Determination of urinary nucleosides by direct injection and coupled-column high-performance liquid chromatography

A coupled-column liquid chromatographic method for the direct analysis of 14 urinary nucleosides is described. Efficient on-line clean-up and concentration of 14 nucleosides from urine samples were obtained by using a boronic acid-substituted silica column (40 turn x 4.0 mm I.D.) as the first column (Col-1) and a Hypersil ODS2 column (250 mm x 4.6 mm I.D.) as the second column (Col-2). The mobile phases applied consisted of 0.25 mol/L ammonium acetate (pH 8.5) on Col-1, and of 25 mmol/L potassium dihydrogen phosphate (pH 4.5) on Col-2, respectively. Determination of urinary nucleosides was performed on Col-2 column by using a linear gradient elution comprising 25 mmol/L potassium dihydrogen phosphate (pH 4.5) and methanol-water (60:40, v/v) with UV detection at 260 nm. Urinary nucleosides analysis can be carried out by this procedure in 50 min requiring only pH adjustment and the protein precipitation by centrifugation of urine samples. Calibration plots of 14 standard nucleosides showed excellent linearity (r > 0.995) and the limits of detection were at micromolar levels. Both of intra- and inter-day precisions of the method were better than 6.6% for direct determination of 14 nucleosides. The validated method was applied to quantify 14 nucleosides in 20 normal urines to establish reference ranges. (c) 2005 Elsevier B.V. All rights reserved.

Quantitative determination of compounds in tobacco essential oils by comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry

A quantitative analysis of the individual compounds in tobacco essential oils is performed by comprehensive two-dimensional gas chromatography (GC x GC) combined with flame ionization detector (FID). A time-of-flight mass spectrometer (TOF/MS) was coupled to GC x GC for the identification of the resolved peaks. The response of a flame ionization detector to different compound classes was calibrated using multiple internal standards. In total, 172 compounds were identified with good match and 61 compounds with high probability value were reliably quantified. For comparative purposes, the essential oil sample was also quantified by one-dimensional gas chromatography-mass spectrometry (GC/MS) with multiple internal standards method. The results showed that there was close agreement between the two analysis methods when the peak purity and match quality in one-dimensional GC/MS are high enough. (c) 2005 Elsevier B.V. All rights reserved.

Cluster-assistant generation of multiply charged atomic ions in nanosecond laser ionization of seeded methyl iodide beam

The photoionization of methyl iodide beam seeded in argon and helium is studied by time-of-flight mass spectrometry using a 25 ns, 532 nm Nd-YAG laser with intensities in the range of 2 x 10(10)-2 x 10(11) W/cm(2). Multiply charged ions Of Iq+ (q = 2-3) and C2+ with tens of eV kinetic energies have been observed when laser interacts with the middle part of the pulsed molecular beam, whose peak profiles are independent on the laser polarization directions. Strong evidences show that these ions are coming from the Coulomb explosion of multiply charged CH3I clusters, and laser induced inverse bremsstrahlung absorption of caged electrons plays a key role in the formation of multiply charged ions. (C) 2004 Elsevier B.V. All rights reserved.

Cluster-assisted multiple ionization of xenon and krypton by a nanosecond laser

Multicharged xenon and krypton ions with charge states up to Xe11+ and Kr11+ have been observed in laser ionization of a pulsed xenon or krypton beam by a 25 ns Nd-YAG laser with laser intensity of 10(10)-10(11) W cm(-2) at 532 nm. There is strong evidence to support that those multicharged ions come from cluster-assisted electron recolliding ionizations inside the cluster after multiphoton ionization of atoms in the cluster, the electron can gain its kinetic energy by inverse bremsstrahlung absorption from a laser field quickly.

Interface of chip-based capillary electrophoresis-inductively coupled plasma-atomic emission spectrometry (CE-ICP-AES)

An interface of chip-based capillary electrophoresis (CE)-inductively coupled plasma-atomic emission spectrometry (ICP-AES) that is based on cross-flow nebulization has been developed. A polydimethylsiloxane (PDMS) CE-chip with conventional cross channel layout was used. A stainless steel tube was placed orthogonal to the exit of the CE separation channel for cross flow nebulization. A supplementary flow of buffer solution at the channel exit was used to improve nebulization efficiency. Two capillaries were inserted into the CE chip near the inlet of the separation channel for sample and buffer solution injection. Syringe pumps were used to manipulate the flow rate and flow direction of the sample, buffer, and supplementary buffer solution. Peak broadening due to the shape (bulb and tube-shaped) and size of the spray chambers was studied. The smaller tube-shaped spray chamber was used because of smaller peak broadening effect due to aerosol transport. The nebulization and transport efficiency of the CE-ICP interface was approximately 10%. Ba2+ and Mg2+ ions were eluted from the CE-chip within 30 s. Resolution of the Ba2+ and Mg2+ peaks was 0.7 using the chip-based CE-ICP-AES system.

Data analysis with artificial immune systems, cluster analysis and kohonen networks: some comparisons.

Neal M J Timmis J and Hunt J. Data analysis with artificial immune systems, cluster analysis and kohonen networks: some comparisons. In Proceedings of IEEE international conference of systems, man and cybernetics, pages 922-927, Tokyo, 1999. IEEE.

Topological changes in a two-dimensional foam cluster

Cox, S.J., Vaz, M.F. and Weaire, D. (2003) Topological changes in a two-dimensional foam cluster. The European Physical Journal E - Soft Matter . 11:29-35.

ROMA: Reliable Overlay Multicast with Loosely Coupled TCP Connections

We consider the problem of architecting a reliable content delivery system across an overlay network using TCP connections as the transport primitive. We first argue that natural designs based on store-and-forward principles that tightly couple TCP connections at intermediate end-systems impose fundamental performance limitations, such as dragging down all transfer rates in the system to the rate of the slowest receiver. In contrast, the ROMA architecture we propose incorporates the use of loosely coupled TCP connections together with fast forward error correction techniques to deliver a scalable solution that better accommodates a set of heterogeneous receivers. The methods we develop establish chains of TCP connections, whose expected performance we analyze through equation-based methods. We validate our analytical findings and evaluate the performance of our ROMA architecture using a prototype implementation via extensive Internet experimentation across the PlanetLab distributed testbed.

Cluster-Based Optimizations for Distributed Hash Tables

We consider the problem of performing topological optimizations of distributed hash tables. Such hash tables include Chord and Tapestry and are a popular building block for distributed applications. Optimizing topologies over one dimensional hash spaces is particularly difficult as the higher dimensionality of the underlying network makes close fits unlikely. Instead, current schemes are limited to heuristically performing local optimizations finding the best of small random set of peers. We propose a new class of topology optimizations based on the existence of clusters of close overlay members within the underlying network. By constructing additional overlays for each cluster, a significant portion of the search procedure can be performed within the local cluster with a corresponding reduction in the search time. Finally, we discuss the effects of these additional overlays on spatial locality and other load balancing scheme.

Load Balancing a Cluster of Web Servers using Distributed Packet Rewriting

In this paper, we propose and evaluate an implementation of a prototype scalable web server. The prototype consists of a load-balanced cluster of hosts that collectively accept and service TCP connections. The host IP addresses are advertised using the Round Robin DNS technique, allowing any host to receive requests from any client. Once a client attempts to establish a TCP connection with one of the hosts, a decision is made as to whether or not the connection should be redirected to a different host---namely, the host with the lowest number of established connections. We use the low-overhead Distributed Packet Rewriting (DPR) technique to redirect TCP connections. In our prototype, each host keeps information about connections in hash tables and linked lists. Every time a packet arrives, it is examined to see if it has to be redirected or not. Load information is maintained using periodic broadcasts amongst the cluster hosts.

Explorations in a meaning making system: Kerry as an entrepreneurial platform and the equine sector as a cluster

This Portfolio is about the changes that can be supported and achieved through transformational education that impacts on personal, professional and organisational levels. Having lived through an era of tremendous change over the second half of the twentieth century and into the twenty-first the author has a great drawing board to contemplate in the context of professional career experience as an engineer. The ability to engage in ‘subject-object’ separation is the means by which Kegan (1994, 2009) explains that transformation takes place and the Essays in this Portfolio aim to support and bring about such change. Exploration of aspects of ‘Kerry’ is the material selected to both challenge support change in the way of knowing from being subject to certain information and knowledge that to being able to consider it more objectively. The task of being able to distance judgement about the economy and economic development of Kerry was facilitated by various readings around of a number of key thinkers including Kegan, Drucker, Porter and Penrose. The central themes of Kerry or the potential for economic development are built into each Essay. Essay One focuses on reflections of Kerry life - on Kerry people within and without Kerry - and events as they affected understandings of how people related to and worked with one another. These reflections formed the basis for transformational goals identified which required a shift from an engineering mindset to encompass an economics-based view. In Essay Two knowledge of economic concepts is developed by exploring the writings of Drucker, Penrose, and Porter with pertinence to considering economic development generally, and for Kerry in particular in the form of an ‘entrepreneurial platform’. The concepts and theories were the basis of explorations presented in Essays Three and Four. Essay Three focuses on Kerry’s potential for economic development give its current economic profile and includes results from interviews with selected businesses. Essay Four is an exercise in the application of Porter’s ‘Cluster’ concept to the equine sector.

Hybrid integration and packaging of grating-coupled silicon photonics

This thesis covers both the packaging of silicon photonic devices with fiber inputs and outputs as well as the integration of laser light sources with these same devices. The principal challenge in both of these pursuits is coupling light into the submicrometer waveguides that are the hallmark of silicon-on-insulator (SOI) systems. Previous work on grating couplers is leveraged to design new approaches to bridge the gap between the highly-integrated domain of silicon, the Interconnected world of fiber and the active region of III-V materials. First, a novel process for the planar packaging of grating couplers with fibers is explored in detail. This technology allows the creation of easy-to-use test platforms for laser integration and also stands on its own merits as an enabling technology for next-generation silicon photonics systems. The alignment tolerances of this process are shown to be well-suited to a passive alignment process and for wafer-scale assembly. Furthermore, this technology has already been used to package demonstrators for research partners and is included in the offerings of the ePIXfab silicon photonics foundry and as a design kit for PhoeniX Software’s MaskEngineer product. After this, a process for hybridly integrating a discrete edge-emitting laser with a silicon photonic circuit using near-vertical coupling is developed and characterized. The details of the various steps of the design process are given, including mechanical, thermal, optical and electrical steps. The interrelation of these design domains is also discussed. The construction process for a demonstrator is outlined, and measurements are presented of a series of single-wavelength Fabry-Pérot lasers along with a two-section laser tunable in the telecommunications C-band. The suitability and potential of this technology for mass manufacture is demonstrated, with further opportunities for improvement detailed and discussed in the conclusion.

Investigation of the genetic susceptibility to osteoporosis in the Irish population

Osteoporosis is a complex skeletal disorder characterized by compromised bone strength. Variation in bone mineral density (BMD) is a contributing factor. The aim of this research as to select informative single nucleotide polymorphisms (SNPs) in potential candidate genes from loci suggestively linked to BMD variation for fine mapping. The gene regulated by oestrogen in breast cancer 1 (GREB1), located at 2p25.1, was selected. GREB1 transcription is initiated early in the oestrogen receptor alpha regulated pathway. There was significant association between GREB1_03 and BMD variation at the lumbar spine and femoral neck (FN) in the discovery cohort. Significant association was observed between GREB1_04 and FN BMD in the replication cohort. The development and differentiation enhancing factor 2, the integrin cytoplasmic domain associated protein 1 and A-disintegrin and metalloprotease 17 were selected due to their respective roles in cell mobility and adhesion. There was no linkage or association observed between the Chr2 cluster SNPs and BMD. Two factors in bone remodelling are the attraction of bone cell precursors and endocrine regulation of the process, primarily through the action of parathyroid hormone (PTH). The C-C chemokine receptor type 3 (CCR3) encodes a CC chemokine receptor expressed in osteoclast precursors. The PTH receptor type 1 (PTHR1) encodes a G-protein coupled receptor for PTH. Association was observed between CCR3 haplotypes and BMD variation at the FN. There was no linkage or association observed between PTHR1 SNPs and BMD variation. Population genetic studies with complex phenotypes endeavour to elucidate the traits genetic architecture. This study presents evidence of association between GREB1 and BMD variation and as such, introduces GREB1 as a novel gene target for osteoporosis genetics studies. It affirms that common genomic variants in PTHR1 are not associated with BMD variation in Caucasians and supports the evidence that CCR3 may be contributing to BMD variation

Development of low-cost sensing and separation devices based on macro, micro and nano technology for health applications

The work presented in this thesis described the development of low-cost sensing and separation devices with electrochemical detections for health applications. This research employs macro, micro and nano technology. The first sensing device developed was a tonerbased micro-device. The initial development of microfluidic devices was based on glass or quartz devices that are often expensive to fabricate; however, the introduction of new types of materials, such as plastics, offered a new way for fast prototyping and the development of disposable devices. One such microfluidic device is based on the lamination of laser-printed polyester films using a computer, printer and laminator. The resulting toner-based microchips demonstrated a potential viability for chemical assays, coupled with several detection methods, particularly Chip-Electrophoresis-Chemiluminescence (CE-CL) detection which has never been reported in the literature. Following on from the toner-based microchip, a three-electrode micro-configuration was developed on acetate substrate. This is the first time that a micro-electrode configuration made from gold; silver and platinum have been fabricated onto acetate by means of patterning and deposition techniques using the central fabrication facilities in Tyndall National Institute. These electrodes have been designed to facilitate the integration of a 3- electrode configuration as part of the fabrication process. Since the electrodes are on acetate the dicing step can automatically be eliminated. The stability of these sensors has been investigated using electrochemical techniques with excellent outcomes. Following on from the generalised testing of the electrodes these sensors were then coupled with capillary electrophoresis. The final sensing devices were on a macro scale and involved the modifications of screenprinted electrodes. Screen-printed electrodes (SPE) are generally seen to be far less sensitive than the more expensive electrodes including the gold, boron-doped diamond and glassy carbon electrodes. To enhance the sensitivity of these electrodes they were treated with metal nano-particles, gold and palladium. Following on from this, another modification was introduced. The carbonaceous material carbon monolith was drop-cast onto the SPE and then the metal nano-particles were electrodeposited onto the monolith material