College of Science

A Modified Watermark Synchronisation Code for Robust Embedding of Data in DNA

Sun, 26 May 2013 00:00:00 GMT

A Modified Watermark Synchronisation Code for Robust Embedding of Data in DNA Haughton, David; Balado, Félix DNA data embedding is a newly emerging field aspiring to encode data in deoxyribonucleic acid (DNA). DNA is an inherently digital and noisy medium, undergoing substitution, insertion and deletion mutations. Hence, encoding information in DNA can be seen as a particular case of digital communications in which biological constraints must be observed. In this paper we propose a modification of Davey and MacKay’s watermark synchronisation code (unrelated to digital watermarking) to create an encoding procedure more biocompatible with the host organism than previous methods. In addition, when combined with a low density parity check (LDPC) code, the method provides near-optimum error correction. We also obtain the theoretical embedding capacity of DNA under substitution mutations for the increased biocompatibility constraint. This result, along with an existing bound on capacity for insertion and deletion mutations, is compared to the proposed algorithm’s performance by means of Monte Carlo simulations Poster presentation at the 38th IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP 2013), May 23-31, 2013, Vancouver, Canada

Permutation Codes and Steganography

Sun, 26 May 2013 00:00:00 GMT

Permutation Codes and Steganography Balado, Félix; Haughton, David We show that Slepian’s Variant I permutation codes implement first-order perfect steganography (i.e., histogram-preserving steganography). We give theoretical expressions for the embedding distortion, embedding rate and embedding efficiency of permutation codes in steganography, which demonstrate that these codes conform to prior analyses of the properties of capacity-achieving perfect stegosystems with a passive warden. We also propose a modification of adaptive arithmetic coding that near optimally implements permutation coding with a low complexity, confirming all our theoretical predictions. Finally we discuss how to control the embedding distortion. Permutation coding turns out to be akin to Sallee’s model-based steganography, and to supersede both this method and LSB matching. 38th IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), Vancouver, Canada, May, 2013

The Demonstration of the Reviewer's Assistant

Sat, 01 Sep 2012 00:00:00 GMT

The Demonstration of the Reviewer's Assistant Dong, Ruihai; Schaal, Markus; O'Mahony, Michael P.; McCarthy, Kevin; Smyth, Barry User generated reviews are now a familiar and valuable part of most e-commerce sites since high quality reviews are known to influence purchasing decisions. In this demonstration we describe work on the Reviewer's Assistant (RA), which is a recommendation system that is designed to help users to write better quality reviews. It does this by suggesting relevant topics that they may wish to discuss based on the product they are reviewing and the content of their review so far. ACM Conference on Recommender Systems (RecSys '12), Dublin, Ireland, 9-13 September, 2012

Bogtrotters in Space

Sun, 01 Jan 2012 00:00:00 GMT

Bogtrotters in Space Carr, Dominic; Russell, Sean E.; Pete, Balazs; O'Hare, G. M. P. (Greg M. P.); Collier, Rem This is the fourth year in which a team from University College Dublin has participated in the Multi-Agent Programming Contest. This paper describes the system that was created to participate in the contest, along with observations of the team’s experiences in the contest. The system itself was built using the AF-TeleoReactive and AF-AgentSpeak agent programming languages running on the Agent Factory platform. Unlike in previous years where a hybrid control architecture was used, this year the system was implemented using only agent code and associated actions, sensors, modules and platform services. In Proceedings of Programming Multi-Agent Systems, 00, 2012

Visualizing molecular polar order in tissues via electromechanical coupling

Sat, 01 Dec 2012 00:00:00 GMT

Visualizing molecular polar order in tissues via electromechanical coupling Denning, Denise; Alilat, Sofiane; Habelitz, S.; Fertala, A.; Rodriguez, Brian J. Electron microscopy (EM) and atomic force microscopy (AFM) techniques have long been used to characterize collagen fibril ordering and alignment in connective tissues. These techniques, however, are unable to map collagen fibril polarity, i.e., the polar orientation that is directed from the amine to the carboxyl termini. Using a voltage modulated AFM-based technique called piezoresponse force microscopy (PFM), we show it is possible to visualize both the alignment of collagen fibrils within a tissue and the polar orientation of the fibrils with minimal sample preparation. We demonstrate the technique on rat tail tendon and porcine eye tissues in ambient conditions. In each sample, fibrils are arranged into domains whereby neighboring domains exhibit opposite polarizations, which in some cases extend to the individual fibrillar level. Uniform polarity has not been observed in any of the tissues studied. Evidence of anti-parallel ordering of the amine to carboxyl polarity in bundles of fibrils or in individual fibrils is found in all tissues, which has relevance for understanding mechanical and biofunctional properties and the formation of connective tissues. The technique can be applied to any biological material containing piezoelectric biopolymers or polysaccharides.

Electromechanical properties of dried tendon and iso-electrically focused collagen hydrogels

Wed, 01 Aug 2012 00:00:00 GMT

Electromechanical properties of dried tendon and iso-electrically focused collagen hydrogels Denning, Denise; Abu-Rub, M. T.; Zeugolis, D. I.; Habelitz, S.; Pandit, A.; Fertala, A.; Rodriguez, Brian J. Assembling artificial collagenous tissues with structural, functional, and mechanical properties which mimic natural tissues is of vital importance for many tissue engineering applications. While the electro-mechanical properties of collagen are thought to play a role in, for example, bone formation and remodeling, this functional property has not been adequately addressed in engineered tissues. Here the electro-mechanical properties of rat tail tendon are compared with those of dried isoelectrically focused collagen hydrogels using piezoresponse force microscopy under ambient conditions. In both the natural tissue and the engineered hydrogel D-periodic type I collagen fibrils are observed, which exhibit shear piezoelectricity. While both tissues also exhibit fibrils with parallel orientations, Fourier transform analysis has revealed that the degree of parallel alignment of the fibrils in the tendon is three times that of the dried hydrogel. The results obtained demonstrate that isoelectrically focused collagen has similar structural and electro-mechanical properties to that of tendon, which is relevant for tissue engineering applications.

Growth mechanism of photoreduced silver nanostructures on periodically proton exchanged lithium niobate: Time and concentration dependence

Wed, 08 May 2013 00:00:00 GMT

Growth mechanism of photoreduced silver nanostructures on periodically proton exchanged lithium niobate: Time and concentration dependence Craig Carville, N.; Manzo, Michele; Denning, Denise; Gallo, Katia; Rodriguez, Brian J. Photodeposition of metallic nanostructures onto ferroelectric surfaces, which have been chemically patterned using a proton exchange process, has recently been demonstrated. By varying the molar concentration of the AgNO3 solution and the illumination time, one can determine the initial nucleation sites, control the rate of nucleation and the height of silver nanostructures formed, and study the mechanisms by which these processes occurs. The nanoparticles are found to deposit preferentially in the boundary between ferroelectric and proton exchanged regions, in an area proton exchanged via lateral diffusion under the masking layer used for chemical patterning, consistent with our previous results. Using a short illumination time (3 min), we are able to determine that the initial nucleation of the silver nanostructure, having a width of 0.17±0.02µm and a height of 1.61±0.98nm, occurs near the edge of the reactive ion etched area within this lateral diffusion region. Over longer illumination times (15 min), we find that the silver deposition has spread to a width of 1.29±0.06µm, extending across the entire lateral diffusion region. We report that at a high molar concentration of AgNO3 (10¯² M), the amount of silver deposition for 5 min UV illumination is greater (2.88±0.58nm) compared to that at low (10¯4M) concentrations (0.78±0.35nm), however, this is not the case for longer time periods. With increasing illumination time (15 min), experiments at 10¯4 M had greater overall deposition, 6.90±1.52nm, compared to 4.50±0.76nm at 10 ¯² M. For longer exposure times (30min) at 10 ¯² M the nanostructure height is 4.72±0.59nm, suggesting a saturation in the nanostructure height. The results are discussed in terms of the electric double layer that forms at the crystal surface. There is an order of magnitude difference between the Debye lengths for 10¯² and 10¯4 M solutions, i.e., 3.04 vs. 30.40nm, which suggests the Debye length plays a role in the availability of Ag+ ions at the surface.

Characterising the metric and topological evolution of OpenStreetMap network representations

Tue, 01 Jan 2013 00:00:00 GMT

Characterising the metric and topological evolution of OpenStreetMap network representations Corcoran, Padraig; Mooney, Peter OpenStreetMap (OSM) is a collaborative project to create a free editable map database of the world. This paper presents an analysis of the evolution of OSM street network representations. Three urban areas in Ireland were analysed where each evolves from containing little street network detail to a highly detailed street network. In order to characterise this evolution a number of metric and topological characteristics were computed. Some characteristics exhibited broadly similar behaviour in each region. This may be a attributed to similarities in the degree of contributor activity and intrinsic universal mapping procedures exhibited by contributors

Interactive cartographic route descriptions

Mon, 01 Apr 2013 00:00:00 GMT

Interactive cartographic route descriptions Corcoran, Padraig; Mooney, Peter; Bertolotto, Michela Providing an adequate route description requires in-depth spatial knowledge of the route in question. In this article we demonstrate that despite having travelled a route recently and having much experience of the area in question, an individual may lack such a degree of knowledge. Previous research and experience informs us that a map is an effective tool for bridging gaps in one’s spatial knowledge. In this article we propose an approach, known as an Interactive Route Description, for defining and interpreting route descriptions interactively with a map. This approach is based on the concept of annotating the map in question and allows the aforementioned gap in one’s spatial knowledge to be bridged. An additional benefit of defining route descriptions in this way is that it facilitates automatic parsing and in turn offers many potential applications. One such application, illustrated in this paper, is the automatic transformation to other representations of the description such as turn-by-turn instructions.

Utilizing geometric coherence in the computation of map transformations

Mon, 01 Oct 2012 00:00:00 GMT

Utilizing geometric coherence in the computation of map transformations Corcoran, Padraig; Mooney, Peter; Bertolotto, Michela Adaptive mapping and real-time spatial data delivery are currently major research topics in the fields of Web-GIS and Location Based Services (LBS). In order to successfully implement these paradigms a methodology to progressively adopt or transform an arbitrary map representation in an arbitrary fashion on-the-fly is necessary. Such a methodology was previously considered not feasible due to the high computational complexity associated with existing automated map generalisation methodologies. This paper presents a methodology, inspired by related research in the field of computer graphics, which offers the potential to reduce such associated computational complexity. This is achieved using an approach to map transformation which takes advantage of the geometric coherence between a user's spatial data requirements.

Immersive human-robot interaction

Thu, 01 Mar 2012 00:00:00 GMT

Immersive human-robot interaction Sandygulova, Anara; Campbell, Abraham G.; Dragone, Mauro; O'Hare, G. M. P. (Greg M. P.) Networked robotic applications enable robots to operate in distant, hazardous, or otherwise inaccessible environments, such as search and rescue, surveillance, and exploration applications. The most difficult challenge which persists for such systems is that of supporting effective human-robot interaction, as this usually demands managing dynamic views, changeable interaction modalities, and adaptive levels of robotic autonomy. In contrast of sophisticated screen-based graphical user interfaces (GUIs), the solution proposed herein is to enable more natural human-robot interaction modalities through a networked immersive user interface. This paper describes the creation of one such shared space where to test such an approach, with both simulated and real robots. HRI 2012 7th ACM/IEEE International Conference on Human-Robot Interaction, Boston, USA, March 5-8, 2012

HeyStaks: A Real-World deployment of Social Search

Sun, 01 Jan 2012 00:00:00 GMT

HeyStaks: A Real-World deployment of Social Search Smyth, Barry; Coyle, Maurice; Briggs, Peter The purpose of this paper is to provide a deployment update for the HeyStaks social search system which uses recommendation techniques to add collaboration to mainstream search engines such as Google, Bing, and Yahoo. We describe our the results of initial deployments, including an assessment of the quality of HeyStaks' recommendations, and highlight some lessons learned in the marketplace. 6th ACM Conference on Recommender Systems (RecSys '12), Dublin, Ireland, 9th-13th September, 2012

Exploiting Extended Search Sessions for Recommending Search Experiences in the Social Web

Mon, 03 Sep 2012 00:00:00 GMT

Exploiting Extended Search Sessions for Recommending Search Experiences in the Social Web Saaya, Zurina; Schaal, Markus; Coyle, Maurice; Briggs, Peter; Smyth, Barry HeyStaks is a case-based social search system that allows users to create and share case bases of search experiences (called staks) and uses these staks as the basis for result recommendations at search time. These recommendations are added to conventional results from Google and Bing so that searchers can benefit from more focused results from people they trust on topics that matter to them. An important point of friction in HeyStaks is the need for searchers to select their search context (that is, their active stak) at search time. In this paper we extend previous work that attempts to eliminate this friction by automatically recommending an active stak based on the searchers context (query terms, Google results, etc.) and demonstrate significant improvements in stak recommendation accuracy. 20th International Conference, ICCBR 2012, Lyon, France, September 3-6, 2012.

The Reviewer's Assistant: Recommending Topics to Writers by Association Rule Mining and Case-base Reasoning

Mon, 17 Sep 2012 00:00:00 GMT

The Reviewer's Assistant: Recommending Topics to Writers by Association Rule Mining and Case-base Reasoning Dong, Ruihai; Schaal, Markus; O'Mahony, Michael P.; Smyth, Barry Today, online reviews for products and services have become an important class of user-generated content and they play a valuable role for countless online businesses by helping to convert casual browsers into informed and satisfied buyers. As users gravitate towards sites that offer insightful and objective reviews, the ability to source helpful reviews from a community of users is increasingly important. In this extended abstract we describe the Reviewer’s Assistant, a case-based reasoning inspired recommender system designed to help people to write more helpful reviews on sites such as Amazon and TripAdvisor. In particular, we describe two approaches to helping users during the review writing process and evaluate each as part of a blind live-user study. Our results point to high levels of user satisfaction and improved review quality compared to a control-set of Amazon reviews. The 23rd Irish Conference on Artificial Intelligence and Cognitive Science (AICS 2012), Dublin City University, Dublin, Ireland, 17-19 September, 2012

Advances in pervasive health

Sun, 01 Jul 2012 00:00:00 GMT

Advances in pervasive health O'Grady, Michael J.; Caulfield, Brian; O'Hare, G. M. P. (Greg M. P.) Pervasive Health seeks to harness developments in pervasive computing technologies and harness them in the health domain. This domain may be interpreted in its widest possible sense, including the medical aspect both physical and mental, but also that of care management, education, community and occupational health. Such is the potential of pervasive computing technologies that the domain of pervasive health itself may ultimately fracture into a number of specialised domains, as the potential of the technology is being increasingly realised in practice. Indeed, this is already occurring with increased research activity being directed towards Ambient Assisted Living (AAL) in response to ongoing societal aging patterns

Supporting Problem-based Learning in Moodle using Personalised, Context- specific Learning Episode Generation

Fri, 14 Sep 2012 00:00:00 GMT

Supporting Problem-based Learning in Moodle using Personalised, Context- specific Learning Episode Generation Brabazon, Dermot; Donovan, Lynda; Melia, Mark; O'Mahony, Michael P.; Egan, Andrew; Smyth, Barry Providing learners with a list of disparate search results is not always conducive to learning. In particular, this approach lacks learning structure, and learners have to sift through lists of resources in order to make sense of them and to find the level of detail they require. In this paper we outline the Moodle Help Block, a Moodle block plug-in that provides learners with Just-In-Time context relevant learning material using a defined pedagogical strategy. The Moodle Help Block uses a combination of Semantic Web, Social Web and learning composition technology to generate learning episodes as needed by learners. The Moodle help block conducts a dialogue with the learner to extrapolate where a given learner’s knowledge gaps lie and generate learning episodes with learning material to help the learner overcome their knowledge deficit. It is thought that the Moodle Help Block can assist learners with targeted help when a teacher is not available. 1st Moodle Research Conference, Heraklion, Crete, Greece, September 14-15, 2012

Harnessing the Experience Web to Support User-Generated Product Reviews

Mon, 03 Sep 2012 00:00:00 GMT

Harnessing the Experience Web to Support User-Generated Product Reviews Dong, Ruihai; Schaal, Markus; O'Mahony, Michael P.; McCarthy, Kevin; Smyth, Barry Today, online reviews for products and services have become an important class of user-generated content and they play a valuable role for countless online businesses by helping to convert casual browsers into informed and satisfied buyers. In many respects, the content of user reviews is every bit as important as the catalog content that describes a given product or service. As users gravitate towards sites that offer insightful and objective reviews, the ability to source helpful reviews from a community of users is increasingly important. In this work we describe the Reviewer’s Assistant, a case-based reasoning inspired recommender system designed to help people to write more helpful reviews on sites such as Amazon and TripAdvisor. In particular, we describe two approaches to helping users during the review writing process and evaluate each as part of a blind live-user study. Our results point to high levels of user satisfaction and improved review quality compared to a control-set of Amazon reviews. Proceedings of the 20th International Conference, ICCBR 2012, Lyon, France, September 3-6, 2012.

Practical Problem-Based Learning in Computing Education

Sun, 01 Jul 2012 00:00:00 GMT

Practical Problem-Based Learning in Computing Education O'Grady, Michael J. Computer Science (CS) is a relatively new disciple and how best to introduce it to new students remains an open question. Likewise, the identification of appropriate instructional strategies for the diverse topics that constitute the average curriculum remains open to debate. One approach considered by a number of practitioners in CS education involves Problem Based Learning (PBL), a radical departure from the conventional lecturing format. PBL has been adopted in other domains with success, but whether these positive experiences will be replicated in CS remains to be seen. In this paper, a systematic review of PBL initiatives in undergraduate and postgraduate CS is presented from a Computing Education Research (CER) perspective. This includes analyses of a range of practical didactic issues, including the degree to which PBL has been systematically evaluated, practical problem description in the literature, as well as a survey of topics for which a PBL approach has been adopted.

Robotic UBIquitous COgnitive Network

Sun, 01 Jan 2012 00:00:00 GMT

Robotic UBIquitous COgnitive Network Amato, G.; Broxvall, M.; Dragone, Mauro; Gennaro, C.; Lopez, R.; Maguire, L.; McGinnity, T. M.; Micheli, A.; Renteria, A.; O'Hare, G. M. P. (Greg M. P.); Pecora, F. Robotic ecologies are networks of heterogeneous robotic devices pervasively embedded in everyday environments, where they cooperate to perform complex tasks. While their potential makes them increasingly popular, one fundamental problem is how to make them self-adaptive, so as to reduce the amount of preparation, pre-programming and human supervision that they require in real world applications. The EU FP7 project RUBICON develops self-sustaining learning solutions yielding cheaper, adaptive and efficient coordination of robotic ecologies. The approach we pursue builds upon a unique combination of methods from cognitive robotics, agent control systems, wireless sensor networks and machine learning. This paper briefly illustrates how these techniques are being extended, integrated, and applied to AAL applications. 3rd International Symposium on Ambient Intelligence, Salamanca, Spain, 2012

Robotic UBIquitous COgnitive Networks (RUBICON)

Wed, 22 Feb 2012 00:00:00 GMT

Robotic UBIquitous COgnitive Networks (RUBICON) Abdel-Naby, S.; Amato, G.; Bacciu, D.; Chessa, S.; Coleman, S.; Di Rocco, M.; Dragone, Mauro; Gallicchio, C.; Gennaro, C.; Guzman, R.; Lopez, R.; Lozano, H.; Maguire, L.; McGinnity, T. M.; Micheli, A.; O'Hare, G. M. P. (Greg M. P.); Pecora, F.; Ray, A.; Renteria, A.; Saffiotti, A.; Swords, D.; Vairo, C. Poster presentation at the 5th International Conference on Cognitive Systems (CogSys 2012), TU Vienna, Vienna, 22-23 February, 2012

Content on demand for fourth year advanced materials and manufacturing students

Wed, 18 Jul 2012 00:00:00 GMT

Content on demand for fourth year advanced materials and manufacturing students Brabazon, Dermot; Donovan, Lynda; Egan, Andrew; O'Mahony, Michael P.; Melia, Mark; Smyth, Barry There is growing recognition of the key role that social and informal learning play in Higher Education. There is also increasing interest in technologies that enable, capture and channel this type of learning to students at their point of need and personalised to their ability. The objective of this project was to leverage research technologies from the areas of adaptive hypermedia, social and semantic search to create an application to deliver learning resources to students tailored to their specific learning needs. In this project, some 130 digital learning resources, specific to a final year advanced materials and manufacturing module, were made available to the students via a Help Block plugin in the Moodle Virtual Learning Environment. The students were required to use the Help Block as a just-in-time learning resource to help them complete a continuous assessment assignment. The assignment required the students to select an advanced manufacturing process and associated material describing the manufacturing process steps, control and specifications and presenting the technological benefits of the process and material used relative to competing processes and materials. Post-trial, students were asked to complete a questionnaire to describe their experience with the Help Block in terms of whether it assisted them in completing the assignment, for example, and its ease of use. The system, evaluation findings, and some suggestions for future system enhancements are presented in the paper. ISEE 2012, 4th International Symposium of Engineering Education, The University of Sheffield, UK, 18th -20th July 2012

Quaternarized pdppz: synthesis, DNA-binding and biological studies of a novel dppz derivative that causes cellular death upon light irradiation.

Sat, 01 Jan 2011 00:00:00 GMT

Quaternarized pdppz: synthesis, DNA-binding and biological studies of a novel dppz derivative that causes cellular death upon light irradiation. Elmes, Robert B.P.; Erby, Marialuisa; Cloonan, Suzanne M.; Quinn, Susan J.; Williams, D. Clive; Gunnlaugsson, Thorfinnur The quaternarized pdppz derivative 1 was shown to bind strongly to DNA with concomitant changes in its ground and excited state photophysical properties. Furthermore, the compound also showed rapid cellular uptake, and induced apoptosis upon light irradiation in various cancer cell lines after 24 hours of incubation.

Synthesis and photophysical evaluations of fluorescent quaternary bipyridyl-1,8-naphthalimide conjugates as nucleic acid targeting agents

Mon, 16 Jan 2012 00:00:00 GMT

Synthesis and photophysical evaluations of fluorescent quaternary bipyridyl-1,8-naphthalimide conjugates as nucleic acid targeting agents Ryan, Gary J.; Elmes, Robert B.P.; Quinn, Susan J.; Gunnlaugsson, Thorfinnur A family of organic molecules containing the DNA intercalating chromophores, 4-nitro- and 4-amino 1,8-naphthalimide, conjugated to a diquat derivative by an ‘orthogonal’ phenyl spacer have been prepared and characterised. Their binding interactions with double-stranded DNA were studied by a variety of spectroscopic techniques. These charged organic compounds are found to exhibit excellent binding affinities to DNA with binding constants comparable to those exhibited by metal complexes.

A comparative picosecond transient infrared study of 1-methylcytosine and 5'-dCMP that sheds further light on the excited states of cytosine derivatives

Tue, 01 Mar 2011 00:00:00 GMT

A comparative picosecond transient infrared study of 1-methylcytosine and 5'-dCMP that sheds further light on the excited states of cytosine derivatives Keane, Páraic M.; Wojdyla, Michal; Doorley, Gerard W.; Watson, Graeme W.; Clark, Ian P.; Greetham, Gregory M.; Parker, Anthony W.; Towrie, Michael; Kelly, John M.; Quinn, Susan J. The role of N1-substitution in controlling the deactivation processes in photoexcited cytosine derivatives has been explored using picosecond time-resolved IR spectroscopy. The simplest N1-substituted derivative, 1-methylcytosine, exhibits relaxation dynamics similar to the cytosine nucleobase and distinct from the biologically relevant nucleotide and nucleoside analogues, which have longer-lived excited-state intermediates. It is suggested that this is the case because the sugar group either facilitates access to the long-lived (1)n(O)Ï * state or retards its crossover to the ground state.

Ultrafast IR spectroscopy of polymeric cytosine nucleic acids reveal the long-lived species is due to a localised state

Wed, 22 Feb 2012 00:00:00 GMT

Ultrafast IR spectroscopy of polymeric cytosine nucleic acids reveal the long-lived species is due to a localised state Keane, Páraic M.; Wojdyla, Michal; Doorley, Gerard W.; Kelly, John M.; Clark, Ian P.; Parker, Anthony W.; Greetham, Gregory M.; Towrie, Michael; Magno, Luís M.; Quinn, Susan J. The decay pathways of UV-excited cytosine polymers are investigated using picosecond time-resolved infrared spectroscopy. Similar yields of a non-emissive (1)nÏ * state are found in the single-stranded dC(30) polymer as in the dCMP monomer, but with a longer lifetime in the polymer (80 ps vs. 39 ps). A longer lifetime is also found in the d(CpC) dinucleotide. No evidence of excimer states is observed, suggesting that localised (1)nÏ * excited states are the most significant intermediates present on the picosecond timescale.

Excited state behaviour of substituted dipyridophenazine Cr(III) complexes in the presence of nucleic acids

Fri, 01 Jan 2010 00:00:00 GMT

Excited state behaviour of substituted dipyridophenazine Cr(III) complexes in the presence of nucleic acids Wojdyla, Michal; Smith, Jayden A.; Vasudevan, Suni; Quinn, Susan J.; Kelly, John M. The photophysics and photochemistry of [Cr(phen)2(dppz)]3+ and its 11,12-substituted derivatives [Cr(phen)2(X2dppz)]3+ {X = Me or F} have been studied in the presence of purine nucleotides or DNA using steady state and time-resolved absorption and luminescence spectroscopy. 5'-Adenosine monophosphate (5'-AMP) shows only a weak interaction with the excited states of each complex. By contrast they are efficiently quenched by 5'-guanosine monophosphate (5'-GMP), consistent with photo-induced electron transfer. Laser flash photolysis spectroscopy in the presence of 5'--GMP suggests that both forward and back electron-transfers are rapid. All complexes also display a strong affinity for DNA and evidence for both static and dynamic quenching mechanisms is provided.

Incandescent Porous Carbon Microspheres to Light up Cells: Solution Phenomena and Cellular Uptake

Sun, 01 Jan 2012 00:00:00 GMT

Incandescent Porous Carbon Microspheres to Light up Cells: Solution Phenomena and Cellular Uptake Duffy, Paul; Magno, Luís M.; Yadavc, Rahul B.; Roberts, Selene K.; Ward, Andrew D.; Botchway, Stanley W.; Colavita, Paula E.; Quinn, Susan J. Carbon based materials are attractive for biological applications because of their excellent biocompatibility profile. Porous carbons with high specific surface area are particularly interesting because it is possible in principle to leverage their properties to deliver high drug payloads. In this work, porous carbon microspheres with high specific surface area were prepared and studied in solution and in cells. Raman optical tweezer trapping of microspheres, excited by 532 nm, results in graphitization and incandescence in solvents that display poor heat conduction. Fluorescence confocal microscopy imaging was used to demonstrate the uptake of fluorescently labelled microspheres by cells and the ability to leverage their optical absorptivity in order to cause carbon graphitization and cell death.

Photophysical studies of CdTe quantum dots in the presence of a zinc cationic porphyrin

Mon, 24 Sep 2012 00:00:00 GMT

Photophysical studies of CdTe quantum dots in the presence of a zinc cationic porphyrin Keane, Páraic M.; Gallagher, Shane A.; Magno, Luís M.; Leising, Miriam J.; Clark, Ian P.; Greetham, Gregory M.; Towrie, Michael; Gun'ko, Yurii; Kelly, John M.; Quinn, Susan J. The photophysical properties of 2.3 nm thioglycolic acid (TGA) coated CdTe quantum dots (QDs) prepared by a reflux method have been studied in the presence of cationic meso-tetrakis(4-N-methylpyridyl) zinc porphyrin (ZnTMPyP4). Addition of the CdTe QDs to the porphyrin in H2O results in a marked red-shift and hypochromism in the porphyrin absorption spectrum, indicative of a non-covalent binding interaction with the QD surface. Only low equivalents of the quantum dot were required for complete quenching of the porphyrin fluorescence revealing that one quantum dot may quench more than one porphyrin. Similarly addition of porphyrin to the quantum dot provided evidence for very efficient quenching of the CdTe photoluminescence, suggesting the formation of CdTe'porphyrin aggregates. Definitive evidence for such aggregates was gathered using small angle X-ray spectroscopy (SAXS). Ultrafast transient absorption data are consistent with very rapid photoinduced electron transfer (1.3 ps) and the resultant formation of a long-lived porphyrin species.

The Microbial Cell Factory

Wed, 14 Mar 2012 00:00:00 GMT

The Microbial Cell Factory Murphy, Cormac D. Microorganisms have been used for decades as sources of antibiotics, vitamins and enzymes and for the production of fermented foods and chemicals. In the 21st century microorganisms will play a vital role in addressing some of the problems faced by mankind. In this article three of the current applications in which microbes have a significant role to play are highlighted: the discovery of new antibiotics, manufacture of biofuels and bioplastics, and production of fine chemicals via biotransformation.

Production of human metabolites of the anti-cancer drug flutamide via biotransformation in Cunninghamella species

Tue, 01 Feb 2011 00:00:00 GMT

Production of human metabolites of the anti-cancer drug flutamide via biotransformation in Cunninghamella species Amadio, Jessica; Murphy, Cormac D. Fungi belonging to the genus Cunninghamella have enzymes similar to those employed by mammals for the detoxification of xenobiotics, thus they are useful as models of mammalian drug metabolism, and as a source for drug metabolites. We report the transformation of the anti-cancer drug flutamide in Cunninghamella sp. The most predominant phase I metabolites present in the plasma of humans, 2-hydroxyflutamide and 4-nitro-3-(trifluoromethyl)aniline, were also produced in Cunninghamella cultures. Other phase I and phase II metabolites were also detected using a combination of HPLC, GC–MS and 19F-NMR.

Production of the Novel Lipopeptide Antibiotic Trifluorosurfactin via Precursor-Directed Biosynthesis.

Thu, 01 Nov 2012 00:00:00 GMT

Production of the Novel Lipopeptide Antibiotic Trifluorosurfactin via Precursor-Directed Biosynthesis. O'Connor, Neil K.; Rai, Dilip K.; Clark, Benjamin R.; Murphy, Cormac D. Incorporation of fluorine into antibiotics can moderate their biological activity, lipophilicity and metabolic stability. The introduction of fluorine into an antimicrobial lipopeptide produced by Bacillus sp. CS93 via precursor-directed biosynthesis is described. The lipopeptide surfactin is synthesised non-ribosomally by various Bacillus species and is known for its biological activity. Administering 4,4,4-trifluoro-dl-valine to cultures of Bacillus sp. CS93 results in the formation of trifluorosurfactin in quantities sufficient for detection by LC–MS/MS. 19F NMR analysis of the culture supernatant revealed that the bulk of the fluorinated amino acid was transformed and thus was unavailable for incorporation into surfactin. Detection of ammonia, and MS analysis indicated that the transformation proceeds with deamination and reduction of the keto acid, yielding 4,4,4-trifluoro-2-hydroxy-3-methylbutanoic acid.

Synthesis and spectroscopic studies of chiral CdSe quantum dots

Sun, 01 Aug 2010 00:00:00 GMT

Synthesis and spectroscopic studies of chiral CdSe quantum dots Gallagher, Shane A.; Moloney, Mícheál P.; Wojdyla, Michal; Quinn, Susan J.; Kelly, John M.; Gun'ko, Yurii K. Using microwave irradiation, water soluble, optically active, penicillamine (Pen) capped CdSe nanocrystals with broad spectral distribution (430-780 nm) of photoluminescence have been produced and studied by a range of instrumental techniques including absorption, circular dichroism and both steady state and time resolved photoluminescence spectroscopy. The photoluminescence of these nanocrystals is attributed to emission from surface defect states. The decay of the excited state in the nanosecond region, which can be analysed as a triple exponential, depends strongly on the emission wavelength selected, but only weakly on the excitation wavelength.

Anisotropic spatial clustering of TB in cattle - the implications for control policy

Sat, 01 Jan 2011 00:00:00 GMT

Anisotropic spatial clustering of TB in cattle - the implications for control policy Kelly, Gabrielle E. Bovine TB is a disease that affects cattle and the wildlife badger, species Meles meles, in Ireland and the UK, and badgers have been implicated in the spread of the disease in cattle. Efforts to eradicate the disease that have included localized badger culling, have not been successful. In a study to understand how the disease spreads, Kelly and More [1] determined that the disease spatially clusters in cattle herds and estimated the practical spatial ranges at which this occurs. We extend this work by examining possible anisotropy in clustering and the consequences for TB control policy. 1st Conference on Spatial Statistics 2011 – Mapping Global Change, Enschede, The Netherlands, March, 2011

Clustering Ordinal Data via Latent Variable Models

Mon, 01 Apr 2013 00:00:00 GMT

Clustering Ordinal Data via Latent Variable Models McParland, Damien; Gormley, Claire Item response modelling is a well established method for analysing ordinal response data. Ordinal data are typically collected as responses to a number of questions or items. The observed data can be viewed as discrete versions of an underlying latent Gaussian variable. Item response models assume that this latent variable (and therefore the observed ordinal response) is a function of both respondent specific and item specific parameters. However, item response models assume a homogeneous population in that the item specific parameters are assumed to be the same for all respondents. Often a population is heterogeneous and clusters of respondents exist; members of different clusters may view the items differently. A mixture of item response models is developed to provide clustering capabilities in the context of ordinal response data. The model is estimated within the Bayesian paradigm and is illustrated through an application to an ordinal response data set resulting from a clinical trial involving self-assessment of arthritis. IFCS 2013 Conference of the International Federation of Classification Societies, Tilburg University, The Netherlands, from July 14-17, 2013

A long term observational study of the impact of badger removal on herd restrictions due to bovine TB in the Irish midlands during 1989-2004

Wed, 01 Oct 2008 00:00:00 GMT

A long term observational study of the impact of badger removal on herd restrictions due to bovine TB in the Irish midlands during 1989-2004 Kelly, Gabrielle E.; Condon, J.; More, Simon John; Dolan, L.; Higgins, I.; Eves, J. An observational study was carried out, using data collected from four areas in the Irish midlands, between 1989 and 2004, to critically evaluate the long-term effects of proactive badger culling and to provide insights into reactive badger culling tuberculosis (TB) prevalence in cattle. Confirmed cattle herd TB incidence is the outcome measure used throughout. Relative to reactive culling, proactive badger culling was associated with a decrease in incidence in each of the 16 years of observation, which encompassed periods of both intensive and less-intensive badger removal. By 2004, we observed a decrease of 22% [95% confidence interval (CI) 15-29, P<0.001] in the entire proactive and 37% (95% CI 25–47, P<0.001), in the inner proactive removal areas. The size of the decrease increased with time (P=0.055). There was a decrease (constant over time) of at least 14% (95% CI 76–97, P=0.013) in incidence in the inner compared to the outer control area (herds ≤2 km, >2 km, from proactive removal area boundaries, respectively). Incidence in the outer proactive removal area (herds <1.6 km from the proactive removal boundary) was similar to the inner control area (P=0.890). Incidence in the outer control area and total control area, compared to a neighbouring area some distance away, increased over the course of the study. Differences with the total control area were not statistically significant but the outer control area was 11% higher than the neighbouring area by 2004 (borderline significance P=0.057).

Body mass index and height over three generations: evidence from the Lifeways cross-generational cohort study

Sun, 01 Jan 2012 00:00:00 GMT

Body mass index and height over three generations: evidence from the Lifeways cross-generational cohort study Murrin, Celine; Kelly, Gabrielle E.; Tremblay, Richard E.; Kelleher, Cecily Background: Obesity and its measure of body mass index are strongly determined by parental body size. Debate continues as to whether both parents contribute equally to offspring body mass which is key to understanding the aetiology of the disease. The aim of this study was to use cohort data from three generations of one family to examine the relative maternal and paternal associations with offspring body mass index and how these associations compare with family height to demonstrate evidence of genetic or environmental cross-generational transmission. Methods: 669 of 1082 families were followed up in 2007/8 as part of the Lifeways study, a prospective observational cross-generation linkage cohort. Height and weight were measured in 529 Irish children aged 5 to 7 years and were self-reported by parents and grandparents. All adults provided information on self-rated health, education status, and indicators of income, diet and physical activity. Associations between the weight, height, and body mass index of family members were examined with mixed models and heritability estimates computed using linear regression analysis. Results: Self-rated health was associated with lower BMI for all family members, as was age for children. When these effects were accounted for evidence of familial associations of BMI from one generation to the next was more apparent in the maternal line. Heritability estimates were higher (h2 = 0.40) for mother-offspring pairs compared to father-offspring pairs (h2 = 0.22). In the previous generation, estimates were higher between mothersparents (h2 = 0.54-0.60) but not between fathers-parents (h2 = -0.04-0.17). Correlations between mother and offspring across two generations remained significant when modelled with fixed variables of socioeconomic status, health, and lifestyle. A similar analysis of height showed strong familial associations from maternal and paternal lines across each generation. Conclusions: This is the first family cohort study to report an enduring association between mother and offspring BMI over three generations. The evidence of BMI transmission over three generations through the maternal line in an observational study corroborates the findings of animal studies. A more detailed analysis of geno and phenotypic data over three generations is warranted to understand the nature of this maternal-offspring relationship.

Spatial clustering of TB-infected cattle herds prior to and following proactive badger removal

Mon, 01 Aug 2011 00:00:00 GMT

Spatial clustering of TB-infected cattle herds prior to and following proactive badger removal Kelly, Gabrielle E.; More, Simon John Bovine tuberculosis (TB) is primarily a disease of cattle. In both Ireland and the UK, badgers (Meles meles) are an important wildlife reservoir of infection. This paper examined the hypothesis that TB is spatially correlated in cattle herds, established the range of correlation and the effect, if any, of proactive badger removal on this. We also re-analysed data from the Four Area Project in Ireland, a large-scale intervention study aimed at assessing the effect of proactive badger culling on bovine TB incidence in cattle herds, taking possible spatial correlation into account. We established that infected herds are spatially correlated (the scale of spatial correlation is presented), but at a scale that varies with time and in different areas. Spatial correlation persists following proactive badger removal.

Estimating the extent of spatial association of Mycobacterium bovis infection in badgers in Ireland

Mon, 01 Feb 2010 00:00:00 GMT

Estimating the extent of spatial association of Mycobacterium bovis infection in badgers in Ireland Kelly, Gabrielle E.; McGrath, Guy; More, Simon John Mycobacterium bovis infects the wildlife species badgers Meles meles who are linked with the spread of the associated disease tuberculosis (TB) in cattle. Control of livestock infections depends in part on the spatial and social structure of the wildlife host. Here we describe spatial association of M. bovis infection in a badger population using data from the first year of the Four Area Project in Ireland. Using second-order intensity functions, we show there is strong evidence of clustering of TB cases in each the four areas, i.e. a global tendency for infected cases to occur near other infected cases. Using estimated intensity functions, we identify locations where particular strains of TB cluster. Generalized linear geostatistical models are used to assess the practical range at which spatial correlation occurs and is found to exceed 6 in all areas. The study is of relevance concerning the scale of localized badger culling in the control of the disease in cattle.

Spatio-Temporal Modelling of TB in Cattle Herds

Wed, 01 Aug 2012 00:00:00 GMT

Spatio-Temporal Modelling of TB in Cattle Herds Kelly, Gabrielle E. We examine spatial association of bovine TB in cattle herds using data from Ireland. Badgers (Meles meles), a protected species under the Wildlife Act 1976 (OAG 2012), have been implicated in the spread of the disease in cattle. Current disease control policies include reactive culling (in response to TB outbreaks) of badgers in the index and neighbouring farms. Kelly and More (2011) using generalized linear geostatistical models, established that TB clusters in cattle herds and estimated the practical spatial ranges at which this occurs. Here this work is extended by taking into account possible anisotropy. Changes in spatial association over two time periods are also examined. The results have direct implications for establishing scale and direction in reactive culling. They are also of import regarding the evaluation of vaccines for badgers and cattle.

Towards selective catalytic oxidations using in-situ generated H2O2

Fri, 29 Mar 2013 00:00:00 GMT

Towards selective catalytic oxidations using in-situ generated H2O2 Sullivan, James A.; O'Callaghan, Niamh A series of Ti-modified mesoporous SiO2 materials (SBA-15 and MCF) are prepared, characterised and used as catalysts in the selective epoxidation of a probe alkene (cyclohexene) using H2O2 as an oxidising agent. Similarly, a series of mesoporous SiO2-supported monometallic and bimetallic DMAP-stabilized Au and Pd nanoparticles were prepared, characterised and used as catalysts in the production of H2O2 from dilute H2(g) + O2(g) mixtures.The metallic nanoparticles were then supported on the Ti-modified mesoporous SiO2 and these hybrid materials were characterised and their activities in the selective epoxidation of alkenes in the presence of H2 (g) + O2 (g) mixtures (where H2O2 would be formed in situ) were studied. The bimetallic Au / Pd nanoparticles (which were most active in the production of H2O2 from H2 and O2) were not the most active or selective in the combined reaction. This was ascribed to the Pd component of the nanoparticles promoting hydrogenation of the probe alkene more rapidly than the formation of H2O2. The selectivity of Au nanoparticles in the presence of H2(g) + O2(g) was higher than that of the same catalysts in the presence of H2O2(aq).

Rare earth (La, Nd, Pr) doped ceria zirconia solid solutions for soot combustion

Fri, 01 Feb 2013 00:00:00 GMT

Rare earth (La, Nd, Pr) doped ceria zirconia solid solutions for soot combustion Dulgheru, Petrica; Sullivan, James A. A series of rare earth (RE) (La, Nd, Pr) ceria zirconia materials were analysed for their soot combustion activity in air and in NO/O2. The materials were characterised using DRIFT spectroscopy. In general the presence of the RE dopant increases the activity of undoped CexZr1-xO2. The La and Pr doped catalysts showed increased low temperature activity in the presence of NO/O2 while the effect was less pronounced in case of Nd - doped samples. FTIR data has shown that the catalysts interact differently to NO/O2 mixtures in that they do not form significant quantities of adsorbed nitrite-type species. We postulate that this species is a precursor to NO2 formation which in turn increases soot combustion.

Influence of Surface Groups on Poly(propylene imine) Dendrimers Antiprion Activity

Wed, 12 Dec 2012 00:00:00 GMT

Influence of Surface Groups on Poly(propylene imine) Dendrimers Antiprion Activity McCarthy, James M.; Moreno, Beatriz Rasines; Filippini, Damien; Komber, Hartmut; Maly, Marek; Cernescu, Michaela; Brutschy, Bernhard; Appelhans, Dietmar; Rogers, Mark S. Prion diseases are characterized by the accumulation of PrP(Sc), an aberrantly folded isoform of the host protein PrP(C). Specific forms of synthetic molecules known as dendrimers are able to eliminate protease-resistant PrP(Sc) in both an intracellular and in vitro setting. The properties of a dendrimer which govern this ability are unknown. We addressed the issue by comparing the in vitro antiprion ability of numerous modified poly(propylene-imine) dendrimers, which varied in size, structure, charge, and surface group composition. Several of the modified dendrimers, including an anionic glycodendrimer, reduced the level of protease resistant PrP(Sc) in a prion strain-dependent manner. This led to the formulation of a new working model for dendrimer/prion interactions which proposes dendrimers eliminate PrP(Sc) by destabilizing the protein and rendering it susceptible to proteolysis. This ability is not dependent on any particular charge of dendrimer, but does require a high density of reactive surface groups.

Influence of surface functionality of poly(propylene imine) dendrimers on protease resistance and propagation of the scrapie prion protein

Tue, 20 Apr 2010 00:00:00 GMT

Influence of surface functionality of poly(propylene imine) dendrimers on protease resistance and propagation of the scrapie prion protein Fischer, Marlies; Appelhans, Dietmar; Schwarz, Simona; Klajnert, Barbara; Bryszewska, Maria; Voit, Brigitte; Rogers, Mark S. Accumulation of PrP(Sc), an insoluble and protease-resistant pathogenic isoform of the cellular prion protein (PrP(C)), is a hallmark in prion diseases. Branched polyamines, including PPI (poly(propylene imine)) dendrimers, are able to remove protease resistant PrP(Sc) and abolish infectivity, offering possible applications for therapy. These dendrimer types are thought to act through their positively charged amino surface groups. In the present study, the molecular basis of the antiprion activity of dendrimers was further investigated, employing modified PPI dendrimers in which the positively charged amino surface groups were substituted with neutral carbohydrate units of maltose (mPPI) or maltotriose (m3PPI). Modification of surface groups greatly reduced the toxicity associated with unmodified PPI but did not abolish its antiprion activity, suggesting that the presence of cationic surface groups is not essential for dendrimer action. PPI and mPPI dendrimers of generation 5 were equally effective in reducing levels of protease-resistant PrP(Sc) (PrP(res)) in a dose- and time-dependent manner in ScN2a cells and in pre-existing aggregates in homogenates from infected brain. Solubility assays revealed that total levels of PrP(Sc) in scrapie-infected mouse neuroblastoma (ScN2a) cells were reduced by mPPI. Coupled with the known ability of polyamino dendrimers to render protease-resistant PrP(Sc) in pre-existing aggregates of PrP(Sc) susceptible to proteolysis, these findings strongly suggest that within infected cells dendrimers reduce total amounts of PrP(Sc) by mediating its denaturation and subsequent elimination.

Differentiating prion strains using dendrimers

Thu, 01 Nov 2012 00:00:00 GMT

Differentiating prion strains using dendrimers McCarthy, James M.; Rasines, Beatriz; Appelhans, Dietmar; Rogers, Mark S. A panel of repetitively branched synthetic molecules known as dendrimers is used to identify and differentiate between different strains of the prion infectious agent, the protein-based pathogen responsible for prion disorders—a group of invariably fatal neurodegenerative diseases

The nature of surface deposits following valeric acid interactions with Al2O3-supported Alkaline Earth Oxide catalysts: Towards cellulosic biofuels

Mon, 01 Apr 2013 00:00:00 GMT

The nature of surface deposits following valeric acid interactions with Al2O3-supported Alkaline Earth Oxide catalysts: Towards cellulosic biofuels Sullivan, James A.; Sherry, Linda Two Al2O3-supported alkaline earth metal oxide catalysts (MgO and BaO) were contacted with valeric acid at 250 °C. Each formed amounts of 5-nonanone (BaO more than MgO). A significant deposition of hydrocarbonaceous material onto the catalyst surface is noted. This adsorbed material is characterised using TGA and FTIR and relates to a carboxylate species.

The Preparation of Group II Oxide Catalysts Through Acetate Calcination: The Influence of a Support on the Nature of the Final Catalyst.

Fri, 01 Mar 2013 00:00:00 GMT

The Preparation of Group II Oxide Catalysts Through Acetate Calcination: The Influence of a Support on the Nature of the Final Catalyst. Sullivan, James A.; Sherry, Linda The preparation of supported and unsupported group II oxide catalysts through oxidation of analogous group II acetates (Mg, Ca and Ba) in the presence and absence of a mesoporous silica material (SBA-15) was analysed using TGA. In the absence of the mesoporous support the acetates oxidised at different temperatures with a stability trend whereby Mg

Anti-prion drug mPPIg5 inhibits PrPC conversion to PrPSc

Mon, 28 Jan 2013 00:00:00 GMT

Anti-prion drug mPPIg5 inhibits PrPC conversion to PrPSc McCarthy, James M.; Franke, Markus; Resenberger, Ulrike K.; Waldron, Sibeal; Simpson, Jeremy C.; Tatzelt, Jörg; Appelhans, Dietmar; Rogers, Mark S. Prion diseases, also known as transmissible spongiform encephalopathies, are a group of fatal neurodegenerative diseases that include scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle and Creutzfeldt-Jakob disease (CJD) in humans. The 'protein only hypothesis' advocates that PrPSc, an abnormal isoform of the cellular protein PrPC, is the main and possibly sole component of prion infectious agents. Currently, no effective therapy exists for these diseases at the symptomatic phase for either humans or animals, though a number of compounds have demonstrated the ability to eliminate PrPSc in cell culture models. Of particular interest are synthetic polymers known as dendrimers which possess the unique ability to eliminate PrPSc in both an intracellular and in vitro setting. The efficacy and mode of action of the novel anti-prion dendrimer mPPIg5 was investigated through the creation of a number of innovative bio-assays based upon the scrapie cell assay. These assays were used to demonstrate that mPPIg5 is a highly effective anti-prion drug which acts, at least in part, through the inhibition of PrPC to PrPSc conversion. Understanding how a drug works is a vital component in maximising its performance. By establishing the efficacy and method of action of mPPIg5, this study will help determine which drugs are most likely to enhance this effect and also aid the design of dendrimers with anti-prion capabilities for the future.

Direct shape control of photoreduced nanostructures on proton exchanged ferroelectric templates

Thu, 31 Jan 2013 00:00:00 GMT

Direct shape control of photoreduced nanostructures on proton exchanged ferroelectric templates Balobaid, Laila; Craig Carville, N.; Manzo, Michele; Gallo, Katia; Rodriguez, Brian J. Photoreduction on a periodically proton exchanged ferroelectric crystal leads to the formation of periodic metallic nanostructures on the surface. By varying the depth of the proton exchange (PE) from 0.59 to 3.10 µm in congruent lithium niobate crystals, the width of the lateral diffusion region formed by protons diffusing under the mask layer, can be controlled. The resulting deposition occurs in the PE region with the shallowest PE depth, and preferentially in the lateral diffusion region for greater PE depths. PE depth-control provides a route for the fabrication of complex metallic nanostructures with controlled dimensions on chemically patterned ferroelectric templates.

Photoreduction of SERS-active metallic nanostructures on chemically-patterned ferroelectric crystals

Tue, 28 Aug 2012 00:00:00 GMT

Photoreduction of SERS-active metallic nanostructures on chemically-patterned ferroelectric crystals Craig Carville, N.; Manzo, Michele; Damm, Signe; Castiella, Marion; Collins, Liam; Denning, Denise; Weber, Stefan A. L.; Gallo, Katia; Rice, James H.; Rodriguez, Brian J. Photodeposition of metallic nanostructures onto ferroelectric surfaces is typically based on patterning local surface reactivity via electric field poling. Here, we demonstrate metal deposition onto substrates which have been chemically patterned via proton exchange (i.e., without polarization reversal). The chemical patterning provides the ability to tailor the electrostatic fields near the surface of lithium niobate crystals and these engineered fields are used to fabricate metallic nanostructures. The effect of the proton exchange process on the piezoelectric and electrostatic properties of the surface is characterized using voltage modulated atomic force microscopy techniques, which combined with modeling of the electric fields at the surface of the crystal, reveal that the deposition occurs preferentially along the boundary between ferroelectric and proton exchanged regions. The metallic nanostructures have been further functionalized with a target probe molecule, 4-aminothiophenol, from which surface enhanced Raman scattering (SERS) signal is detected, demonstrating the suitability of chemically patterned ferroelectrics as SERS-active templates.

Production of anticancer polyenes through precursor-directed biosynthesis

Thu, 01 Sep 2011 00:00:00 GMT

Production of anticancer polyenes through precursor-directed biosynthesis Clark, Benjamin R.; O'Connor, Stephen; Fox, Deirdre; Leroy, Jacques; Murphy, Cormac D. The biosynthesis of the pyrrolyl moiety of the fungal metabolite rumbrin originates from pyrrole-2-carboxylic acid. In an effort to produce novel derivatives with enhanced biological activity a series of substituted pyrrole-2-carboxylates were synthesised and incubated with the producing organism, Auxarthron umbrinum. Several 4-halo-pyrrole-2-carboxylic acids were incorporated into the metabolite yielding three new derivatives: 3-fluoro-, 3-chloro- and 3-bromo-isorumbrin, which were generated in milligram quantities enabling cytotoxicity assays to be conducted. The 3-chloro- and 3-bromo-isorumbrins had improved activity against HeLa cells compared with rumbrin; 3-bromoisorumbrin also showed dramatically improved activity towards a lung cancer cell line (A549).