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Publication Machine learning methods for quantitative analysis of Raman spectroscopy data(Society of Photo-optical Instrumentation Engineers (SPIE), 2003-08-27) Madden, Michael G.; Ryder, Alan G.; |~|The automated identification and quantification of illicit materials using Raman spectroscopy is of significant importance for law enforcement agencies. This paper explores the use of Machine Learning (ML) methods in comparison with standard statistical regression techniques for developing automated identification methods. In this work, the ML task is broken into two sub-tasks, data reduction and prediction. In well-conditioned data, the number of samples should be much larger than the number of attributes per sample, to limit the degrees of freedom in predictive models. In this spectroscopy data, the opposite is normally true. Predictive models based on such data have a high number of degrees of freedom, which increases the risk of models over-fitting to the sample data and having poor predictive power. In the work described here, an approach to data reduction based on Genetic Algorithms is described. For the prediction sub-task, the objective is to estimate the concentration of a component in a mixture, based on its Raman spectrum and the known concentrations of previously seen mixtures. Here, Neural Networks and k-Nearest Neighbours are used for prediction. Preliminary results are presented for the problem of estimating the concentration of cocaine in solid mixtures, and compared with previously published results in which statistical analysis of the same dataset was performed. Finally, this paper demonstrates how more accurate results may be achieved by using an ensemble of prediction techniques.Publication Fluorescence lifetime based pH sensing using Resorufin(2003) Ryder, Alan G.; Power, Sarah; Glynn, Thomas J.; |~|Accurate, non-contact pH sensing is of particular importance in the biological and clinical sciences. Fluorescence lifetime based pH sensing is potentially more useful than intensity based methods because of the reduced sensitivity to excitation source intensity variations, scattering effects, and photobleaching. In this work, we investigate the variation of fluorescence lifetime with pH for resorufin. The intensity averaged lifetime (τ) of resorufin sodium salt in 0.1M phosphate buffer shows an increase of > 3 ns over the 2 -10 pH range, with 90% of the signal change occurring between pH 4 and 8. The fluorescence is not quenched by chloride or oxygen and was unaffected by the ionic strength of the buffer. Resorufin is relatively insoluble in non-alkaline phosphate buffered solutions, but was estimated to increase by ~2 ns between pH 6 and 8. Resorufin and its sodium salt were both incorporated into sol-gels by either acid or base hydrolysis of tetra-methoxysilane (TMOS). Various surfactants were also added to the sol-gels in an attempt to optimise the fluorescence properties and pH sensitivity of the dyes, and to prevent cracking. The sols were then cast from petri-dishes or dip-coated onto acrylic and glass slides. The dyes retained their pH sensitivity, with showing an increase of approximately 2 ns over the pH range 6 - 8. However, leaching of the dye is observed at higher pH and attempt to minimise dye leaching and sol-gel cracking, poly(vinyl alcohol) (PVA) was cross-linked to the silica gel to form a more flexible matrix.Publication Anisotropy resolved multidimensional emission spectroscopy (ARMES): A new tool for protein analysis(Elsevier, 2015-07-30) Groza, Radu Constantin; Ryder, Alan G.; Li, Boyan; |~|6201984|~|Structural analysis of proteins using the emission of intrinsic fluorophores is complicated by spectral overlap. Anisotropy resolved multidimensional emission spectroscopy (ARMES) overcame the overlap problem by the use of anisotropy, with chemometric analysis, to better resolve emission from different fluorophores. Total synchronous fluorescence scan (TSFS) provided information about all the fluorophores that contributed to emission while anisotropy provided information about the environment of each fluorophore. Here the utility of ARMES was demonstrated via study of the chemical and thermal denaturation of human serum albumin (HSA).Multivariate curve resolution (MCR) analysis of the constituent polarized emission ARMES data resolved contributions from four emitters: fluorescence from tryptophan (Trp), solvent exposed tyrosine (Tyr), Tyr in a hydrophobic environment, and room temperature phosphorescence (RTP) from Trp. The MCR scores, anisotropy, and literature validated these assignments and showed all the expected transitions during HSA unfolding. This new methodology for comprehensive intrinsic fluorescence analysis of proteins is applicable to any protein containing multiple fluorophores. (C) 2015 Elsevier B.V. All rights reserved.Publication Fluorescence study of bovine serum albumin and Ti and Sn Oxide nanoparticles interactions.(The Optical Society, 2007) Togashi, Denisio M.; Ryder, Alan G.; Mc Mahon, Deirdre; Dunne, Peter; McManus, James; |~|1267883|~|Nanochemistry offers stimulating opportunities for a wide variety of applications in the biosciences. Understanding of the interaction of nanoparticles with biomolecules such as proteins is very important as it can help better design and fabricate nanocomposites for applications in diagnostics, drug delivery, and cell monitoring. In this work, the interaction of Bovine Serum Albumin (BSA) and two types of metal oxide nanoparticles (titanium and tin) have been studied using the intrinsic fluorescence of tryptophan residue from the proteins measured by steady state and time resolved fluorescence techniques. The nanoparticles which were fabricated using a novel synthetic process have average sizes of ~2 nm (SnO2) and ~6 nm (estimated for TiO2) and have very high solubilities in a variety of solvents. The Stern-Volmer plots indicate an effective quenching process by TiO2 nanoparticles whereas SnO2 nanoparticles have a lower quenching efficiency for BSA fluorescence. Static quenching is the major contribution in the overall process which may indicate a high degree of association between protein and nanoparticles. The difference in BSA fluorescence quenching efficiency between the two types of nanoparticles can be explained by the non-covalent interaction differences and the thermal stability of protein-nanoparticle associated species for both materials.Publication The third dimension of reading the sugar code by lectins: design of glycoclusters with cyclic scaffolds as tools with the aim to define correlations between spatial presentation and activity.(MDPI, 2013-04-04) Murphy, Paul V.; |~|Coding of biological information is not confined to nucleic acids and proteins. Endowed with the highest level of structural versatility among biomolecules, the glycan chains of cellular glycoconjugates are well-suited to generate molecular messages/signals in a minimum of space. The sequence and shape of oligosaccharides as well as spatial aspects of multivalent presentation are assumed to underlie the natural specificity/selectivity that cellular glycans have for endogenous lectins. In order to eventually unravel structure-activity profiles cyclic scaffolds have been used as platforms to produce glycoclusters and afford valuable tools. Using adhesion/growth-regulatory galectins and the pan-galectin ligand lactose as a model, emerging insights into the potential of cyclodextrins, cyclic peptides, calixarenes and glycophanes for this purpose are presented herein. The systematic testing of lectin panels with spatially defined ligand presentations can be considered as a biomimetic means to help clarify the mechanisms, which lead to the exquisite accuracy at which endogenous lectins select their physiological counterreceptors from the complexity of the cellular glycome.