems from the Thermophilic Fungus Talaromyces emersonii for Sugar Beet Bioconversion. Bioresources 3 (3), 2008 898-909. Patrick G. Murray, Sara Fernandes and Maria G. Tuohy.

    Molecular cloning and expression analysis of two distinct β-glucosidase genes, bg1 and aven1, with very different biological roles from the thermophilic, saprophytic fungus Talaromyces emersonii. Mycological Research, Volume 111, Issue 7, July 2007, Pages 840-849. Catherine M. Collins, Patrick G. Murray, Stuart Denman, John P. Morrissey, Lucy Byrnes, Tuula T. Teeri and Maria G. Tuohy

    Cloning, characterisation and expression analysis of α-glucuronidase from the thermophilic fungus Talaromyces emersonii. Enzyme and Microbial Technology, Volume 41, Issues 6-7, 1 November 2007, Pages 677-682.M.N. Heneghan, L. McLoughlin, P.G. Murray and M.G. Tuohy.

    ‘Talaromyces emersonii enzyme systems’ Patent Filing date February 10th 2006 Application No. S2006/0090. M.G. Tuohy., P.G. Murray, Caroline Gilleran, Catherine M. Collins, F. J. Reen, et al.

    3-Dimensional structure of a thermostable native cellobiohydrolase, CBH IB, and molecular characterisation of the cel7 gene from the filamentous fungus, Talaromyces emersonii. Eur. J. Biochem. 271, 4495-4506 (2004). Alice Grassick‡*& Patrick G. Murray‡* (Both authors contributed equally to this work) Roisin Thompson§, Catherine M. Collins‡, Lucy, M. Byrnes||, Gabriel Birrane, Timothy M. Higgins§ and Maria G. Tuohy‡¶.

    Expression in Trichoderma reesei and characterisation of a thermostable Family 3 -glucosidase from the moderately thermophilic fungus Talaromyces emersonii. Protein Purification and Expression 38, 248-257 (2004). Patrick Murray§, Nina Aro¥, Catherine Collins§, Alice Grassick§, Merja Penttilä¥, Markku Saloheimo¥ and Maria Tuohy§+

    Mitochondrial malate dehydrogenase from the thermophilic, filamentous fungus Talaromyces emersonii: Purification of the native enzyme, cloning and overexpression of the corresponding gene. Eur. J. Biochem. 271, 1–11 (2004). Alan P. Maloney, Susan M. Callan, Patrick G. Murray and Maria G. Tuohy

    Crystallisation and preliminary crystallographic analysis of the catalytic domain Cellobiohydrolase IB from Talaromyces emersonii. Biological Crystallography: Acta Crystal D: (2003). D59, 1283-1284. Alice Grassick,, Maria Tuohy, Patrick Murray and Timothy Higgins.

    Molecular characterisation and expression analysis of the first hemicellulase gene (bxl1) encoding-xylosidase from the thermophilic fungus Talaromyces emersonii, Biochemical and Biophysical Research Communications, Volume 305, Issue 3, 6 June 2003, Pages 579-585 F. J. Reen, P. G. Murray and M. G. Tuohy

    Molecular cloning, transcriptional, and expression analysis of the first cellulase gene (cbh2), encoding cellobiohydrolase II, from the moderately thermophilic fungus Talaromyces emersonii and structure prediction of the gene product, Biochemical and Biophysical Research Communications, Volume 301, Issue 2, 7 February 2003, Pages 280-286 P. G. Murray, C. M. Collins, A. Grassick and M. G. Tuohy

    Paper waste saccharification by the thermophilic aerobic fungus, Talaromyces emersonii CBS814.70. Presented to 8TH European Roundtable on Cleaner Production Cork, Ireland Oct. 2002. Gilleran, C. Murray PG. And Tuohy M.G.

    Kinetic parameters and mode of action of the cellobiohydrolases produced by Talaromyces emersonii. Biochim Biophys Acta. 2002 Apr 29;1596(2):366-80. Tuohy MG, Walsh DJ, Murray PG, Claeyssens M, Cuffe MM, Savage AV, Coughlan MP.

    Isolation and characterization of a thermostable endo-beta-glucanase active on 1,3-1,4-beta-D-glucans from the aerobic fungus Talaromyces emersonii CBS 814.70.Enzyme Microb Technol. 2001 Jul 5;29(1):90-98.Murray PG, Grassick A, Laffey CD, Cuffe MM, Higgins T, Savage AV, Planas A, Tuohy MG.

    Professional Affiliation

    Senior research fellow and Strand leader Shannon Applied Biotechnology Centre

    Supervisor

    Not applicable

  • Regina Kelly

    Postgraduate Researcher

    regina.kelly@lit.ie

    Qualifications

    Bachelor of Science (Education) in Biological Sciences and Physics

    Current Research

    Third Level Physics Education

    Publications

    The use of Classroom Response Systems and Multimedia Presentations to enhance Teaching and Learning in First Year, Regina Kelly, Dr Liam Boyle and Leah Wallace, SMEC, (2010). Changing Minds: challenging student attitudes to introductory physics, Regina Kelly and Leah Wallace, LIN, (2011).

    Conferences and Presentations

    Science and Mathematics Education Conference 2010. Learning Innovation Network 2011.

    Professional Affiliation

    Centre of Expertise in Mathematics and Science Teaching and Learning

    Supervisor

    Dr Siobhan Moane, Leah Wallace
  		 
 

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