Monolithic optical gates based on integration of evanescently-coupled uni-traveling-carrier photodiodes and electroabsorption modulators

We report on chip-scale optical gates based on the integration of evanescent waveguide unitraveling-carrier photodiodes (EC-UTC-PDs) and intra-step quantum well electroabsorption modulators (IQW-EAMs) on n-InP substrates. These devices exhibit simultaneously 2.1 GHz and -16.2 dB RF-gain at 21 GHz with a 450 Omega thin-film resistor and a bypass capacitor integrated on a chip.

A Novel Optical Gate by Integration of a Photodiode and an Electroabsorption Modulator

A compact and stable three-port optical gate has been successfully fabricated by monolithically integrating asimple photodiode and an electroabsorption modulator. The gate shows an excellent DC logic "and" function with differ-ent load resistors. Its dynamical characteristics without packaging have also been measured. We observed a dynamic extinc-tion ratio of over 7dB with a 950Ω load resistor and a 7mW control light power at 622Mbit/s.

Integration of genomic and phenotypic data

Clare, A. (2005) Integration of genomic and phenotypic data. In Data Analysis and Visualization in Genomics and Proteomics, Eds. Francisco Azuaje and Joaquin Dopazo, Wiley, London. ISBN: 0-470-09439-7

Grid integration of wave energy & generic modelling of ocean devices for power system studies

The work presented in this thesis covers four major topics of research related to the grid integration of wave energy. More specifically, the grid impact of a wave farm on the power quality of its local network is investigated. Two estimation methods were developed regarding the flicker level Pst generated by a wave farm in relation to its rated power as well as in relation to the impedance angle ψk of the node in the grid to which it is connected. The electrical design of a typical wave farm design is also studied in terms of minimum rating for three types of costly pieces of equipment, namely the VAr compensator, the submarine cables and the overhead line. The power losses dissipated within the farm's electrical network are also evaluated. The feasibility of transforming a test site into a commercial site of greater rated power is investigated from the perspective of power quality and of cables and overhead line thermal loading. Finally, the generic modelling of ocean devices, referring here to both wave and tidal current devices, is investigated.

Integration of micro- and macroscopic models for pedestrian evacuation simulation

Simulation of pedestrian evacuations of smart buildings in emergency is a powerful tool for building analysis, dynamic evacuation planning and real-time response to the evolving state of evacuations. Macroscopic pedestrian models are low-complexity models that are and well suited to algorithmic analysis and planning, but are quite abstract. Microscopic simulation models allow for a high level of simulation detail but can be computationally intensive. By combining micro- and macro- models we can use each to overcome the shortcomings of the other and enable new capability and applications for pedestrian evacuation simulation that would not be possible with either alone. We develop the EvacSim multi-agent pedestrian simulator and procedurally generate macroscopic flow graph models of building space, integrating micro- and macroscopic approaches to simulation of the same emergency space. By “coupling” flow graph parameters to microscopic simulation results, the graph model captures some of the higher detail and fidelity of the complex microscopic simulation model. The coupled flow graph is used for analysis and prediction of the movement of pedestrians in the microscopic simulation, and investigate the performance of dynamic evacuation planning in simulated emergencies using a variety of strategies for allocation of macroscopic evacuation routes to microscopic pedestrian agents. The predictive capability of the coupled flow graph is exploited for the decomposition of microscopic simulation space into multiple future states in a scalable manner. By simulating multiple future states of the emergency in short time frames, this enables sensing strategy based on simulation scenario pattern matching which we show to achieve fast scenario matching, enabling rich, real-time feedback in emergencies in buildings with meagre sensing capabilities.

Time use, daily activities, and health-related quality of life of school-going late adolescents in Cork city and county: A cross-sectional study

Aim: This thesis examines a question posed by founding occupational scientist Dr. Elizabeth Yerxa (1993) – “what is the relationship between human engagement in a daily round of activity (such as work, play, rest and sleep) and the quality of life people experience including their healthfulness” (p. 3). Specifically, I consider Yerxa’s question in relation to the quotidian activities and health-related quality of life (HRQoL) of late adolescents (aged 15 - 19 years) in Ireland. This research enquiry was informed by an occupational perspective of health and by population health, ecological, and positive youth development perspectives. Methods: This thesis is comprised of five studies. Two scoping literature reviews informed the direction of three empirical studies. In the latter, cross-sectional time use and HRQoL data were collected from a representative sample of 731 school-going late adolescents (response rate 52%) across 28 schools across Cork city and county (response rate 76%). In addition to socio-demographic data, time use data were collected using a standard time diary instrument while a nationally and internationally validated instrument, the KIDSCREEN-52, was used to measure HRQoL. Variable-centred and person-centred analyses were used. Results: The scoping reviews identified the lack of research on well populations or an adolescent age range within occupational therapy and occupational science; limited research testing the popular assumption that time use is related to overall well-being and quality of life; and the absence of studies that examined adolescent 24-hour time use and quality of life. Established international trends were mirrored in the findings of the examination of weekday and weekend time use. Aggregate-level, variable-centred analyses yielded some significant associations between HRQoL and individual activities, independent of school year, school location, family context, social class, nationality or diary day. The person-centred analysis of overall time use identified three male profiles (productive, high leisure and all-rounder) and two female profiles (higher study/lower leisure and moderate study/higher leisure). There was tentative support for the association between higher HRQoL and more balanced time use profiles. Conclusion: The findings of this thesis highlight the gendered nature of adolescent time use and HRQoL. Participation in daily activities, singly and in combination, appears to be associated with HRQoL. However, the nature of this relationship is complex. Individually and collectively, adolescents need to be educated and supported to create health through their everyday patterns of doing.

Cancer associated malnutrition: prevalence of cachexia, sarcopenia and impact on treatment outcomes, survival and health related quality of life

Malnutrition, sarcopenia and cancer cachexia (CC) are prevalent among cancer patients and can have detrimental effects on clinical outcomes such as quality of life (QoL) and overall survival. Cachexia is associated with lower tolerance for chemotherapy, which limits the total dose that can be delivered, the number of symptomatic responses and any survival advantage that might be accrued. Moreover, for the majority who do not respond, cachexia may be exacerbated by systemic chemotherapy, thus increasing the net symptom burden experienced by patients. The multitude of interactions between cancer location, treatments, nutritional status and QoL has never been thoroughly explored in an Irish cancer cohort. The objectives of this thesis were to further understand nutritional status, especially body composition in ambulatory cancer patients and determine the relationship between nutritional status using different assessment criteria and QoL, chemotherapy toxicity and survival among cancer patients undergoing chemotherapy. Results aimed to identify baseline factors that may be predictive of poor outcome, toxicities to chemotherapy and disease-free and overall survival. This thesis broadly divides into two sections. The first section (Chapters 3 & 4) focuses on improving our knowledge of the nutritional status of Irish cancer outpatients using a cross sectional study design. A study of 517 patients referred for chemotherapy was conducted using computed tomography (CT) imaging (body composition) and a survey that documented oncologic data, weight loss (WL) data and QoL data. We revealed that a significant proportion of Irish cancer patients undergoing chemotherapy experience unintentional WL over the previous 6 months (62%), sarcopenia (45%) and CC (43%), and the distribution of WL and nutritional risk were associated with site of primary tumour and treatment intent. Patients that had sarcopenia, nutritional risk, or CC had significantly reduced functional abilities, more symptoms and adverse global QoL. In the second section of this thesis (Chapters 5 & 6) the potential link between developing toxicity to antineoplastic regimens in patients with sarcopenia was conducted by way of retrospective studies. A retrospective serial CT analysis defined the prevalence of sarcopenia in patients with metastatic renal cell carcinoma (mRCC) and metastatic castrate resistant prostate cancer (mCRPC), which was then correlated with dose limiting toxicities of sunitinib and docetaxel respectively. Sarcopenia was prevalent in patients with mRCC and mCRPC, was an occult condition in patients with normal/high BMI, was associated with less treatment days, was a significant predictor of DLT in patients receiving sunitinib and a significant predictor of neutropenia and neurosensory toxicities in patients receiving docetaxel. This thesis attempted to address the underlying research deficiencies in Irish oncology nutritional data at national level. The findings from this thesis have implications for the planning of cancer care interventions and indicate that further research is required to improve nutritional screening, in particular for CC and sarcopenia, in the hope that timely intervention can improve both patient-centered and oncologic outcomes.

When a trauma becomes a key to identity: Enhanced integration of trauma memories predicts posttraumatic stress disorder symptoms

The Centrality of Event Scale (CES) measures the extent to which a traumatic memory forms a central component of personnal identity, a turning point in the life story and a reference point for everyday inferences. In two studies, we show that the CES is positively correlated with severity of PTSD symptoms, even when controlling for measures of anxiety, depression, dissociation and self-consciousness. The findings contradict the widespread view that poor integration of the traumatic memory into one's life story is a main cause of PTSD symptoms. Instead, enhanced integration appears to be a key issue. Copyright © 2006 John Wiley & Sons, Ltd.

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged before the Cretaceous-Paleogene mass extinction event 66 million years ago instead of after. However, their interpretations of the fossil record and timetrees are incorrect.

Differential scanning calorimetry in life science: thermodynamics, stability, molecular recognition and application in drug design

All biological phenomena depend on molecular recognition, which is either intermolecular like in ligand binding to a macromolecule or intramolecular like in protein folding. As a result, understanding the relationship between the structure of proteins and the energetics of their stability and binding with others (bio)molecules is a very interesting point in biochemistry and biotechnology. It is essential to the engineering of stable proteins and to the structure-based design of pharmaceutical ligands. The parameter generally used to characterize the stability of a system (the folded and unfolded state of the protein for example) is the equilibrium constant (K) or the free energy (deltaG(o)), which is the sum of enthalpic (deltaH(o)) and entropic (deltaS(o)) terms. These parameters are temperature dependent through the heat capacity change (deltaCp). The thermodynamic parameters deltaH(o) and deltaCp can be derived from spectroscopic experiments, using the van't Hoff method, or measured directly using calorimetry. Along with isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC) is a powerful method, less described than ITC, for measuring directly the thermodynamic parameters which characterize biomolecules. In this article, we summarize the principal thermodynamics parameters, describe the DSC approach and review some systems to which it has been applied. DSC is much used for the study of the stability and the folding of biomolecules, but it can also be applied in order to understand biomolecular interactions and can thus be an interesting technique in the process of drug design.

The integration of an intelligent knowledge-based system into engineering software using the blackboard structure

Over recent years there has been an increase in the use of generic Computational Fluid Dynamics (CFD) software packages spread across various application fields. This has created the need for the integration of expertise into CFD software. Expertise can be integrated into CFD software in the form of an Intelligent Knowledge-Based System (IKBS). The advantages of integrating intelligence into generic engineering software are discussed with a special view to software engineering considerations. The software modelling cycle of a typical engineering problem is identified and the respective expertise and user control needed for each modelling phase is shown. The requirements of an IKBS for CFD software are discussed and compared to current practice. The blackboard software architecture is presented. This is shown to be appropriate for the integration of an IKBS into an engineering software package. This is demonstrated through the presentation of the prototype CFD software package FLOWES.

A design pattern for integration of business process management systems

A cross-domain workflow application may be constructed using a standard reference model such as the one by the Workflow Management Coalition (WfMC) [7] but the requirements for this type of application are inherently different from one organization to another. The existing models and systems built around them meet some but not all the requirements from all the organizations involved in a collaborative process. Furthermore the requirements change over time. This makes the applications difficult to develop and distribute. Service Oriented Architecture (SOA) based approaches such as the BPET (Business Process Execution Language) intend to provide a solution but fail to address the problems sufficiently, especially in the situations where the expectations and level of skills of the users (e.g. the participants of the processes) in different organisations are likely to be different. In this paper, we discuss a design pattern that provides a novel approach towards a solution. In the solution, business users can design the applications at a high level of abstraction: the use cases and user interactions; the designs are documented and used, together with the data and events captured later that represents the user interactions with the systems, to feed an intermediate component local to the users -the IFM (InterFace Mapper) -which bridges the gaps between the users and the systems. We discuss the main issues faced in the design and prototyping. The approach alleviates the need for re-programming with the APIs to any back-end service thus easing the development and distribution of the applications

Creating a suitable and successful solution for the integration of podcasting and vidcasting in a higher education e-learning environment

A small research project is currently taking place within a department of the University of Greenwich. The project involves using current technology (Apple’s xServe, iPhones, iPod touch, Podcast Producer application and some 3rd party capture software) with the intention to provide a solution for quick and simple podcasting. This paper also aims to investigate the use of podcasting to help promote and extend the e-learning provision within the school. In short this project aims to justify the use of podcasting as a teaching and learning tool to help enhance student learning while identifying the most appropriate manner to integrate podcasting within an e-learning environment.

Perspectives and Integration in SOLAS Science

Why a chapter on Perspectives and Integration in SOLAS Science in this book? SOLAS science by its nature deals with interactions that occur: across a wide spectrum of time and space scales, involve gases and particles, between the ocean and the atmosphere, across many disciplines including chemistry, biology, optics, physics, mathematics, computing, socio-economics and consequently interactions between many different scientists and across scientific generations. This chapter provides a guide through the remarkable diversity of cross-cutting approaches and tools in the gigantic puzzle of the SOLAS realm. Here we overview the existing prime components of atmospheric and oceanic observing systems, with the acquisition of ocean–atmosphere observables either from in situ or from satellites, the rich hierarchy of models to test our knowledge of Earth System functioning, and the tremendous efforts accomplished over the last decade within the COST Action 735 and SOLAS Integration project frameworks to understand, as best we can, the current physical and biogeochemical state of the atmosphere and ocean commons. A few SOLAS integrative studies illustrate the full meaning of interactions, paving the way for even tighter connections between thematic fields. Ultimately, SOLAS research will also develop with an enhanced consideration of societal demand while preserving fundamental research coherency.

Integration Of Strength and Process Modelling of Friction-Stir-Welded Fuselage Panels

In order to reduce potential uncertainties and conservatism in welded panel analysis procedures, understanding of the relationships between welding process parameters and static strength is required. The aim of this study is to determine and characterize the key process induced properties of advanced welding assembly methods on stiffened panel local buckling and collapse performance. To this end, an in-depth experimental and computational study of the static strength of a friction stir welded fuselage skin-stiffener panel subjected to compression loading has been undertaken. Four welding process effects, viz. the weld joint width, the width of the weld Heat Affected Zone, the strength of material within the weld Heat Affected Zone and the magnitude of welding induced residual stress, are investigated. A fractional factorial experiment design method (Taguchi) has been applied to identify the relative importance of each welding process effect and investigate effect interactions on both local skin buckling and crippling collapse performance. For the identified dominant welding process effects, parametric studies have been undertaken to identify critical welding process effect magnitudes and boundaries. The studies have shown that local skin buckling is principally influenced by the magnitude of welding induced residual stress and that the strength of material in the Heat Affected Zone and the magnitude of the welding induced residual stress have the greatest influence on crippling collapse behavior.


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