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University College Dublin - formally known as University College Dublin - National University of Ireland, Dublin is Ireland's largest, and the island of Ireland's second largest, university, with over 1,300 faculty and 17,000 undergraduate students. It is located in Dublin, the Irish capital. Wikipedia.


Hone D.W.E.,University College Dublin
Historical Biology | Year: 2012

A previously undescribed and near-complete specimen of the non-pterodactyloid pterosaur Rhamphorhynchus is briefly described. Although purchased in 1878 and held in a public collection in Dublin, Ireland ever since, this specimen has never been described and was not even mentioned in the literature until 2010. © 2012 Copyright Taylor and Francis Group, LLC.


De Vleeschouwer D.,Vrije Universiteit Brussel | Parnell A.C.,University College Dublin
Geology | Year: 2014

Dealing with uncertainties is inherent to the scientifi c process. In the process of building geologic time scales, the reported uncertainties are at least as important as the estimates of the numerical ages. Currently all time scales for the Devonian are based on conventional age-depth models, constructed by linear or cubic interpolation between different dated positions. Unfortunately, such models tend to produce overoptimistic confi dence intervals. In this study we apply Bayesian statistics to the Devonian time scale to better incorporate stratigraphic and radioisotopic uncertainty. This approach yields a Devonian time scale characterized by increasing uncertainty with growing stratigraphic distance from a radioisotopically dated sample. This feature is absent from The Geologic Time Scale 2012; therefore, that time scale is overoptimistic. We further constrain the obtained time scale by incorporating astrochronological duration estimates for the Givetian and Frasnian stages. The combination of radioisotopic dating and astrochronology results in a reduction of the uncertainty on the numerical age of the stage boundaries concerned by several million years. For example, we estimate the age of the Frasnian-Famennian boundary at 373.9 ± 1.4 Ma.© 2014 Geological Society of America.


Heckman J.J.,University of Chicago | Heckman J.J.,University College Dublin
Health Economics | Year: 2012

The developmental approach to the study of health promises to produce a deeper understanding of both prevention and remediation strategies. Understanding the dynamic mechanisms of causation is essential for devising wise policies. It is not enough to know that early-life conditions help shape later-life outcomes. We need to trace the effects of early-life outcomes on intermediate-life investments and environments to understand when and for what intervention can be effective. © 2011 John Wiley & Sons, Ltd.


Phillips A.D.,University College Dublin
Organometallic Chemistry | Year: 2014

This article covers the progress of β-diketiminates as supporting ligands in transition metal complexes from the seminal review published by Lappert et al. in 2002 to the middle of 2013.1 Due to the tremendous number of reports since 2002 involving this class of ligand, this review focuses on the early transition metals, with elements from groups 3 to 5. β-diketiminate ligands are sterically demanding and thus stabilise highly reactive metal environments engendering both low-coordinate and multiply-bonded motifs. Recent publications also demonstrate the utility of this ligand class to build early transition catalysts with unique and interesting reactivity. © The Royal Society of Chemistry 2014.


Obesity is now considered the new world epidemic. In an attempt to face this menace to public health, several treatments, apart from the traditional nutritional modification and oral medication, have been introduced, among them bariatric surgery and gut hormone-based treatments. The gastrointestinal (GI) tract is a powerful endocrine organ, releasing active peptides and influencing appetite and glycaemic control. Alteration of the GI tract, in ways that exaggerate the secretion and levels of the gut hormones, creates a new functional equilibrium that further contributes to weight loss. The purpose of this review is to explore the mechanisms that drive this gut hormone-derived body regulation, as well as the changes that occur to them after bariatric surgery. Close to that, leptin, a hormone secreted by adipose tissue will be analysed, as its pathways are closely related to those of the gut hormones. Gut hormones are strongly implicated in energy control, and various effects of bariatric surgery in weight loss are directly related to the alteration of the levels of these hormones. © 2012 Springer Science + Business Media, LLC.


Walsh C.A.,National Maternity Hospital | McAuliffe F.M.,University College Dublin
Ultrasound in Obstetrics and Gynecology | Year: 2012

ABSTRACT Objectives Selective fetoscopic laser photocoagulation (SFLP) is now the treatment of choice for twin-twin transfusion syndrome (TTTS). The incidence of recurrent TTTS following SFLP has been inconsistently reported across different studies.We performed a systematic review of TTTS recurrence following SFLP. Methods PubMed and MEDLINE online databases were searched for articles published between 2000 and August 2011, using combinations of the terms .twin-twin transfusion', .TTTS', .laser', .recur' and .outcome'. Citations identified in the primary search were screened for eligibility. Studies reporting outcomes from selective SFLP for TTTS in twin pregnancies, which addressed specifically the issue of TTTS recurrence, were included. The primary outcome was rate of TTTS recurrence. Secondary outcomes were therapeutic preference and fetal outcomes in cases of recurrent TTTS. Results The primary search identified 22 eligible studies that are included in this review (n=2447 twin pregnancies). Two studies included a minority of non-selective procedures. The published incidence of recurrent TTTS ranged from 0 to 16%. Clinical management was reported in 65.7% (71/108) cases, with repeat SFLP the most commonly performed secondary intervention. Only three studies provided comprehensive outcome data for cases of recurrent TTTS. The overall rate of neurologically-intact survival was 44% (23/52). The data were inadequate to determine the effects of secondary therapeutic approach, placental location or gestational age on perinatal outcome in cases of recurrent TTTS. Conclusions The published rate of TTTS recurrence following SFLP in monochorionic twin pregnancies ranges from 0 to 16%. Although limited follow-up data suggest that recurrence is associated with significant perinatalmortality and morbidity, further study is needed. Currently, there are insufficient data available to guide recommendations for clinical management of TTTS recurrence. Future studies on SFLP for TTTS must include details on recurrence rates and provide outcome data specific to the recurrent subset. Copyright ©2012 ISUOG. Published by John Wiley & Sons, Ltd.


Miras A.D.,Imperial College London | Le Roux C.W.,University College Dublin
International Journal of Obesity | Year: 2014

The number of bariatric surgical procedures performed has increased dramatically. This review discusses the clinical and physiological changes, and in particular, the mechanisms behind weight loss and glycaemic improvements, observed following the gastric bypass, sleeve gastrectomy and gastric banding bariatric procedures. The review then examines how close we are to mimicking the clinical or physiological effects of surgery through less invasive and safer modern interventions that are currently available for clinical use. These include dietary interventions, orlistat, lorcaserin, phentermine/topiramate, glucagon-like peptide-1 receptor agonists, dipeptidyl peptidase-4 inhibitors, pramlintide, dapagliflozin, the duodenal-jejunal bypass liner, gastric pacemakers and gastric balloons. We conclude that, based on the most recent trials, we cannot fully mimic the clinical or physiological effects of surgery; however, we are getting closer. A 'medical bypass' may not be as far in the future as we previously thought, as the physician's armamentarium against obesity and type 2 diabetes has recently got stronger through the use of specific dietary modifications, novel medical devices and pharmacotherapy. Novel therapeutic targets include not only appetite but also taste/food preferences, energy expenditure, gut microbiota, bile acid signalling, inflammation, preservation of β-cell function and hepatic glucose output, among others. Although there are no magic bullets, an integrated multimodal approach may yield success. Non-surgical interventions that mimic the metabolic benefits of bariatric surgery, with a reduced morbidity and mortality burden, remain tenable alternatives for patients and health-care professionals. © 2014 Macmillan Publishers Limited.


Smith W.J.,University College Dublin
Energy Policy | Year: 2013

Gas demand projections for the EU27 from a variety of sources are compared. Projected demand varies widely between sources, even when similar rates of economic growth and policy strength are assumed. The divergence is shown to result from differing assumptions concerning future energy intensity, on the one hand, and the future contribution of nuclear power and renewables (RES) to electricity generation on the other. The variation with time of some of these projections is also examined. It is found that the gas demand projected by both the International Energy Agency (IEA) and the European Commission (EC) for 2020 and for 2030 has tended to decrease with each successive projection. This is understandable, since the penetration of RES-E has continued to exceed expectations. However, in an economically depressed, post-Fukushima Europe, estimates of future growth in both RES and nuclear generation may need significant revision. The Energy Efficiency Directive, as agreed by the Council of the European Union and the European Parliament in April 2012 (Council of the European Union, 2012), will also impact significantly on future gas demand, even though the measures incorporated are weaker than the original proposal. The analysis presented here shows that a "nuclear decline" due to the Fukushima disaster is seen to moderate, rather than reverse, projected demand decay. A significant shortfall in projected RES capacity, if it were to occur, constitutes a potential source of additional gas demand.Although the emphasis in this paper is on the EU27 as a whole, consideration is given to the regional heterogeneity of each of these impacts. Hence, although aggregate demand growth for the next decade or two is likely to be moderate or (more probably) negative, local demand growth in some regions may be significant. Ensuring adequate access to these specific regions - via interconnection to their EU27 neighbours, and/or directly from extra-EU sources - will therefore be essential. Hence, implementation of the Third Energy Plan should remain a priority. © 2013 Elsevier Ltd.


Jordan E.J.,Waterford Regional Hospital | Kelly C.M.,University College Dublin
Expert Opinion on Pharmacotherapy | Year: 2012

Introduction: Metastatic melanoma is an aggressive disease resistant to chemotherapy. Recent clinical trials have reported improved survival for two novel agents; ipilimumab, a humanized, IgG1 monoclonal antibody that blocks cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and vemurafenib, a BRAF (v-raf murine sarcoma viral oncogene homolog B1) inhibitor targeting an activating mutation in the serine-threonine-protein kinase BRAF gene. Areas covered: The authors reviewed preclinical and clinical data examining the safety of vemurafenib in melanoma. MEDLINE and EMBASE were searched using the medical subject heading 'vemurafenib' and the following text terms: melanoma, BRAF inhibition, vemurafenib. This review provides the reader with an overview of current data examining the efficacy and safety of vemurafenib in metastatic melanoma. Expert opinion: Vemurafenib is an oral agent licensed for patients with BRAF V600E mutation-positive inoperable and metastatic melanoma. The most common adverse effects observed in Phase III clinical trials were dermatological events, arthralgia and fatigue. Specific dermatological toxicities included development of cutaneous squamous cell cancers and keratoacanthomas. Prolongation of the QT interval was also reported. Regular dermatological assessments and electrocardiograms are recommended. Ongoing trials are examining vemurafenib in both the adjuvant setting and metastatic setting in combination with ipilimumab and MEK inhibitors (mitogen-activated protein kinase/extracellular signal-regulated kinase). Understanding and overcoming mechanisms of resistance to BRAF inhibitors is the focus of ongoing research. © Informa UK, Ltd.


Cowley C.,University College Dublin
Journal of Medical Ethics | Year: 2016

A recent issue of the journal Bioethics discussed whether conscientious objectors within the healthcare context should be required to give their reasons to a specially convened tribunal, who would have the power to reject the objection. This is modeled on the context of military conscription. Advocates for such a tribunal offer two different justifications, one based on determining the genuineness of the applicant's beliefs, the other based on determining their reasonableness. I limit my discussion to a doctor's objection to abortion in the UK, and argue against both justifications: I thereby defend the status quo, where such doctors are not formally required to defend their beliefs. My argument has to do with the particular nature of the abortion debate in the UK, and the more general nature of ethical disagreement.


Nguyen L.K.,University College Dublin
Cell communication and signaling : CCS | Year: 2013

Ubiquitination, the covalent attachment of ubiquitin to target proteins, has emerged as a ubiquitous post-translational modification (PTM) whose function extends far beyond its original role as a tag for protein degradation identified three decades ago. Although sharing parallel properties with phosphorylation, ubiquitination distinguishes itself in important ways. Nevertheless, the interplay and crosstalk between ubiquitination and phosphorylation events have become a recurrent theme in cell signalling regulation. Understanding how these two major PTMs intersect to regulate signal transduction is an important research question. In this review, we first discuss the involvement of ubiquitination in the regulation of the EGF-mediated ERK signalling pathway via the EGF receptor, highlighting the interplay between ubiquitination and phosphorylation in this cancer-implicated system and addressing open questions. The roles of ubiquitination in pathways crosstalking to EGFR/MAPK signalling will then be discussed. In the final part of the review, we demonstrate the rich and versatile dynamics of crosstalk between ubiquitination and phosphorylation by using quantitative modelling and analysis of network motifs commonly observed in cellular processes. We argue that given the overwhelming complexity arising from inter-connected PTMs, a quantitative framework based on systems biology and mathematical modelling is needed to efficiently understand their roles in cell signalling.


Ilten P.,University College Dublin
Nuclear Physics B - Proceedings Supplements | Year: 2014

As of version 8.150 of Pythia, the isotropic decay model of τ-leptons has been replaced with sophisticated τ- lepton decay machinery. The decays and spin correlations for τ-leptons in Pythia 8 are described, including the spin correlation algorithm, the available τ-lepton production processes, the τ-lepton decay models, the user interface, and the implementation. © 2014 Elsevier B.V.


Iacopino D.,Tyndall National Institute | Redmond G.,University College Dublin
Chemical Communications | Year: 2011

A novel photo-switching system based on fluorescent polymer nanotubes incorporating spirooxazine molecules has been designed. Reversible photoluminescence modulation of up to 60% has been shown in individual nanotubes subjected to repeated photo-conversion cycles. © 2011 The Royal Society of Chemistry.


Grada C.O.,University College Dublin
Development and Change | Year: 2011

Famine, like poverty, has always been with us. No region and no century has been immune. Its scars - economic, psychological and political - can long outlast its immediate impact on mortality and health. Famines are a hallmark of economic backwardness, and were thus more likely to occur in the pre-industrialized past. Yet the twentieth century suffered some of the most devastating ever recorded. That century also saw shifts in both the causes and symptoms of famine. This new century's famines have been 'small' by historical standards, and the threat of major ones seemingly confined to ever-smaller pockets of the globe. Are these shifts a sign of hope for the future?© 2011 International Institute of Social Studies.


Don MacElroy J.M.,University College Dublin
Ambio | Year: 2016

In this paper, a brief overview is presented of natural gas as a fuel resource with subsequent carbon capture and re-use as a means to facilitate reduction and eventual elimination of man-made carbon emissions. A particular focus is shale gas and, to a lesser extent, methane hydrates, with the former believed to provide the most reasonable alternative as a transitional fuel toward a low-carbon future. An emphasis is placed on the gradual elimination of fossil resource usage as a fuel over the coming 35 to 85 years and its eventual replacement with renewable resources and nuclear power. Furthermore, it is proposed that synthesis of chemical feedstocks from recycled carbon dioxide and hydrogen-rich materials should be undertaken for specific applications in the transport sector which require access to high energy density fuels. To achieve the latter, carbon dioxide capture is imperative and possible synthetic routes for chemical feedstock production are briefly reviewed. © 2016, The Author(s).


O'Sullivan C.,University College Dublin | O'Sullivan S.,Dublin Institute of Technology
Journal of Computational Finance | Year: 2016

The accelerated trinomial tree (ATT) is a derivatives pricing lattice method that circumvents the restrictive time step condition inherent in standard trinomial trees and explicit finite difference methods (FDMs), in which the time step must scale with the square of the spatial step. ATTs consist of L uniform supersteps, each of which contains an inner lattice/trinomial tree with N nonuniform subtime steps. Similarly to implicit FDMs, the size of the superstep in ATTs, a function of N, is constrained primarily by accuracy demands. ATTs can price options up toN times faster than standard trinomial trees (explicit FDMs). ATTs can be interpreted as using risk-neutral extended probabilities: extended in the sense that values can lie outside the range [0; 1] on the substep scale but aggregate to probabilities within the range [0; 1] on the superstep scale. Hence, it is only strictly at the end of each superstep that a practically meaningful solution may be extracted from the tree. We demonstrate that ATTs with L supersteps are more efficient or have comparable efficiency to competing implicit methods that use L time steps in pricing Black–Scholes American put options and two-dimensional American basket options. Crucially, this performance is achieved using an algorithm that requires only a modest modification of a standard trinomial tree. This is in contrast to implicit FDMs, which may be relatively complex in their implementation. We also extend ATTs to the pricing of American options under the Heston model and the Bates model in order to demonstrate the general applicability of the approach. © 2016 Incisive Risk Information (IP) Limited.


Miras A.D.,Institute of Clinical science | Le Roux C.W.,University College Dublin
Nature Reviews Gastroenterology and Hepatology | Year: 2013

The clinical efficacy of bariatric surgery has encouraged the scientific investigation of the gut as a major endocrine organ. Manipulation of gastrointestinal anatomy through surgery has been shown to profoundly affect the physiological and metabolic processes that control body weight and glycaemia. The most popular bariatric surgical procedures are gastric bypass, adjustable gastric banding and vertical sleeve gastrectomy. Even though these procedures were designed with the aim of causing restriction of food intake and nutrient malabsorption, evidence suggests that their contributions to weight loss are minimal. Instead, these interventions reduce body weight by decreasing hunger, increasing satiation during a meal, changing food preferences and energy expenditure. In this Review, we have explored these mechanisms as well as their mediators. The hope is that that their in-depth investigation will enable the optimization and individualization of surgical techniques, the development of equally effective but safer nonsurgical weight-loss interventions, and even the understanding of the pathophysiology of obesity itself. © 2013 Macmillan Publishers Limited.


Duffy D.J.,University College Dublin
Briefings in Bioinformatics | Year: 2016

The 'precision medicine (systems medicine)' concept promises to achieve a shift to future healthcare systems with a more proactive and predictive approach to medicine, where the emphasis is on disease prevention rather than the treatment of symptoms. The individualization of treatment for each patient will be at the centre of this approach, with all of a patient's medical data being computationally integrated and accessible. Precision medicine is being rapidly embraced by biomedical researchers, pioneering clinicians and scientific funding programmes in both the European Union (EU) and USA. Precision medicine is a key component of both Horizon 2020 (the EU Framework Programme for Research and Innovation) and the White House's Precision Medicine Initiative. Precision medicine promises to revolutionize patient care and treatment decisions. However, the participants in precision medicine are faced with a considerable central challenge. Greater volumes of data from a wider variety of sources are being generated and analysed than ever before; yet, this heterogeneous information must be integrated and incorporated into personalized predictive models, the output of which must be intelligible to non-computationally trained clinicians. Drawing primarily from the field of 'oncology', this article will introduce key concepts and challenges of precision medicine and some of the approaches currently being implemented to overcome these challenges. Finally, this article also covers the criticisms of precision medicine overpromising on its potential to transform patient care. © The Author 2015. Published by Oxford University Press.


De Gascun C.F.,Frimley Park Hospital | Carr M.J.,University College Dublin
Clinical and Developmental Immunology | Year: 2013

JC and BK polyomaviruses were discovered over 40 years ago and have become increasingly prevalent causes of morbidity and mortality in a variety of distinct, immunocompromised patient cohorts. The recent discoveries of eight new members of the Polyomaviridae family that are capable of infecting humans suggest that there are more to be discovered and raise the possibility that they may play a more significant role in human disease than previously understood. In spite of this, there remains a dearth of specific therapeutic options for human polyomavirus infections and an incomplete understanding of the relationship between the virus and the host immune system. This review summarises the human polyomaviruses with particular emphasis on pathogenesis in those directly implicated in disease aetiology and the therapeutic options available for treatment in the immunocompromised host. © 2013 Cillian F. De Gascun and Michael J. Carr.


Miller I.,University College Dublin
Social History of Medicine | Year: 2013

Historians have castigated the British medical profession for endorsing forcible feeding during the suffragette hunger strike campaigns of 1909 to 1914. This article reconsiders the importance of medical opposition to forcible feeding by closely analysing its agendas and, importantly, by positing that the medico-ethical debates sparked in that period set the stage for ethical discourses that have recurrently resurfaced ever since. Although leading contemporary medical institutions and figures did indeed turn a blind eye to forcible feeding, the nature of medical opposition where it did arise, and the complex medico-ethical dilemmas posed by the procedure, demand fuller investigation, not least because they illuminate concerns still raised today. More specifically, I explore historical disagreement on forcible feeding as a therapeutic or coercive technique, the complex positioning of the prison doctor who performed the procedure and contestation over the extent to which the state ought to intervene in prison medicine. © 2013 The Author 2013. Published by Oxford University Press on behalf of the Society for the Social History of Medicine. All rights reserved.


Bartelmess J.,Italian Institute of Technology | Quinn S.J.,University College Dublin | Giordani S.,Italian Institute of Technology
Chemical Society Reviews | Year: 2015

Carbon based nanomaterials have emerged over the last few years as important agents for biomedical fluorescence and Raman imaging applications. These spectroscopic techniques utilize either fluorescently labelled carbon nanomaterials or the intrinsic photophysical properties of the carbon nanomaterial. In this review article we present the utilization and performance of several classes of carbon nanomaterials, namely carbon nanotubes, carbon nanohorns, carbon nanoonions, nanodiamonds and different graphene derivatives, which are currently employed for in vitro as well as in vivo imaging in biology and medicine. A variety of different approaches, imaging agents and techniques are examined and the specific properties of the various carbon based imaging agents are discussed. Some theranostic carbon nanomaterials, which combine diagnostic features (i.e. imaging) with cell specific targeting and therapeutic approaches (i.e. drug delivery or photothermal therapy), are also included in this overview. This journal is © The Royal Society of Chemistry 2015.


Mooney C.,University College Dublin
Bioinformatics (Oxford, England) | Year: 2013

Peptides play important roles in signalling, regulation and immunity within an organism. Many have successfully been used as therapeutic products often mimicking naturally occurring peptides. Here we present PeptideLocator for the automated prediction of functional peptides in a protein sequence. We have trained a machine learning algorithm to predict bioactive peptides within protein sequences. PeptideLocator performs well on training data achieving an area under the curve of 0.92 when tested in 5-fold cross-validation on a set of 2202 redundancy reduced peptide containing protein sequences. It has predictive power when applied to antimicrobial peptides, cytokines, growth factors, peptide hormones, toxins, venoms and other peptides. It can be applied to refine the choice of experimental investigations in functional studies of proteins. PeptideLocator is freely available for academic users at http://bioware.ucd.ie/.


Reilly C.,University College Dublin
Journal of Intellectual Disability Research | Year: 2012

Background A number of genetic conditions with associated intellectual disability and/or special educational needs have increasingly well-defined behavioural phenotypes. Thus, the concept of 'behavioural phenotype' and aetiology of intellectual disability may be important with regard to school-based interventions. Method The evidence for distinctive cognitive and behavioural aspects of five of the most common genetic syndromes (Down syndrome, fragile X syndrome, Williams syndrome, Prader-Willi syndrome and velo-cardio-facial syndrome) associated with special educational needs is reviewed with respect to key studies and findings. The possible utility of aetiology-related interventions in education is discussed with reference to arguments for and against such approaches with respect to published guidelines and published research. Results Behavioural phenotypes are probabilistic and many children with a specific genetic syndrome will share commonalities with other children with other genetic syndromes and within syndrome variability is not uncommon. There is evidence that teachers and parents have limited knowledge of aspects of the proposed cognitive and behaviour profiles associated with the reviewed syndromes. While there are published guidelines in the area of learning and behaviour for each of the five reviewed syndromes there is a limited amount of evidence of the efficacy of such approaches in school settings. Conclusion It is likely that knowing the aetiology of a child's special educational needs will be helpful for staff who work in school settings in relation to cognitive and behavioural implications. However, how such knowledge might inform teaching practice or behavioural interventions has not been studied. A model is proposed that might help inform educators about the possible role of aetiology in the classroom. © 2012 Blackwell Publishing Ltd.


Kelly B.D.,University College Dublin
Transcultural Psychiatry | Year: 2011

There are significant points of similarity between considerations of self-harm and suicide in Buddhist and non-Buddhist traditions, including qualified acceptance of certain forms of self-harm, altruism as a motivation for suicide, and self-immolation as a form of political protest. Differences include specific contexts in which certain forms of selfharm are accepted and the predominant frameworks used to interpret such acts. The integration of Buddhist concepts of dukkha (unsatisfactoriness or suffering) and sati (mindfulness) into Western psychotherapeutic paradigms represents a significant point of convergence between the two traditions, and suggests the possibility of greater dialogue and therapeutic benefit in the future. © The Author(s) 2011.


Mauger A.,University College Dublin
Journal of the History of Medicine and Allied Sciences | Year: 2012

The period 182060 marked an era of transition and diversity in Ireland that rapidly transformed the face of Irish society. Inextricably linked with these processes was the expansion of Irelands private asylum system. This system diverged from its British counterpart both in the socioeconomic cohort it served and in the role it played within the mental health-care system as a whole. The implementation of the 1842 Private Asylums (Ireland) Act, the first legislative measure geared exclusively toward the system, highlighted the growing importance of private care in Ireland as well as providing for the licensing and regulation of these institutions for the first time. To date, historians of Irish medicine have focused almost exclusively on the pauper insane. This article aims to shift this emphasis toward other categories of the Irish insane through exploration of the Irish private asylum system, its growth throughout the period, and the social profile of private patients. I shall also interrogate the trade in lunacy model through exploration of financial considerations, discharge and recovery rates, and conditions of care and argue that while Irish private institutions were a lucrative business venture, the quality of care upheld was apparently high. Finally, I shall argue that Irish private asylums catered primarily for the upper classes and briefly explore alternative provisional measures for other non-pauper sectors of society. © 2011 The Author. Published by Oxford University Press. All rights reserved.


Ramos C.,Polytechnic Institute of Porto | Liu C.-C.,University College Dublin
IEEE Intelligent Systems | Year: 2011

The power industry performs the engineering design, installation, operation, and maintenance tasks to provide a high-quality, secure energy supply while accounting for its systems' abilities to withstand uncertain events, such as weather-related outages. In addition, the inherent uncertainties of wind and solar energy lead to technical challenges such as forecasting, scheduling, operation, control, and risk management. Power system experts are fully aware that there is a risk of degradation with increasingly complex power systems. Intelligent systems are natural decision support tools for planning, operation, maintenance, market monitoring, and risk management. This new generation of technologies must combine the technical operation of the power grid with the trading activities of electricity markets. Neural networks have been extensively used for forecasting tasks.


Vohnsen B.,University College Dublin
Biomedical Optics Express | Year: 2014

Photoreceptor outer segments have been modeled as stacked arrays of discs or membrane infoldings containing visual pigments with light-induced dipole moments. Waveguiding has been excluded so fields diffract beyond the physical boundaries of each photoreceptor cell. Optical reciprocity is used to argue for identical radiative and light gathering properties of pigments to model vision. Two models have been introduced: one a macroscopic model that assumes a uniform pigment density across each layer and another microscopic model that includes the spatial location of each pigment molecule within each layer. Both models result in highly similar directionality at the pupil plane which proves to be insensitive to the exact details of the outer-segment packing being predominantly determined by the first and last contributing layers as set by the fraction of bleaching. The versatility of the microscopic model is demonstrated with an array of examples that includes the Stiles-Crawford effect, visibility of a focused beam of light and the role of defocus. ©2014 Optical Society of America.


Tuohy A.,EPRI | O'Malley M.,University College Dublin
Energy Policy | Year: 2011

This paper examines the operation of the Irish power system with very high levels of wind energy, with and without pumped storage. A unit commitment model which accounts for the uncertainty in wind power is used. It is shown that as wind penetration increases, the optimal operation of storage depends on wind output as well as load. The main benefit from storage is shown to be a decrease in wind curtailment. The economics of the system are examined to find the level at which storage justifies its capital costs and inefficiencies. It is shown that the uncertainty of wind makes the option of storage more attractive. The size of the energy store has an impact on results. At lower levels of installed wind (up to approximately 50% of energy from wind in Ireland), the reduction in curtailment is insufficient to justify building storage. At greater levels of wind, storage reduces curtailment sufficiently to justify the additional capital costs. It can be seen that if storage replaces OCGTs in the plant mix instead of CCGTs, then the level at which it justifies itself is lower. Storage increases the level of carbon emissions at wind penetration below 60%. © 2011 Elsevier Ltd.


Ip B.C.,Boston University | Hogan A.E.,University College Dublin | Nikolajczyk B.S.,Boston University
Trends in Endocrinology and Metabolism | Year: 2015

Type 2 diabetes (T2D) is a metabolic disease associated with obesity-related insulin resistance (IR) and chronic inflammation. Animal studies indicate that IR can be caused and/or exacerbated by systemic and/or tissue-specific alterations in lymphocyte differentiation and function. Human studies also indicate that obesity-associated inflammation promotes IR. Nevertheless, clinical trials with anti-inflammatory therapies have yielded modest impacts on established T2D. Unlike mouse models, where obesity is predominantly associated with IR, 20-25% of obese humans are metabolically healthy with high insulin sensitivity. The uncoupling of obesity from IR in humans but not in animal models advocates for a more comprehensive understanding of mediators and mechanisms of human obesity-promoted IR, and better integration of knowledge from human studies into animal experiments to efficiently pursue T2D prevention and treatment. © 2014 Elsevier Ltd.


Kirwan R.P.,University College Dublin
Investigative ophthalmology & visual science | Year: 2012

Vascular hypoperfusion, extracellular matrix remodeling and axon loss are pathological characteristics of the glaucomatous optic nerve head. We report a novel study demonstrating transcriptional responses in optic nerve lamina cribrosa (LC) cells exposed to in vitro hypoxic stress. Primary cultures of human glial fibrillary acid protein (GFAP) negative LC cells were generated from four donors. Cells were exposed to 24 hours of hypoxic stress (1% O2) or normoxia (21% O2). Hypoxia responsive genes were identified using Affymetrix HG-U133A microarrays (n = 3) and validated with real time PCR (n = 3). Secreted protein was measured by ELISA (n = 4) and cellular protein by Western blot (n = 4). Expression data were annotated with NIH DAVID software and putative transcription factor sites in hypoxia-responsive gene promoters were identified using Core_TF software. Hypoxia-sensitive genes included those involved in apoptosis (e.g., BNIP3), neurogenesis (e.g., STC1), extracellular matrix (e.g., MIF, DDR1/TrkE, and IGFR2), mitochondrion (e.g., CYP1B1) and angiogenesis (e.g., VEGF). Real time PCR for selected genes supported the expression changes identified by microarray. ELISA and Western blot validated corresponding changes in protein production. Promoter sequence interrogation revealed putative conserved transcription factor binding sites (e.g., HIF and CREB) in the promoters of the hypoxia responsive genes. Our data show that LC cell gene expression is sensitive to reduced oxygen levels in vitro and provides bioinformatic evidence of the potential transcriptional regulators of this response.


Ulusoy H.S.,University of California at Irvine | Feng M.Q.,University of California at Irvine | Fanning P.J.,University College Dublin
Earthquake Engineering and Structural Dynamics | Year: 2011

This paper describes the identification of finite dimensional, linear, time-invariant models of a 4-story building in the state space representation using multiple data sets of earthquake response. The building, instrumented with 31 accelerometers, is located on the University of California, Irvine campus. Multiple data sets, recorded during the 2005 Yucaipa, 2005 San Clemente, 2008 Chino Hills and 2009 Inglewood earthquakes, are used for identification and validation. Considering the response of the building as the output and the ground motion as the input, the state space models that represent the underlying dynamics of the building in the discrete-time domain corresponding to each data set are identified. The time-domain Eigensystem Realization Algorithm with the Observer/Kalman filter identification procedure are adopted in this paper, and the modal parameters of the identified models are consistently determined by constructing stabilization diagrams. The four state space models identified demonstrate that the response of the building is amplitude dependent with the response frequency and damping, being dependent on the magnitude of ground excitation. The practical application of this finding is that the consistency of this building response to future earthquakes can be quickly assessed, within the range of ground excitations considered (0.005g-0.074g), for consistency with prior response-this assessment of consistent response is discussed and demonstrated with reference to the four earthquake events considered in this study. Inclusion of data sets relating to future earthquakes will enable the findings to be extended to a wider range of ground excitation magnitudes. © 2010 John Wiley & Sons, Ltd. Copyright © 2010 John Wiley & Sons, Ltd..


Dowler E.A.,University of Warwick | O'Connor D.,University College Dublin
Social Science and Medicine | Year: 2012

Food poverty is an important contributing factor to health inequalities in industrialised countries; it refers to the inability to acquire or eat an adequate quality or sufficient quantity of food in socially acceptable ways (or the uncertainty of being able to do so). Synonymous with household food insecurity, the issue needs to be located within a social justice framework. Recognising the clear interdependence between the right to food and the right to health, this paper explores how international human rights obligations could inform approaches to addressing food poverty and insecurity with specific reference to Ireland and the UK. Little attention has been paid to how countries should meet their obligations to respect, protect and fulfil the right to food in developed countries. The paper contributes by examining the social and policy circumstances which inhibit poor households from obtaining sufficient food to eat healthily, along with strategies and interventions from State and civil society actors in the two countries. In practice, problems and potential solutions have largely been directed towards the individual rather than at social determinants, particularly as research on environmental factors such as distance to shops has produced equivocal results. Other key structural aspects such as income sufficiency for food are broadly ignored by the State, and anti-poverty strategies are often implemented without monitoring for effects on food outcomes. Thus scant evidence exists for either Ireland or the UK meeting its rights to food obligations to date, in terms of roles and responsibilities in ensuring access to affordable, available and appropriate food for all. © 2011 Elsevier Ltd.


Matallanas D.,University College Dublin | Crespo P.,University of Cantabria
Current Opinion in Molecular Therapeutics | Year: 2010

Ras proteins are key elements in the regulation of cellular proliferation, differentiation and survival. Mutational activation of Ras or of components of its effector pathways are detected in one-third of human cancers and are essential for the genesis and maintenance of the tumoral phenotype. Research efforts have been dedicated to the development of therapeutic agents that inhibit aberrant Ras signals and, subsequently, tumor progression. However, many of these initiatives have proven less successful than expected. This review summarizes the current status of developments in Ras research, the challenges that have arisen during preclinical and clinical stages, and how novel approaches to targeting Ras pathways have introduced new strategies toward the development of antitumoral agents that are alternative or complementary to those currently in use. These new approaches would be aimed at disrupting key protein-protein interactions that are essential for the conveyance of Ras aberrant signals or would be directed against new proteins recently demonstrated to be critical participants in Ras-regulated pathways. © Thomson Reuters.


Stanek G.,Medical University of Vienna | Wormser G.P.,New York Medical College | Gray J.,University College Dublin | Strle F.,University of Ljubljana
The Lancet | Year: 2012

Lyme borreliosis (Lyme disease) is caused by spirochaetes of the Borrelia burgdorferi sensu lato species complex, which are transmitted by ticks. The most common clinical manifestation is erythema migrans, which eventually resolves, even without antibiotic treatment. However, the infecting pathogen can spread to other tissues and organs, causing more severe manifestations that can involve a patient's skin, nervous system, joints, or heart. The incidence of this disease is increasing in many countries. Laboratory evidence of infection, mainly serology, is essential for diagnosis, except in the case of typical erythema migrans. Diagnosed cases are usually treated with antibiotics for 2-4 weeks and most patients make an uneventful recovery. No convincing evidence exists to support the use of antibiotics for longer than 4 weeks, or for the persistence of spirochaetes in adequately treated patients. Prevention is mainly accomplished by protecting against tick bites. There is no vaccine available for human beings. © 2012 Elsevier Ltd.


Deering B.M.,University College Dublin
Journal of cardiopulmonary rehabilitation and prevention | Year: 2011

Chronic obstructive pulmonary disease (COPD) is characterized by airflow limitation and by both systemic and airway inflammation. In COPD, acupuncture has been shown to improve quality-of-life scores and decrease breathlessness; similar findings have also been reported after pulmonary rehabilitation (PR). The hypothesis of this study was that acupuncture in conjunction with pulmonary rehabilitation would improve COPD outcome measures compared to pulmonary rehabilitation alone. The design was a randomized prospective study; all subjects had COPD. There were 19 controls, 25 who underwent PR, and 16 who had both acupuncture and PR. The primary outcome measure was a change in measures of systemic inflammation at the end of PR and at 3 month followup. Lung function, including maximum inspiratory pressure (PiMax), quality-of-life scores, functional capacity including steps taken, dyspnea scores, and exercise capacity, were secondary endpoints. After PR, both groups had significantly improved quality-of-life scores, reduced dyspnea scores, improved exercise capacity, and PiMax, but no change in measures of systemic inflammation compared with the controls. There were no differences in most of the outcome measures between the 2 treatment groups except that subjects who had both acupuncture and PR remained less breathless for a longer period. The addition of acupuncture to PR did not add significant benefit in most of the outcomes measured.


Schaffer K.,St Vincents University Hospital | Taylor C.T.,University College Dublin
FEBS Journal | Year: 2015

Tissue hypoxia is a common microenvironmental feature during inflammation associated with bacterial infection. Hypoxia has recently been shown to play an important role in both innate and adaptive host immunity through the regulation of transcription factors, including hypoxia-inducible factor and nuclear factor-κB, in both infiltrating immunocytes and inflamed resident cells. Recent studies have suggested that, by regulating these important immune effector pathways in host tissues, hypoxia can significantly alter the process of bacterial infection and subsequent disease progression. Although hypoxia is often beneficial in terms of reducing the development of infection, its net effect depends on a number of factors, including the nature of the pathogen and the characteristics of the infection encountered. In this minireview, we will discuss the impact of local tissue hypoxia and the resulting activation of hypoxia-sensitive pathways on bacterial infection by a range of pathogens. Furthermore, we will review how this knowledge may be used to develop new approaches to anti-infective therapeutics. Hypoxia is a common microenvironmental feature during a range of bacterial infections. In this review, we discuss the implications of local hypoxia on the host, the pathogen and the host-pathogen interactions during bacterial infection. © 2015 FEBS.


Mansouri-Attia N.,University College Dublin
Biology of reproduction | Year: 2012

In mammals, successful pregnancy is dependent in part on the adaptation or regulation of the maternal immune system to prevent the rejection of the embryonic semiallograft. A modification in Th cell function and secretion is a requirement for the establishment and maintenance of pregnancy. Although there is strong evidence from studies in humans and mice linking successful pregnancy with the predominance of Th2-type immunity, the situation in cattle remains unclear. This study describes the characterization of the immune response of the bovine maternal endometrium to the presence of a developing embryo, with specific emphasis on the macrophage and dendritic cell populations and associated factors, using quantitative real-time PCR, in situ hybridization, and immunohistochemistry. Furthermore, in vivo and in vitro models were developed to investigate the potential role of progesterone and interferon-tau (IFNT) in the regulation of these immune factors. There was a marked increase in the population of CD14(+) cells and CD172a-CD11c(+) cells in the endometrium in response to pregnancy, which was paralleled by increased mRNA expression of a number of non-Th-associated factors, including IL12B and IL15, and downregulation of IL18. In addition, we identified several novel IFNT- and progesterone-regulated factors, including IL12B, MCP1, MCP2, PTX3, RSAD2, and TNFA, whose regulation may be critical to pregnancy outcome. Our findings give center stage to non-Th cells, such as monocytes/macrophages and dendritic cells, in the bovine immune response to the semiallogenic embryo. In conclusion, we propose that in cattle, successful pregnancy establishment is associated with a dramatic regulation of the cytokine network, primarily by endometrial monocytes/macrophages and dendritic cells.


Murphy S.,University College Dublin
Irish journal of medical science | Year: 2013

Traditional care pathways for patients with low back pain (LBP) where general practitioners (GPs) refer to consultant specialists can lead to excessive waiting times for patients and questionable use of health care resources. The evaluation of more cost effective pathways is a priority. The study aims to determine if clinical specialist physiotherapists can allocate patients into the three distinct diagnostic triage categories in line with international guidelines. A secondary aim is to examine the utility of baseline domains to inform clinical decision making. A review of LBP patients (n = 1,532) consecutively referred between 2008 and 2010 to a physiotherapy led spinal triage clinic was undertaken. Baseline demographics, pain severity (Visual Analogue Scale), disability (Roland Morris Disability Questionnaire), distress (Distress and Risk Assessment Method), mobility and function were assessed. Relationships between these factors were analysed. Eighty-five percent of the population were deemed suitable for conservative management and were referred for either group exercise intervention (n = 1,125, 73 %) or individual treatment (n = 178, 12 %), in line with clinical guidelines. Fourteen percent were discharged and only 1 % required a specialist opinion. Patients allocated to the three management streams could be clearly discriminated by baseline measures of pain, distress, disability and function (p < 0.01). Clinical Specialist physiotherapists are effective in assessing and selecting appropriate care pathways for LBP patients in line with international LBP clinical guidelines. The utility of the physical and psychological measures to differentiate between groups of varying clinical severity has important implications for treatment selection and management.


Barclay R.S.,Northwestern University | McElwain J.C.,University College Dublin | Sageman B.B.,Northwestern University
Nature Geoscience | Year: 2010

The Cretaceous Ocean Anoxic Event 2 (about 94 million years ago) is thought to be linked to extensive volcanism, which triggered a biogeochemical chain of events that eventually led to widespread marine anoxia and a remarkable increase in carbon burial in marine sediments. It has been suggested that the event was accompanied by a substantial decrease in atmospheric CO 2 concentrations, but the quantification of the drawdown remains controversial. Here we reconstruct atmospheric CO 2 concentrations throughout the ocean anoxic event from counts of the stomata in fossil leaves, and use terrestrial carbon isotopes to link the reconstruction to marine records of the event. We find that before the onset of ocean anoxia, atmospheric CO 2 concentrations increased by 20% over background levels of 370 +100 / 70 ppm. This was part of a long-term rise in atmospheric CO 2 levels, presumably caused by volcanism, which reached a peak of 500 +400 / 180 ppm. However, two pulses of extensive carbon burial during the ocean anoxic event, as indicated by positive carbon isotope excursions, are associated with decreased atmospheric CO 2 concentrations. We conclude that the sequestration of marine organic carbon led to a decrease in atmospheric CO 2 concentration of up to 26% during Ocean Anoxic Event 2. © 2010 Macmillan Publishers Limited. All rights reserved.


Swords L.,Trinity College Dublin | Heary C.,National University of Ireland | Hennessy E.,University College Dublin
Journal of Child Psychology and Psychiatry and Allied Disciplines | Year: 2011

Background: Research suggests that children's reactions to peers with mental health problems are related to the maintenance and outcomes of these problems. However, children's perceptions of such peers, particularly those with internalising problems, are neither well researched nor understood. The present study aimed to test a series of models relating socio-demographic and attributional variables to the acceptance of hypothetical boys and girls with attention deficit hyperactivity disorder (ADHD) and depression. Methods: A sample of 595 participants, drawn from five different age-groups spanning early childhood to late adolescence, completed a booklet of questions in response to two vignettes describing the behaviour of hypothetical target peers with depression and ADHD. The sample was drawn from schools randomly selected in the east of Ireland. Results: The models indicated that age and gender of the participant, and the perceived responsibility of the target character for his/her condition, were the three most important predictors of acceptance in all models. However, the relationship between these variables and acceptance varied depending on the gender of the target child and the condition (depression or ADHD) in the models tested. Conclusions: The findings of the study suggest that the relationships between socio-demographic and attributional variables and acceptance of peers with mental health problems depend on the type of mental health problem under consideration. The findings have implications for the development of information and education programmes to improve the integration of children with mental health problems. © 2011 Association for Child and Adolescent Mental Health.


Mallon P.W.G.,University College Dublin | Mallon P.W.G.,Materials Misericordiae University Hospital
Current Opinion in Infectious Diseases | Year: 2010

PURPOSE OF REVIEW: This review details the clinical aspects and pathogenesis of low bone mineral density (BMD) in HIV, discusses broad management issues and outlines areas in which our understanding of this condition is incomplete. RECENT FINDINGS: Low BMD is prevalent in HIV-infected patients, with traditional risk factors, HIV infection and exposure to antiretroviral therapy all contributing. The role of specific antiretrovirals in the development of low BMD remains controversial, but most changes arise at either antiretroviral therapy initiation or switch. SUMMARY: Further research is needed to clarify mechanisms underlying low BMD in HIV, whether low BMD will translate to increased fractures and to determine the correct therapeutic approach to low BMD in HIV, particularly in younger HIV-infected patients. © 2010 Wolters Kluwer Health | Lippincott Williams & Wilkins.


McNulty R.,University College Dublin
International Journal of Modern Physics A | Year: 2014

The LHCb detector and LHC running conditions are ideally suited to measuring central exclusive production. Several recent measurements of exclusive dimuon, single and double charmonia are reviewed. The potential for future measurements across a broad range of physics channels is discussed. © World Scientific Publishing Company.


Albrecht M.,University College Dublin
Advances in Organometallic Chemistry | Year: 2014

Similarities and differences of normal versus abnormal carbene complexes are highlighted, with an emphasis on effects that can be directly attributed to the different bonding mode and which are thus not imparted by potential stereoelectronic effects such as more or less shielding of the M. C bond. While generally, the bonding scheme is similar throughout all classes of carbenes, distinctly different behaviors have been noted in some reactivity patterns, in particular when comparing different bonding modes of imidazolylidenes. This distinction is blurred with triazolylidenes, and the normal/abnormal nomenclature is not particularly meaningful in these cases. With pyridylidenes, structural differences are noted in the ground state, while reactivity patterns are not significantly dependent on the metal binding site. Common denominators for all normal and abnormal heterocyclic carbene complexes include (i) a strongly mesoionic character of both normal and abnormal bonding modes of the ligand, and (ii) a negligibly small carbenic character. Accordingly "carbene" is a rather debatable name for this class of ligands, and "mesoionic C-donor" may be more accurate. © 2014 Elsevier Inc.


Lennon M.,University College Dublin
Local Environment | Year: 2014

Advocates of the green infrastructure (GI) concept claim it offers a progressive planning approach that facilitates synergies between economic growth, environmental conservation and social development. Although widely endorsed by both planning practitioners and academics, little academic literature exists critically evaluating what GI entails or the potential implications of its institutionalisation within planning practice. This paper addresses this deficit by critically examining the interpretation and representation of the GI concept in planning policy. The paper first critically analyses international interpretations of GI. Following this, the particular attributes of GI's interpretation in the Republic of Ireland are investigated. The paper demonstrates how the emergence of GI in Ireland relates to broader debates on attempts to reconcile environmental concerns with development aspirations in planning policy. It is deduced that GI may represent an approach to planning policy formulation wherein habitat conservation initiatives are primarily designed and justified relative to the ecosystems services they are seen to provide to society. The paper also cautions against the risks posed by confining GI debates to the deliberations of technical specialist. The paper concludes by identifying some issues that may arise in the implementation of a GI approach and suggests ways to enhance the potential benefit of the concept's use in spatial planning. © 2014 © 2014 Taylor & Francis.


Barrios-O'neill D.,University of Ulster | Schuitema G.,University College Dublin
Renewable and Sustainable Energy Reviews | Year: 2016

This paper addresses the question, how can sustainable energy projects increase engagement from consumers using interactive media communications? To this end, a systematic literature review was conducted in order to synthesise findings across four major disciplines, with the goal of identifying current and imminent challenges, as well as potential solutions, to engaging consumers with sustainable energy projects in the era of interactive media. The authors propose a Socially Dynamic Communications Framework (SDCF) that can be used organisationally to address core challenges and generate solutions within a single iterative cycle. Initial findings indicate that consumer behaviours are most likely to be influenced through strategic social interactions using diverse, networked platforms, in order to be meaningful in contemporary social and technological contexts. Furthermore, this type of interaction is likely to become integral to future energy delivery systems, making interactive, online engagement with energy initiatives an important area for investigation. While many organisations may cite a lack of control in digital and social media as a risk justifying avoidance, the majority of engagement and marketing literature emphasise the greater risk inherent in not engaging effectively online. © 2015 Elsevier Ltd. All rights reserved.


McNicholas P.D.,University of Guelph | Murphy T.B.,University College Dublin
Bioinformatics | Year: 2010

Motivation: In recent years, work has been carried out on clustering gene expression microarray data. Some approaches are developed from an algorithmic viewpoint whereas others are developed via the application of mixture models. In this article, a family of eight mixture models which utilizes the factor analysis covariance structure is extended to 12 models and applied to gene expression microarray data. This modelling approach builds on previous work by introducing a modified factor analysis covariance structure, leading to a family of 12 mixture models, including parsimonious models. This family of models allows for the modelling of the correlation between gene expression levels even when the number of samples is small. Parameter estimation is carried out using a variant of the expectation-maximization algorithm and model selection is achieved using the Bayesian information criterion. This expanded family of Gaussian mixture models, known as the expanded parsimonious Gaussian mixture model (EPGMM) family, is then applied to two well-known gene expression data sets. Results: The performance of the EPGMM family of models is quantified using the adjusted Rand index. This family of models gives very good performance, relative to existing popular clustering techniques, when applied to real gene expression microarray data. © The Author 2010. Published by Oxford University Press. All rights reserved.


Parnell A.C.,University College Dublin | Inger R.,University of Exeter | Bearhop S.,University of Exeter | Jackson A.L.,Trinity College Dublin
PLoS ONE | Year: 2010

Background: Stable isotope analysis is increasingly being utilised across broad areas of ecology and biology. Key to much of this work is the use of mixing models to estimate the proportion of sources contributing to a mixture such as in diet estimation. Methodology: By accurately reflecting natural variation and uncertainty to generate robust probability estimates of source proportions, the application of Bayesian methods to stable isotope mixing models promises to enable researchers to address an array of new questions, and approach current questions with greater insight and honesty. Conclusions: We outline a framework that builds on recently published Bayesian isotopic mixing models and present a new open source R package, SIAR. The formulation in R will allow for continued and rapid development of this core model into an all-encompassing single analysis suite for stable isotope research. © 2010 Parnell et al.


There are no standardised serving/portion sizes defined for foods consumed in the European Union (EU). Typical serving sizes can deviate significantly from the 100 g/100 ml labelling specification required by the EU legislation. Where the nutritional value of a portion is specified, the portion size is determined by the manufacturers. Our objective was to investigate the potential for standardising portion sizes for specific foods, thereby ensuring complementarity across countries. We compared portion size for 156 food items measured using a food frequency questionnaire across the seven countries participating in the Food4me study. The probability of consuming a food and the frequency of consumption differed across countries for 93% and 58% of the foods, respectively. However, the individual country mean portion size differed from the average across countries in only 16% of comparisons. Thus, although dietary choices vary markedly across countries, there is much less variation in portion sizes. Our results highlight the potential for standardisation of portion sizes on nutrition labels in the EU.European Journal of Clinical Nutrition advance online publication, 3 February 2016; doi:10.1038/ejcn.2015.227. © 2016 Macmillan Publishers Limited


Drakakis K.,University College Dublin | Drakakis K.,Claude Shannon Institute for Discrete Mathematics
IEEE Transactions on Information Theory | Year: 2010

Given that frequency-hopping filters cannot easily implement big frequency hops instantaneously, those Costas permutations are determined in which the maximal frequency hop prescribed is as small as possible, as well as those that do contain the maximal hop possible, and are, consequently, less suitable for applications. It turns out that exponential Welch permutations not only lead in general to the smallest hops, but are also relatively easy to study, as a closed formula exists for the maximal hop. Through extensive collection of data for logarithmic Welch and Golomb permutations, on the other hand, it is found that: a) these two families behave (almost) identically; and that b) their maximal hops do not get as small as in exponential Welch permutations. © 2006 IEEE.


Meegahapola L.G.,Queens University of Belfast | Littler T.,Queens University of Belfast | Flynn D.,University College Dublin
IEEE Transactions on Sustainable Energy | Year: 2010

This paper proposes a decoupled fault ride-through strategy for a doubly fed induction generator (DFIG) to enhance network stability during grid disturbances. The decoupled operation proposes that a DFIG operates as an induction generator (IG) with the converter unit acting as a reactive power source during a fault condition. The transition power characteristics of the DFIG have been analyzed to derive the capability of the proposed strategy under various system conditions. The optimal crowbar resistance is obtained to exploit the maximum power capability from the DFIG during decoupled operation. The methods have been established to ensure proper coordination between the IG mode and reactive power compensation from the grid-side converter during decoupled operation. The viability and benefits of the proposed strategy are demonstrated using different test network structures and different wind penetration levels. Control performance has been benchmarked against existing grid code standards and commercial wind generator systems, based on the optimal network support required (i.e., voltage or frequency) by the system operator from a wind farm installed at a particular location. © 2010 IEEE.


Balmond E.I.,University of Bristol | Coe D.M.,Glaxosmithkline | Galan M.C.,University of Bristol | McGarrigle E.M.,University of Bristol | McGarrigle E.M.,University College Dublin
Angewandte Chemie - International Edition | Year: 2012

Alpha rules: A thiourea acts as an efficient organocatalyst for the glycosylation of protected galactals to form oligosaccharides containing a 2-deoxymonosaccharide moiety (see scheme). The reaction is highly stereoselective for α-linkages and proceeds by way of a syn-addition mechanism. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Murphy C.D.,University College Dublin
Organic and Biomolecular Chemistry | Year: 2012

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. © 2012 The Royal Society of Chemistry.


Nielsen J.E.,University College Dublin | Gunner M.R.,City College of New York | Garcia-Moreno E. B.,Johns Hopkins University
Proteins: Structure, Function and Bioinformatics | Year: 2011

The pK a Cooperative was organized to advance development of accurate and useful computational methods for structure-based calculation of pK a values and electrostatic energies in proteins. The Cooperative brings together laboratories with expertise and interest in theoretical, computational, and experimental studies of protein electrostatics. To improve structure-based energy calculations, it is necessary to better understand the physical character and molecular determinants of electrostatic effects. Thus, the Cooperative intends to foment experimental research into fundamental aspects of proteins that depend on electrostatic interactions. It will maintain a depository for experimental data useful for critical assessment of methods for structure-based electrostatics calculations. To help guide the development of computational methods, the Cooperative will organize blind prediction exercises. As a first step, computational laboratories were invited to reproduce an unpublished set of experimental pK a values of acidic and basic residues introduced in the interior of staphylococcal nuclease by site-directed mutagenesis. The pK a values of these groups are unique and challenging to simulate owing to the large magnitude of their shifts relative to normal pK a values in water. Many computational methods were tested in this first Blind Prediction Challenge and critical assessment exercise. A workshop was organized in the Telluride Science Research Center to objectively assess the performance of many computational methods tested on this one extensive data set. This volume of Proteins: Structure, Function, and Bioinformatics introduces the pK a Cooperative, presents reports submitted by participants in the Blind Prediction Challenge, and highlights some of the problems in structure-based calculations identified during this exercise. © 2011 Wiley-Liss, Inc.


Powderly W.G.,University College Dublin
Journal of Antimicrobial Chemotherapy | Year: 2010

Agents active against HIV type 1 (HIV-1) that target the viral integrase by inhibiting the strand transfer step of integration have now entered the clinical arena. Raltegravir is the first in this new class. Clinical trials in treatment-experienced and in treatment-naive patients have shown that raltegravir-containing regimens have potent antiretroviral activity and are well tolerated. Drug resistance emerges relatively frequently in patients who fail therapy and is associated with mutations in the gene encoding the integrase enzyme. Although such mutations often confer cross-resistance to other integrase inhibitors, newer agents in development, such as S/GSK1349572, show promise as potential second-generation integrase inhibitors. Given their potency, safety and novel mechanism of action, integrase inhibitors represent an important advance in HIV-1 therapy. © The Author 2010. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved.


Whelan K.,University College Dublin
Economic Policy | Year: 2014

The eurozone's TARGET2 payments system has featured heavily in academic and popular discussions of the euro crisis. Some of this commentary has described the system as being responsible for a 'secret bailout' of Europe's periphery. Another common theme has been that the system has built up large credit risks for Germany should the euro break up. This paper discusses the TARGET2 system, focusing in particular on how it impacts the balance sheets of the central banks that participate in the system. It discusses the factors driving TARGET2 balances, considers some counterfactual cases in which eurozone monetary policy might have operated differently, examines the risks to Germany and considers proposals for settlement of these balances. © CEPR, CES, MSH, 2014.


Persoons T.,University College Dublin | Persoons T.,Purdue University
AIAA Journal | Year: 2012

Synthetic jets are used in various applications from flowcontrol to thermal management of electronics. Controlling the jet operating point using a simple voltage to velocity calibration becomes unreliable in case of external pressure field disturbances or varying actuator characteristics. This paper presents a general lumped parameter model for a synthetic jet actuator with an electromagnetic or piezoelectric driver. The fluidic model accurately predicts the synthetic jet operating point (i.e., Reynolds number and stroke length) based on the measured cavity pressure. The model requires only two empirical coefficients characterizing nozzle fluid damping and inertia. These can be obtained via calibration or estimated from pressure loss correlations and the governing acoustic radiation impedance. The model has been validated experimentally for circular and rectangular orifices. The effect of nozzle damping on the nonlinear system response is discussed. Analytical expressions are given for the two resonance frequencies characterizing the system response as a function of the diaphragm and Helmholtz resonance frequencies. The optimal design of an impinging synthetic jet actuator is discussed in terms of the thermal and acoustic efficiencies. Guidelines for selecting the optimum combination of diaphragm and Helmholtz resonance frequency are presented and compared with previous studies.Copyright © 2012 by the American Institute of Aeronautics and Astronautics, Inc.


Huo P.,Boston University | Coker D.F.,Boston University | Coker D.F.,University College Dublin
Journal of Physical Chemistry Letters | Year: 2011

Recent two-dimensional photon-echo experiments suggest that excitation energy transfer in light harvesting systems occurs coherently rather than by incoherent hopping. The signature quantum beating of coherent energy transfer has been observed even at ambient temperatures. In this letter, we use an iterative linearized density matrix (ILDM) propagation approach to study this dynamics in a realistic multistate system-bath model. Our calculations reproduce the observed 400 fs decoherence time, and studies that vary the system Hamiltonian and structured spectral density describing the chromophore network-protein environment interactions give results that enable us to explore the role of initial coherence in energy transfer efficiency of the model network. Our findings suggest that the initial coherence has only a slight effect on energy transfer in this model system. We explore energy transfer optimization of different chromophores in the network by controlling environmental properties. This study points to the importance of stochastic resonance behavior in determining optimal network throughput. © 2011 American Chemical Society.


Anderson B.,University College Dublin | Di Maria C.,Queens University of Belfast
Environmental and Resource Economics | Year: 2011

We use historical industrial emissions data to assess the level of abatement and over-allocation that took place across European countries during the pilot phase (2005-2007) of the European Union Emission Trading Scheme. Using a dynamic panel data model, we estimate the counter factual (business-as-usual) emissions scenario for EU member states. Comparing this baseline to allocated and verified emissions, we find that both over-allocation and abatement occurred, along with under-allocation and emissions inflation. Over the three trading years of the pilot phase we find over-allocation of approximately 280 million EUAs and total abatement of 247 Mt CO2. However, we calculate that emissions inflation of approximately 73 Mt CO2 also occurred, possibly due to uncertainty about future policy design features. © 2010 Springer Science+Business Media B.V.


Caballero R.,University College Dublin | Huber M.,Purdue University
Geophysical Research Letters | Year: 2010

Recent paleoclimate proxy reconstructions show that tropical surface temperatures may have been as high as 35-40C in the Early Cenozoic. Here, we study the tropical atmospheric circulation's response to temperatures in this range using a full-complexity atmospheric general circulation model (AGCM). We find that when equatorial surface temperatures exceed ∼33C, the model undergoes a transition to equatorial superrotation, a state with strong annual-and zonal-mean westerlies on the equator. The transition is driven by zonal momentum convergence due to large-amplitude transient eddies on the equator. These eddies have a structure similar to the observed Madden-Julian Oscillation (MJO). The model's MJO variability is weaker than observed when simulating the modern climate but increases sharply with temperature, coming to dominate the tropical variability and mean state of the warmest climates. Copyright © 2010 by the American Geophysical Union.


Hearty A.,University College Dublin
Food Science and Technology | Year: 2011

The European Commission funded the Flavors, Additives and food Contact materials Exposure Task (FACET) project as part of its Framework Program 7 to develop a surveillance system offering a single platform with the functionality of estimating exposure to three types of food chemicals in Europe such as additives, flavorings and food contact materials. exposure assessment. Within FACET, national food consumption database managers from eight member states have harmonized their food consumption data according to a categorization system related to databases of concentration of food additives, food flavoring substances and to migration of food contact materials. FACET will provide refined dietary exposure for 41 flavoring substances chosen to represent the different typologies of flavorings, and will consider both their presence as added flavorings and/or as natural constituents of the food. FACET will also be an invaluable tool for the packaging industry and the food industry to perform this risk assessment in a systematic and verified way.


Rothwell P.M.,University of Oxford | Howard S.C.,University of Oxford | Dolan E.,Stroke and Hypertension Unit | O'Brien E.,University College Dublin | And 4 more authors.
The Lancet | Year: 2010

Background: The mechanisms by which hypertension causes vascular events are unclear. Guidelines for diagnosis and treatment focus only on underlying mean blood pressure. We aimed to reliably establish the prognostic significance of visit-to-visit variability in blood pressure, maximum blood pressure reached, untreated episodic hypertension, and residual variability in treated patients. Methods: We determined the risk of stroke in relation to visit-to-visit variability in blood pressure (expressed as standard deviation [SD] and parameters independent of mean blood pressure) and maximum blood pressure in patients with previous transient ischaemic attack (TIA; UK-TIA trial and three validation cohorts) and in patients with treated hypertension (Anglo-Scandinavian Cardiac Outcomes Trial Blood Pressure Lowering Arm [ASCOT-BPLA]). In ASCOT-BPLA, 24-h ambulatory blood-pressure monitoring (ABPM) was also studied. Findings: In each TIA cohort, visit-to-visit variability in systolic blood pressure (SBP) was a strong predictor of subsequent stroke (eg, top-decile hazard ratio [HR] for SD SBP over seven visits in UK-TIA trial: 6·22, 95% CI 4·16-9·29, p<0·0001), independent of mean SBP, but dependent on precision of measurement (top-decile HR over ten visits: 12·08, 7·40-19·72, p<0·0001). Maximum SBP reached was also a strong predictor of stroke (HR for top-decile over seven visits: 15·01, 6·56-34·38, p<0·0001, after adjustment for mean SBP). In ASCOT-BPLA, residual visit-to-visit variability in SBP on treatment was also a strong predictor of stroke and coronary events (eg, top-decile HR for stroke: 3·25, 2·32-4·54, p<0·0001), independent of mean SBP in clinic or on ABPM. Variability on ABPM was a weaker predictor, but all measures of variability were most predictive in younger patients and at lower (


Higgins A.,Materials Private Hospital | Hannan M.M.,University College Dublin
Journal of Hospital Infection | Year: 2013

Background: In 2009, the World Health Organization recommended the use of a 'multi-faceted, multi-modal hand hygiene strategy' (Five Moments for Hand Hygiene) to improve hand hygiene compliance among healthcare workers. As part of this initiative, a training programme was implemented using an automated gaming technology training and audit tool to educate staff on hand hygiene technique in an acute healthcare setting. Aim: To determine whether using this automated training programme and audit tool as part of a multi-modal strategy would improve hand hygiene compliance and technique in an acute healthcare setting. Methods: A time-series quasi-experimental design was chosen to measure compliance with the Five Moments for Hand Hygiene and handwashing technique. The study was performed from November 2009 to April 2012. An adenosine triphosphate monitoring system was used to measure handwashing technique, and SureWash (Glanta Ltd, Dublin, Ireland), an automated auditing and training unit, was used to provide assistance with staff training and education. Findings: Hand hygiene technique and compliance improved significantly over the study period (P < 0.0001). Conclusion: Incorporation of new automated teaching technology into a hand hygiene programme can encourage staff participation in learning, and ultimately improve hand hygiene compliance and technique in the acute healthcare setting. © 2013 The Healthcare Infection Society.


Zellentin A.,University College Dublin
Climatic Change | Year: 2015

This contribution looks at those Small Island Developing States that are doomed to disappear due to anthropogenic climate change. The citizens of these states will not only lose their physical homeland but also their social structure and cultural community. The focus here is on cultural loss. While its subjective importance is easy to grasp, it is harder to see cultural loss as a matter of justice. This paper first presents an account of why cultural loss is often seen as merely unfortunate but not unjust. Against these worries, the paper argues that we have a right that no one threatens our social bases of self-respect and that societal cultures are one important base of self-respect. The discussion concludes that anthropogenic climate change affects peoples’ rights with regard to the cultural dimension and that therefore adaptation efforts ought to protect the social bases of self-respect of those climate refugees whose physical, political, and cultural existence is threatened by our inability to keep emissions below safe levels. © 2015 Springer Science+Business Media Dordrecht


Healy J.J.,National University of Ireland, Maynooth | Sheridan J.T.,University College Dublin
Journal of the Optical Society of America A: Optics and Image Science, and Vision | Year: 2011

The product of the spatial and spatial frequency extents of a wave field has proven useful in the analysis of the sampling requirements of numerical simulations. We propose that the ratio of these quantities is also illuminating. We have shown that the distance at which the so-called "direct method" becomes more efficient than the so-called "spectral method" for simulations of Fresnel transforms may be written in terms of this space-bandwidth ratio. We have proposed generalizations of these algorithms for numerical simulations of general ABCD systems and derived expressions for the "transition space-bandwidth ratio," above which the generalization of the spectral method is the more efficient algorithm and below which the generalization of the direct method is preferable. © 2011 Optical Society of America.


Charlton B.D.,University College Dublin
PLoS ONE | Year: 2015

Determining the information content of animal vocalisations can give valuable insights into the potential functions of vocal signals. The source-filter theory of vocal production allows researchers to examine the information content of mammal vocalisations by linking variation in acoustic features with variation in relevant physical characteristics of the caller. Here I used a source-filter theory approach to classify female koala vocalisations into different call-types, and determine which acoustic features have the potential to convey important information about the caller to other conspecifics. A two-step cluster analysis classified female calls into bellows, snarls and tonal rejection calls. Additional results revealed that female koala vocalisations differed in their potential to provide information about a given caller's phenotype that may be of importance to receivers. Female snarls did not contain reliable acoustic cues to the caller's identity and age. In contrast, female bellows and tonal rejection calls were individually distinctive, and the tonal rejection calls of older female koalas had consistently lower mean, minimum and maximum fundamental frequency. In addition, female bellows were significantly shorter in duration and had higher fundamental frequency, formant frequencies, and formant frequency spacing than male bellows. These results indicate that female koala vocalisations have the potential to signal the caller's identity, age and sex. I go on to discuss the anatomical basis for these findings, and consider the possible functional relevance of signalling this type of information in the koala's natural habitat. Copyright: © 2015 Benjamin D. Charlton.


Waples R.S.,National Oceanic and Atmospheric Administration | Do C.,National Oceanic and Atmospheric Administration | Chopelet J.,University College Dublin
Ecology | Year: 2011

The concept of effective population size (N e) was developed under a discretegeneration model, but most species have overlapping generations. In the early 1970s, J. Felsenstein and W. G. Hill independently developed methods for calculating Ne in agestructured populations; the two approaches produce the same answer under certain conditions and have contrasting advantages and disadvantages. Here, we describe a hybrid approach that combines useful features of both. Like Felsenstein's model, the new method is based on agespecific survival and fertility rates and therefore can be directly applied to any species for which life table data are available. Like Hill, we relax the restrictive assumption in Felsenstein's model regarding random variance in reproductive success, which allows more general application. The basic principle underlying the new method is that age structure stratifies a population into winners and losers in the game of life: individuals that live longer have more opportunities to reproduce and therefore have a higher mean lifetime reproductive success. This creates different classes of individuals within the population, and grouping individuals by age at death provides a simple means of calculating lifetime variance in reproductive success of a newborn cohort. The new method has the following features: (1) it can accommodate unequal sex ratio and sex-specific vital rates and overdispersed variance in reproductive success; (2) it can calculate effective size in species that change sex during their lifetime; (3) it can calculate Ne and the ratio Ne/N based on various ways of defining N; (4) it allows one to explore the relationship between Ne and the effective number of breeders per year (Nb), which is a quantity that genetic estimators of contemporary Ne commonly provide information about; and (5) it is implemented in freely available software (AgeNe). © 2011 by the Ecological Society of America.


O'Connor N.E.,Queens University of Belfast | O'Connor N.E.,University College Dublin
Ecological Indicators | Year: 2013

Coastal systems, such as rocky shores, are among the most heavily anthropogenically-impacted marine ecosystems and are also among the most productive in terms of ecosystem functioning. One of the greatest impacts on coastal ecosystems is nutrient enrichment from human activities such as agricultural run-off and discharge of sewage. The aim of this study was to identify and characterise potential effects of sewage discharges on the biotic diversity of rocky shores and to test current tools for assessing the ecological status of rocky shores in line with the EU Water Framework Directive (WFD). A sampling strategy was designed to test for effects of sewage outfalls on rocky shore assemblages on the east coast of Ireland and to identify the scale of the putative impact. In addition, a separate sampling programme based on the Reduced algal Species List (RSL), the current WFD monitoring tool for rocky shores in Ireland and the UK, was also completed by identifying algae and measuring percent cover in replicate samples on rocky shores during Summer. There was no detectable effect of sewage outfalls on benthic taxon diversity or assemblage structure. However, spatial variability of assemblages was greater at sites proximal or adjacent to sewage outfalls compared to shores without sewage outfalls present. Results based on the RSL, show that algal assemblages were not affected by the presence of sewage outfalls, except when classed into functional groups when variability was greater at the sites with sewage outfalls. A key finding of both surveys, was the prevalence of spatial and temporal variation of assemblages. It is recommended that future metrics of ecological status are based on quantified sampling designs, incorporate changes in variability of assemblages (indicative of community stability), consider shifts in assemblage structure and include both benthic fauna and flora to assess the status of rocky shores. © 2013 Elsevier Ltd.


Lubans D.R.,University of Newcastle | Boreham C.A.,University College Dublin | Kelly P.,University of Oxford | Foster C.E.,University of Oxford
International Journal of Behavioral Nutrition and Physical Activity | Year: 2011

Background: Active travel to school (ATS) has been identified as an important source of physical activity for youth. However, the relationship between ATS and health-related fitness (HRF) among youth remains unclear.Methods: A systematic search of seven electronic databases (EMBASE, OVID MEDLINE, PsycINFO, PubMed, Scopus, SPORTDiscus and TRIS on line) was conducted in December 2009 and studies published since 1980 were considered for inclusion.Results: Twenty seven articles were identified that explored the relationship between ATS and the following aspects of HRF: weight status/body composition, cardiorespiratory fitness, muscular fitness and flexibility. Forty-eight percent of the studies that examined the relationship between ATS and weight status/body composition reported significant associations, this increased to 55% once poor quality studies were removed. Furthermore, the findings from five studies, including one longitudinal study, indicate that ATS is positively associated with cardiorespiratory fitness in youth. However, the evidence for the relationships between ATS and muscular fitness or flexibility is equivocal and limited by low study numbers.Conclusions: There is some evidence to suggest that ATS is associated with a healthier body composition and level of cardiorespiratory fitness among youth. Strategies to increase ATS are warranted and should be included in whole-of-school approaches to the promotion of physical activity. © 2011 Lubans et al; licensee BioMed Central Ltd.


Akcay S.,University of Southampton | Warburton N.,University College Dublin | Barack L.,University of Southampton
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

State-of-the-art computations of the gravitational self-force (GSF) on massive particles in black hole spacetimes involve numerical evolution of the metric perturbation equations in the time domain, which is computationally very costly. We present here a new strategy based on a frequency-domain treatment of the perturbation equations, which offers considerable computational saving. The essential ingredients of our method are (i) a Fourier-harmonic decomposition of the Lorenz-gauge metric perturbation equations and a numerical solution of the resulting coupled set of ordinary equations with suitable boundary conditions; (ii) a generalized version of the method of extended homogeneous solutions [L. Barack, A. Ori, and N. Sago, Phys. Rev. D 78, 084021 (2008)] used to circumvent the Gibbs phenomenon that would otherwise hamper the convergence of the Fourier mode sum at the particle's location; (iii) standard mode-sum regularization, which finally yields the physical GSF as a sum over regularized modal contributions. We present a working code that implements this strategy to calculate the Lorenz-gauge GSF along eccentric geodesic orbits around a Schwarzschild black hole. The code is far more efficient than existing time-domain methods; the gain in computation speed (at a given precision) is about an order of magnitude at an eccentricity of 0.2, and up to 3 orders of magnitude for circular or nearly circular orbits. This increased efficiency was crucial in enabling the recently reported calculation of the long-term orbital evolution of an extreme mass ratio inspiral [N. Warburton, S. Akcay, L. Barack, J. R. Gair, and N. Sago, Phys. Rev. D 85, 061501(R) (2012)]. Here we provide full technical details of our method to complement the above report. © 2013 American Physical Society.


Oconnell N.,Technical University of Denmark | Pinson P.,Technical University of Denmark | Madsen H.,Technical University of Denmark | Omalley M.,University College Dublin
Renewable and Sustainable Energy Reviews | Year: 2014

Advances in IT, control and forecasting capabilities have made demand response a viable, and potentially attractive, option to increase power system flexibility. This paper presents a critical review of the literature in the field of demand response, providing an overview of the benefits and challenges of demand response. These benefits include the ability to balance fluctuations in renewable generation and consequently facilitate higher penetrations of renewable resources on the power system, an increase in economic efficiency through the implementation of real-time pricing, and a reduction in generation capacity requirements. Nevertheless, demand response is not without its challenges. The key challenges for demand response centre around establishing reliable control strategies and market frameworks so that the demand response resource can be used optimally. One of the greatest challenges for demand response is the lack of experience, and the consequent need to employ extensive assumptions when modelling and evaluating this resource. This paper concludes with an examination of these assumptions, which range from assuming a fixed linear price-demand relationship for price responsive demand, to modelling the highly diverse, distributed and uncertain demand response resource as a single, centralised negative generator, adopting fixed characteristics and constraints. © 2014 Elsevier Ltd.


English N.J.,University College Dublin | Tse J.S.,University of Saskatchewan
Physical Review Letters | Year: 2011

The density distributions and fluctuations in grids of varying size in liquid water at ambient pressure, both above the freezing point and in the supercooled state, are analyzed from the trajectories obtained from large-scale molecular dynamics simulations. It is found that the occurrence of low- and high-density regions (LDL and HDL) is transient and their respective residence times are dependent on the size of the simulated system. The spatial extent of density-density correlation is found to be within 7 Å or less. The temporal existence of LDL and HDL arises as a result of natural density fluctuations of an equilibrium system. The density of bulk water at ambient conditions is homogenous. © 2011 American Physical Society.


Evans A.C.,University College Dublin
Society of Reproduction and Fertility supplement | Year: 2010

In cattle we have noted that the antral follicle count (AFC, follicles > or = 3 mm in diameter) varies greatly among animals (from 5 to 50), is repeatable within animals, and is highly correlated with the total number of healthy follicles in ovaries. Also, animals with low AFC have higher serum concentrations of FSH and LH, but lower concentrations of Anti-Mullerian Hormone, progesterone and androgens than animals with high AFC. We have investigated the effect of maternal environment during gestation on their offspring AFC by restricting maternal nutrition to 60% of maintenance requirements (compared with 100% in controls) during the first third of gestation. Calves born to nutritionally restricted mothers had 60% lower AFC compared with calves born to mothers fed control diets. In other studies we have evidence to indicate that fertility may be compromised in animals with low AFC due to effects on oocytes, progesterone and the endometrium compared with animals with high AFC. To examine this directly we assessed AFC in post-partum dairy cows and found that cows with a high AFC had higher pregnancy rates, shorter calving to conception intervals and received fewer services during the breeding season compared with cows with a low AFC. In addition, the high variation in follicle numbers in adults may not only be reflective of reproductive disorders and suboptimal fertility, but there is evidence to indicate that it may be associated with alterations in the function of other non-reproductive systems (e.g. cardiovascular) that may have profound effects on the animal's health and welfare.


Sykora J.,Charles University | Rowland M.,University College Dublin
Helicobacter | Year: 2011

This article reviewed the important publications on Helicobacter pylori research with children between April 2010 and March 2011. The most interesting studies in the last year lend further weight to the evidence for vertical transmission of H. pylori. The discovery of a potential role for jhp0562, the gene which encodes for the cell envelope protein glycosyltransferase, in the progression to peptic ulcer disease is also very interesting as it may provide a novel way to distinguish children at risk of peptic ulcer disease from those who are not, and so determine those who requires treatment to eradicate H. pylori. The rise in non-H. pylori-associated ulcers and erosions continues to be reported with no apparent risk factors for these ulcers identified to date. High levels of treatment failure continue to be reported, and there remains an urgent need for more effective treatment regimes for children. © 2011 Blackwell Publishing Ltd.


Human immunodeficiency virus (HIV) infection is associated with increased cardiovascular risk and reduced high-density lipoprotein cholesterol (HDL-c). In vitro, HIV impairs monocyte-macrophage cholesterol efflux, a major determinant of circulating HDL-c, by increasing ABCA1 degradation, with compensatory upregulation of ABCA1 messenger RNA (mRNA). We examined expression of genes involved in cholesterol uptake, metabolism, and efflux in monocytes from 22 HIV-positive subjects on antiretroviral therapy (ART-Treated), 30 untreated HIV-positive subjects (ART-Naive), and 22 HIV-negative controls (HIV-Neg). HDL-c was lower and expression of ABCA1 mRNA was higher in ART-Naive subjects than in both ART-Treated and HIV-Neg subjects (both P < .01), with HDL-c inversely correlated with HIV RNA (ρ = -0.52; P < .01). Expression of genes involved in cholesterol uptake (LDLR, CD36), synthesis (HMGCR), and regulation (SREBP2, LXRA) was significantly lower in both ART-Treated and ART-Naive subjects than in HIV-Neg controls. In vivo, increased monocyte ABCA1 expression in untreated HIV-infected patients and normalization of ABCA1 expression with virological suppression by ART supports direct HIV-induced impairment of cholesterol efflux previously demonstrated in vitro. However, decreased expression of cholesterol sensing, uptake, and synthesis genes in both untreated and treated HIV infection suggests that both HIV and ART affect monocyte cholesterol metabolism in a pattern consistent with accumulation of intramonocyte cholesterol.


McNamara N.,University College Dublin
Interacting with Computers | Year: 2013

Measuring user satisfaction is an important activity for Human-Computer Interaction (HCI) professionals and there exists a plethora of instruments for this purpose. The aim of this paper is to propose three criteria that practitioners can use when evaluating questionnaire quality prior to selecting an instrument for use in an evaluation. These criteria are: (1) the presence of a clear conceptualization of satisfaction based on a sound theoretical framework, (2) the use of the psychometric method in the questionnaire development process and (3) the extent to which the questionnaire developers have considered the usefulness of the final instrument in an evaluation setting. Two recently published satisfaction questionnaire are discussed in light of these three criteria. © 2013 The Author.


Browne M.A.,University of Sydney | Browne M.A.,University College Dublin | Galloway T.S.,University of Exeter | Thompson R.C.,University of Plymouth
Environmental Science and Technology | Year: 2010

The human population generates vast quantities of waste material. Macro (>1 mm) and microscopic (<1 mm) fragments of plastic debris represent a substantial contamination problem. Here, we test hypotheses about the influence of wind and depositional regime on spatial patterns of micro- and macro-plastic debris within the Tamar Estuary, UK. Debris was identified to the type of polymer using Fourier-transform infrared spectroscopy (FT-IR) and categorized according to density. In terms of abundance, microplastic accounted for 65% of debris recorded and mainly comprised polyvinylchloride, polyester, and polyamide. Generally, there were greater quantities of plastic at downwind sites. For macroplastic, there were clear patterns of distribution for less dense items, while for microplastic debris, clear patterns were for denser material. Small particles of sediment and plastic are both likely to settle slowly from the water-column and are likely to be transported by the flow of water and be deposited in areas where the movements of water are slower. There was, however, no relationship between the abundance of microplastic and the proportion of clay in sediments from the strandline. These results illustrate how FT-IR spectroscopy can be used to identify the different types of plastic and in this case was used to indicate spatial patterns, demonstrating habitats that are downwind acting as potential sinks for the accumulation of debris. © 2010 American Chemical Society.


Rothwell P.M.,University of Oxford | Howard S.C.,University of Oxford | Dolan E.,Stroke and Hypertension Unit | O'Brien E.,University College Dublin | And 4 more authors.
The Lancet Neurology | Year: 2010

Background: Analyses of some randomised trials show that calcium-channel blockers reduce the risk of stroke more than expected on the basis of mean blood pressure alone and that β blockers are less effective than expected. We aimed to investigate whether the effects of these drugs on variability in blood pressure might explain these disparities in effect on stroke risk. Methods: The Anglo-Scandinavian Cardiac Outcomes Trial Blood Pressure Lowering Arm (ASCOT-BPLA) compared amlodipine-based regimens with atenolol-based regimens in 19 257 patients with hypertension and other vascular risk factors and the Medical Research Council (MRC) trial compared atenolol-based and diuretic-based regimens versus placebo in 4396 hypertensive patients aged 65-74 years. We expressed visit-to-visit variability of blood pressure during follow-up in the two trials as standard deviation (SD) and as transformations uncorrelated with mean blood pressure. For ASCOT-BPLA, we also studied within-visit variability and variability on 24 h ambulatory blood-pressure monitoring (ABPM). Results: In ASCOT-BPLA, group systolic blood pressure (SBP) SD was lower in the amlodipine group than in the atenolol group at all follow-up visits (p<0·0001), mainly because of lower within-individual visit-to-visit variability. Within-visit and ABPM variability in SBP were also lower in the amlodipine group than in the atenolol group (all p<0·0001). Analysis of changes from baseline showed that variability decreased over time in the amlodipine group and increased in the atenolol group. The lower risk of stroke in the amlodipine group (hazard ratio 0·78, 95% CI 0·67-0·90) was partly attenuated by adjusting for mean SBP during follow-up (0·84, 0·72-0·98), but was abolished by also adjusting for within-individual SD of clinic SBP (0·99, 0·85-1·16). Findings were similar for coronary events. In the ABPM substudy, reduced variability in daytime SBP in the amlodipine group (p<0·0001) partly accounted for the reduced risk of vascular events, but reduced visit-to-visit variability in clinic SBP had a greater effect. In the MRC trial, group SD SBP and all measures of within-individual visit-to-visit variability in SBP were increased in the atenolol group compared with both the placebo group and the diuretic group during initial follow-up (all p<0·0001). Subsequent temporal trends in variability in blood pressure during follow-up in the atenolol group correlated with trends in stroke risk. Interpretation: The opposite effects of calcium-channel blockers and β blockers on variability of blood pressure account for the disparity in observed effects on risk of stroke and expected effects based on mean blood pressure. To prevent stroke most effectively, blood-pressure-lowering drugs should reduce mean blood pressure without increasing variability; ideally they should reduce both. Funding: None. © 2010 Elsevier Ltd. All rights reserved.


Protein adsorption is one of the key parameters influencing the biocompatibility of medical device materials. This study investigates serum protein adsorption and bacterial attachment on polymer coatings deposited using an atmospheric pressure plasma jet system. The adsorption of bovine serum albumin and bovine fibrinogen (Fg) onto siloxane and fluorinated siloxane elastomeric coatings that exhibit water contact angles (θ) ranging from superhydrophilic (θ < 5°) to superhydrophobic (θ > 150°) were investigated. Protein interactions were evaluated in situ under dynamic flow conditions by spectroscopic ellipsometry. Superhydrophilic coatings showed lower levels of protein adsorption when compared with hydrophobic siloxane coatings, where preferential adsorption was shown to occur. Reduced levels of protein adsorption were also observed on fluorinated siloxane copolymer coatings exhibiting hydrophobic wetting behaviour. The lower levels of protein adsorption observed on these surfaces indicated that the presence of fluorocarbon groups have the effect of reducing surface affinity for protein attachment. Analysis of superhydrophobic siloxane and fluorosiloxane surfaces showed minimal indication of protein adsorption. This was confirmed by bacterial attachment studies using a Staphylococcus aureus strain known to bind specifically to Fg, which showed almost no attachment to the superhydrophobic coating after protein adsorption experiments. These results showed the superhydrophobic surfaces to exhibit antimicrobial properties and significantly reduce protein adsorption.


Ilten P.,University College Dublin
Nuclear Physics B - Proceedings Supplements | Year: 2014

Measurements of the Z → ττ and W → τντ cross-sections at the LHC with data taken at √s = 7 TeV are reported for the ATLAS, CMS, and LHCb experiments. All results are found to agree with the Standard Model. © 2014 Elsevier B.V.


Destrade M.,University College Dublin | Ogden R.W.,University of Glasgow
Journal of the Acoustical Society of America | Year: 2010

Consider the constitutive law for an isotropic elastic solid with the strain-energy function expanded up to the fourth order in the strain and the stress up to the third order in the strain. The stress-strain relation can then be inverted to give the strain in terms of the stress with a view to considering the incompressible limit. For this purpose, use of the logarithmic strain tensor is of particular value. It enables the limiting values of all nine fourth-order elastic constants in the incompressible limit to be evaluated precisely and rigorously. In particular, it is explained why the three constants of fourth-order incompressible elasticity μ, Ā, and D̄ are of the same order of magnitude. Several examples of application of the results follow, including determination of the acoustoelastic coefficients in incompressible solids and the limiting values of the coefficients of nonlinearity for elastic wave propagation. © 2010 Acoustical Society of America.


McGovern R.K.,Massachusetts Institute of Technology | Smith W.J.,University College Dublin
Energy Conversion and Management | Year: 2012

Using simple, finite-time, thermodynamic models of solar thermal power plants, the existence of an optimal solar receiver temperature has previously been demonstrated in literature. Scant attention has been paid, however, to the presence of an optimal level of solar concentration at which solar-to-electric efficiency is maximised. This paper addresses that gap. A simple mathematical model is developed to assess the influence of key system temperatures, thermal conductances and the receiver irradiance (radiation striking unit receiver area) upon the optimal receiver temperature and solar-to-electric efficiency of Rankine-cycle, solar-trough and solar-tower, direct-steam and molten-salts, power plants. The analysis shows that, as the thermal resistance of the solar receiver and condenser increases, the optimal receiver temperature increases whilst the optimal receiver irradiance decreases. The optimal level of receiver irradiance, for solar thermal plants employing a service fluid of molten salts, is found to occur within a range of values achievable using current solar tower technologies. The efficiency trade-off involved in using molten salts rather than direct steam is investigated. The optimal receiver temperatures calculated suggest the use of sub-critical Rankine cycles for solar trough plants, but super-critical Rankine cycles for solar tower plants, if the objective is to maximise solar-to-electric efficiency. © 2012 Elsevier Ltd. All rights reserved.


Sudol M.,Weis Center for Research | Sudol M.,Mount Sinai School of Medicine | Shields D.C.,University College Dublin | Farooq A.,University of Miami
Seminars in Cell and Developmental Biology | Year: 2012

YAP (Yes-associated protein) is a potent oncogene and a major effector of the mammalian Hippo tumor suppressor pathway. In this review, our emphasis is on the structural basis of how YAP recognizes its various cellular partners. In particular, we discuss the role of LATS kinase and AMOTL1 junction protein, two key cellular partners of YAP that bind to its WW domain, in mediating cytoplasmic localization of YAP and thereby playing a key role in the regulation of its transcriptional activity. Importantly, the crystal structure of an amino-terminal domain of YAP in complex with the carboxy-terminal domain of TEAD transcription factor was only recently solved at atomic resolution, while the structure of WW domain of YAP in complex with a peptide containing the PPxY motif has been available for more than a decade. We discuss how such structural information may be exploited for the rational development of novel anti-cancer therapeutics harboring greater efficacy coupled with low toxicity. We also embark on a brief discussion of how recent in silico studies led to identification of the cardiac glycoside digitoxin as a potential modulator of WW domain-ligand interactions. Conversely, dobutamine was identified in a screen of known drugs as a compound that promotes cytoplasmic localization of YAP, thereby resulting in growth suppressing activity. Finally, we discuss how a recent study on the dynamics of WW domain folding on a biologically critical time scale may provide a tool to generate repertoires of WW domain variants for regulation of the Hippo pathway toward desired, non-oncogenic outputs. © 2012 Elsevier Ltd.


Gronert S.,Virginia Commonwealth University | Keeffe J.R.,San Francisco State University | More O'Ferrall R.A.,University College Dublin
Journal of the American Chemical Society | Year: 2011

Thermodynamic stabilities of 92 carbenes, singlets and triplets, have been evaluated on the basis of hydrogenation enthalpies calculated at the G3MP2 level. The carbenes include alkyl-, aryl-, and heteroatom-substituted structures as well as cyclic 1,3-diheteroatom carbenes. Over a wide energy range, a good correlation is seen between the singlet-triplet gaps and the hydrogenation enthalpies of the singlets, but there are some clear outliers, which represent cases where the triplet has unusual stability or instability. By use of hydrogenation enthalpies, separate carbene stabilization enthalpy scales (CSEs) have been developed for singlets and triplets, and these highlight structural features that affect the stability of each. The treatment also allows estimates of aromaticity in cyclic carbenes. In this way, imidazol-2-ylidene is estimated to have an aromatic stabilization energy of about 20 kcal/mol. © 2011 American Chemical Society.


Migge B.,University College Dublin
Journal of Pragmatics | Year: 2011

In recent years, Pidgin and Creole languages have made significant inroads into the public domain of the countries where they are spoken. The media, and the radio broadcasting sector in particular, are the areas in which they figure most prominently. Extension of their use has brought about linguistic changes (Garrett, 2000). This paper explores such changes in relation to the Eastern Maroon radio program Loweman Pansu broadcasted in French Guiana. It investigates whether the program assimilates established norms and practices of programs run in European languages or introduces innovative ones based on local practices. Analysis suggests that the program's makeup and linguistic practices contribute to the emergence of an alternative social space that is distinctly Eastern Maroon in character but integrates properties that are linked to the urban context. This contributes to the construction of a modern urban Maroon identity that transcends traditional ethnic and national borders. © 2010 Elsevier B.V.


Gavin K.,University College Dublin
European Journal of Engineering Education | Year: 2011

This paper describes the use of project-based learning to teach design skills to civil engineering students at University College Dublin (UCD). The paper first considers the development of problem-based leaning (PBL) as a tool in higher education. The general issues to be considered in the design of the curriculum for a PBL module are reviewed. Consideration of the literature on the application of PBL in civil engineering suggests that, because of the hierarchical nature of engineering education, PBL is best applied in a hybrid form known as Project Based Learning. A detailed description is given of how hybrid PBL was implemented in the final year of a civil engineering degree programme. In the final section, the results of an evaluation process designed to gain an insight into students' perceptions of the PBL process are reviewed. The module, which was developed at UCD, provided an excellent mechanism for developing many skills, including problem-solving, innovation, group-working and presentation skills desired by graduate employers. It was clear that the students enjoyed the peer to peer teaching and increased interaction with staff and external experts, which the problem-solving nature of the module facilitated. © 2011 Copyright SEFI.


Murphy C.D.,University College Dublin
Biotechnology Letters | Year: 2015

Several wild type and recombinant microorganisms can transform drugs to the equivalent human metabolites. Fungi, such as Cunninghamella spp., and Streptomyces bacteria express cytochrome P450 (CYP) enzymes that enable analogous phase I (oxidative) reactions with a wide range of drugs. The gene encoding the bifunctional CYP102A1 in Bacillus megaterium can be expressed easily in E. coli, and extensive mutagenesis experiments have generated numerous variants that can produce human drug metabolites. Additionally, human CYP isoforms have been expressed in various hosts. The application of microbial CYPs to the production of human drug metabolites is reviewed, and additional applications in the field of drug development are considered. © 2014, Springer Science+Business Media Dordrecht.


Marques-Silva J.,University College Dublin
Proceedings of The International Symposium on Multiple-Valued Logic | Year: 2010

The task of modeling and reasoning about real-world problems often involves analyzing over-constrained representations, where not all constraints of a problem can be simultaneously satisfied. The need to analyze over-constrained (or unsatisfiable) problems occurs in many settings, including data and knowledge bases, artificial intelligence, applied formal methods, operations research and description logics. In most cases, the problem to solve is related with some form of minimal unsatisfi-ability, i.e. an irreducible set of constraints that explains unsatisfiability. This paper provides an overview of some of the computational problems related with minimal unsatisfi-ability in Boolean logic, including the identification of one minimal unsatisfiable sub-formula and the identification of all minimal unsatisfiable sub-formulas. In addition, the paper briefly overviews practical applications of minimal unsatisfiability. Finally, the paper highlights recent work on minimal unsatisfiability in other domains. © 2010 IEEE.


Watson R.W.G.,University College Dublin | Kay E.W.,Beaumont Hospital | Kay E.W.,Royal College of Surgeons in Ireland | Smith D.,Royal College of Surgeons in Ireland
Nature Reviews Cancer | Year: 2010

Cancer is caused by complex interactions between genes, environment and lifestyles. Biobanks of well-annotated human tissues are an important resource for studying the underlying mechanisms of cancer. Although such biobanks exist, their integration to form larger biobanks is now required to provide the diversity of samples that are needed to study the complexity and heterogeneity of cancer. Clear guidelines and policies are also required to address the challenges of integrating individual institutional or national biobanks and build public trust. This Science and Society article highlights some of the main practical and ethical issues that are undergoing discussion in the integration of tissue biobanks for cancer. © 2010 Macmillan Publishers Limited. All rights reserved.


Fair T.,University College Dublin
Frontiers in Immunology | Year: 2015

Immune cells play an integral role in affecting successful reproductive function. Indeed, disturbed or aberrant immune function has been identified as primary mechanisms behind infertility. In contrast to the extensive body of literature that exists for human and mouse, studies detailing the immunological interaction between the embryo and the maternal endometrium are quite few in cattle. Nevertheless, by reviewing the existing studies and extrapolating from sheep, pig, mouse, and human data, we can draw a reasonably comprehensive picture. Key contributions of immune cell populations include granulocyte involvement in follicle differentiation and gamete transfer, monocyte invasion of the peri-ovulatory follicle and their subsequent role in corpus luteum formation and the pivotal roles of maternal macrophage and dendritic cells in key steps of the establishment of pregnancy, particularly, the maternal immune response to the embryo. These contributions are reviewed in detail below and key findings are discussed. © 2015 Fair.


Sheridan G.K.,University of Cambridge | Murphy K.J.,University College Dublin
Open Biology | Year: 2013

An essential aspect of normal brain function is the bidirectional interaction and communication between neurons and neighbouring glial cells. To this end, the brain has evolved ligand-receptor partnerships that facilitate crosstalk between different cell types. The chemokine, fractalkine (FKN), is expressed on neuronal cells, and its receptor, CX3CR1, is predominantly expressed on microglia. This review focuses on several important functional roles for FKN/CX3CR1 in both health and disease of the central nervous system. It has been posited that FKN is involved in microglial infiltration of the brain during development. Microglia, in turn, are implicated in the developmental synaptic pruning that occurs during brain maturation. The abundance of FKN on mature hippocampal neurons suggests a homeostatic non-inflammatory role in mechanisms of learning and memory. There is substantial evidence describing a role for FKN in hippocampal synaptic plasticity. FKN, on the one hand, appears to prevent excess microgli l activation in the absence of injury while promoting activation of microglia and astrocytes during inflammatory episodes. Thus, FKN appears to be neuroprotective in some settings, whereas it contributes to neuronal damage in others. Many progressive neuroinflammatory disorders that are associated with increased microglial activation, such as Alzheimer's disease, show disruption of the FKN/CX3CR1 communication system. Thus, targeting CX3CR1 receptor hyperactivation with specific antagonists in such neuroinflammatory conditions may eventually lead to novel neurotherapeutics. © 2013 The Authors.


Long R.,University College Dublin | Long R.,University of Rochester | Prezhdo O.V.,University of Rochester
Journal of the American Chemical Society | Year: 2014

Photoexcitation of the plasmon band in metallic nanoparticles adsorbed on a TiO2 surface initiates many important photovoltaic and photocatalytic processes. The traditional view on the photoinduced charge separation involves excitation of a surface plasmon, its subsequent dephasing into electron-hole pairs, followed by electron transfer (ET) from the metal nanoparticle into TiO2. We use nonadiabatic molecular dynamics combined with time-domain density functional theory to demonstrate that an electron appears inside TiO2 immediately upon photoexcitation with a high probability (∼50%), bypassing the intermediate step of electron-hole thermalization inside the nanoparticle. By providing a detailed, atomistic description of the charge separation, energy relaxation, and electron-hole recombination processes, the simulation rationalizes why the experimentally observed ultrafast photoinduced ET in an Au-TiO2 system is possible in spite of the fast energy relaxation. The simulation shows that the photogenerated plasmon is highly delocalized onto TiO2, and thus, it is shared by the electron donor and acceptor materials. In the 50% of the cases remaining after the instantaneous photogeneration of the charge-separated state, the electron injects into TiO2 on a sub-100 fs time scale by the nonadiabatic mechanism due to high density of acceptor states. The electron-phonon relaxation parallels the injection and is slower, resulting in a transient heating of the TiO2 surface by 40 K. Driven by entropy, the electron moves further into TiO2 bulk. If the electron remains trapped at the TiO2 surface, it recombines with the hole on a picosecond time scale. The obtained ET and recombination times are in excellent agreement with the experiment. The delocalized plasmon state observed in our study establishes a novel concept for plasmonic photosensitization of wide band gap semiconductors, leading to efficient conversion of photons to charge carriers and to hybrid materials with a wide variety of applications in photocatalysis and photovoltaics. © 2014 American Chemical Society.


O'Donovan D.S.,University College Dublin
Cell death & disease | Year: 2013

Mitotic cell death following prolonged arrest is an important death mechanism that is not completely understood. This study shows that Protein Tyrosine Phosphatase 1B (PTP1B) undergoes phosphorylation during mitotic arrest induced by microtubule-targeting agents (MTAs) in chronic myeloid leukaemia cells. Inhibition of cyclin-dependent kinase 1 (Cdk1) or polo-like kinase 1 (Plk1) during mitosis prevents PTP1B phosphorylation, implicating these kinases in PTP1B phosphorylation. In support of this, Cdk1 and Plk1 co-immunoprecipitate with endogenous PTP1B from mitotic cells. In addition, active recombinant Cdk1-cyclin B1 directly phosphorylates PTP1B at serine 386 in a kinase assay. Recombinant Plk1 phosphorylates PTP1B on serine 286 and 393 in vitro, however, it requires a priming phosphorylation by Cdk1 at serine 386 highlighting a novel co-operation between Cdk1 and Plk1 in the regulation of PTP1B. Furthermore, overexpression of wild-type PTP1B induced mitotic cell death, which is potentiated by MTAs. Moreover, mutation of serine 286 abrogates the cell death induced by PTP1B, whereas mutation of serine 393 does not, highlighting the importance of serine 286 phosphorylation in the execution of mitotic cell death. Finally, phosphorylation on serine 286 enhanced PTP1B phosphatase activity. Collectively, these data reveal that PTP1B activity promotes mitotic cell death and is regulated by the co-operative action of Cdk1 and Plk1 during mitotic arrest.


Taylor C.T.,Conway Institute Systems Biology Ireland | McElwain J.C.,University College Dublin
Physiology | Year: 2010

Metazoan diversification occurred during a time when atmospheric oxygen levels fluctuated between 15 and 30%. The hypoxia-inducible factor (HIF) is a primary regulator of the adaptive transcriptional response to hypoxia. Although the HIF pathway is highly conserved, its complexity increased during periods when atmospheric oxygen concentrations were increasing. Thus atmospheric oxygen levels may have provided a selection force on the development of cellular oxygen-sensing pathways. © 2010 Int. Union Physiol. Sci./Am. Physiol. Soc.


Bates J.R.,University College Dublin
Climate Dynamics | Year: 2012

A theoretical investigation of climate stability and sensitivity is carried out using three simple linearized models based on the top-of-the-atmosphere energy budget. The simplest is the zero-dimensional model (ZDM) commonly used as a conceptual basis for climate sensitivity and feedback studies. The others are two-zone models with tropics and extratropics of equal area; in the first of these (Model A), the dynamical heat transport (DHT) between the zones is implicit, in the second (Model B) it is explicitly parameterized. It is found that the stability and sensitivity properties of the ZDM and Model A are very similar, both depending only on the global-mean radiative response coefficient and the global-mean forcing. The corresponding properties of Model B are more complex, depending asymmetrically on the separate tropical and extratropical values of these quantities, as well as on the DHT coefficient. Adopting Model B as a benchmark, conditions are found under which the validity of the ZDM and Model A as climate sensitivity models holds. It is shown that parameter ranges of physical interest exist for which such validity may not hold. The 2 × CO2 sensitivities of the simple models are studied and compared. Possible implications of the results for sensitivities derived from GCMs and palaeoclimate data are suggested. Sensitivities for more general scenarios that include negative forcing in the tropics (due to aerosols, inadvertent or geoengineered) are also studied. Some unexpected outcomes are found in this case. These include the possibility of a negative global-mean temperature response to a positive global-mean forcing, and vice versa. © 2010 Springer-Verlag.


Kelly B.D.,University College Dublin
British Journal of Psychiatry | Year: 2014

The United Nations Convention on the Rights of Persons with Disabilities is a welcome articulation of the rights of the disabled. However, as its definition of disability appears to include mental illness, the UK appears to violate it by linking mental illness with detention. Clarity and, possibly, change are needed.


The electronic structure of the TiO2(110) surface interfaced with both a semiconducting and metallic carbon nanotube (CNT) was investigated by density functional theory. Our simulations rationalized visible light photocatalytic activity of CNT/TiO2 hybrid materials higher than that under ultraviolent irradiation and showed that the photoactivity of a semiconducting CNT decorating TiO2 is better than that of the metallic CNT/TiO2 system due to efficient charge separation across the interface. This suggests that semiconducting CNT/TiO2 could be a potential photovoltaic material. In contrast, strong interaction between a metallic CNT and TiO2 leads to large charge transfer. Such charge transfer reduces the built-in potential, in turn resulting in inefficient charge separation. Functionalizing the metallic CNT with a small platinum cluster can increase the built-in potential and drive charge separation. These observations indicate that the CNT/TiO2 interface can be a potential photovoltaic material by a metal cluster decorating a CNT despite a real tube being composed of the mixture of metallic and semiconducting CNTs. © 2013 American Chemical Society.


Mooney P.,National University of Ireland, Maynooth | Corcoran P.,University College Dublin
Transactions in GIS | Year: 2012

In this article we describe the analysis of 25,000 objects from the OpenStreetMap (OSM) databases of Ireland, United Kingdom, Germany, and Austria. The objects are selected as exhibiting the characteristics of "heavily edited" objects. We consider "heavily edited" objects as having 15 or more versions over the object's lifetime. Our results indicate that there are some serious issues arising from the way contributors tag or annotate objects in OSM. Values assigned to the "name" and "highway" attributes are often subject to frequent and unexpected change. However, this "tag flip-flopping" is not found to be strongly correlated with increasing numbers of contributors. We also show problems with usage of the OSM ontology/controlled vocabularly. The majority of errors occurring were caused by contributors choosing values from the ontology "by hand" and spelling these values incorrectly. These issues could have a potentially detrimental effect on the quality of OSM data while at the same time damaging the perception of OSM in the GIS community. The current state of tagging and annotation in OSM is not perfect. We feel that the problems identified are a combination of the flexibility of the tagging process in OSM and the lack of a strict mechanism for checking adherence to the OSM ontology for specific core attributes. More studies related to comparing the names of features in OSM to recognized ground-truth datasets are required. © 2012 Blackwell Publishing Ltd.


Veale D.J.,Park University | Veale D.J.,University College Dublin
Arthritis Research and Therapy | Year: 2013

Psoriatic arthritis (PsA) is the second most common inflammatory arthropathy, after rheumatoid arthritis diagnosis, in early arthritis clinics. Most patients have established psoriasis, often for years, prior to the onset of joint pain and swelling; in addition, associated features of nail disease, dactylitis, enthesitis, spondylitis or uveitis may be present. Psoriasis may not be immediately apparent, as small or patchy lesions may occur in the scalp or perineum. PsA presents as a symmetrical polyarthritis, similar to rheumatoid arthritis, or an asymmetrical oligoarthritis with a predilection for the distal interphalangeal joints. Spinal involvement is similar, although not identical, to ankylosing spondylitis. Joint damage occurs early; up to 50% of PsA patients have an 11% annual erosion rate in the first 2 years of disease duration, suggesting it is not a benign condition. There have been significant advances in our understanding of PsA pathogenesis in recent years, in the areas of genetics and molecular biology, implicating both the innate and the adaptive immune systems. This has lead to the introduction of evidence-based targeted therapy, primarily with tumour necrosis factor inhibitor (TNFi) agents. Therapy with disease-modifying anti-rheumatic drugs, such as methotrexate and leflunomide, remains the first-choice therapeutic intervention, even though there are few randomised controlled trials with these agents. In contrast, a number of successful studies of TNFi agents demonstrate excellent efficacy, in combination with methotrexate, and several novel agents are currently in development for the treatment of PsA. © 2013 BioMed Central Ltd.


Hone D.W.E.,University College Dublin
Journal of Vertebrate Paleontology | Year: 2012

Estimating the mass of an extinct organism is naturally difficult. Practicality and simplicity means that often some linear measurement is used as a proxy. In the case of non-avian dinosaurs, the total length of the animal (from the snout to the tip of the tail) is sometimes used for this purpose. However, the total length of the tail is unknown in all but very few dinosaurian taxa. Tail length data taken from specimens and the literature are shown here to have remarkable variation both between and within clades (and even within single species). Comparison with body length data shows that total length (including the tail) is therefore a less reliable measure of size than using the snout-vent length of the animal. Snout-sacrum lengths are suggested as a more reliable alternative. Total length should not be abandoned, however, both to provide a comparison with older works and specimens lacking complete presacral axial columns, and for communication with the general public. © 2012 Taylor & Francis Group, LLC.


Wolfe K.H.,University College Dublin
PLoS Biology | Year: 2015

Whole-genome duplications (WGDs) are rare evolutionary events with profound consequences. They double an organism’s genetic content, immediately creating a reproductive barrier between it and its ancestors and providing raw material for the divergence of gene functions between paralogs. Almost all eukaryotic genome sequences bear evidence of ancient WGDs, but the causes of these events and the timing of intermediate steps have been difficult to discern. One of the best-characterized WGDs occurred in the lineage leading to the baker’s yeast Saccharomyces cerevisiae. Marcet-Houben and Gabaldón now show that, rather than simply doubling the DNA of a single ancestor, the yeast WGD likely involved mating between two different ancestral species followed by a doubling of the genome to restore fertility. © 2015 Kenneth H. Wolfe.


Murphy J.C.,Gaelic Athletic Association | O'Malley E.,University College Dublin | Gissane C.,St. Marys College | Blake C.,Gaelic Athletic Association
American Journal of Sports Medicine | Year: 2012

Background: Gaelic football is a national sport of Ireland. While predominantly played in Ireland, it is recognized in North America, the United Kingdom, Europe, and Australasia. Its high-velocity, multidirectional, and high physical contact elements expose players to a risk of injury. To date, prospective injury data for Gaelic football has been of short duration. Purpose: To describe the incidence and nature of sport-related injuries in elite male Gaelic football players over 4 consecutive seasons. Study Design: Descriptive epidemiology study. Methods: Over the period 2007 to 2010, a total of 851 Gaelic football players were tracked. Players were members of county-level teams who volunteered to be included in the study. Team injury, training, and match play data were submitted by the team physiotherapist on a weekly basis through a dedicated web portal to the National Gaelic Athletic Association (GAA) injury database. Injury was defined using a time loss criterion, in accordance with consensus statements in sports applicable to Gaelic games. Results: A total of 1014 Gaelic football injuries were recorded. Incidence of injury was 4.05 per 1000 hours of football training. Match-play injury rates were 61.86 per 1000 hours. Muscle was the most frequently injured tissue (42.6%) and fractures accounted for 4.4% of Gaelic football injuries. Lower extremity injuries predominated (76.0%). Hamstring injuries were the single most common injury overall, representing almost one quarter (24%) of all injuries and over half of muscle injuries. Anterior cruciate ligament (ACL) injuries accounted for 13% of knee injuries. The majority of injuries were defined as new injuries (74.7%), with recurrent injuries constituting 23% of all injuries. The majority (59%) of match play injuries occurred in the second half of the match. Eighty six percent of injuries caused over one weeks absence from play. Conclusion: These findings illustrate injury patterns in Gaelic football using a prospective methodology, over 4 consecutive seasons. omparison with published literature suggests that Gaelic football match play injury risk is greater han soccer but less than rugby union. © 2012 The Author(s).


Plant D.,University of Manchester | Wilson A.G.,University College Dublin | Barton A.,University of Manchester
Nature Reviews Rheumatology | Year: 2014

Methotrexate and TNF-blocking agents are the DMARDs most commonly prescribed for the treatment of rheumatoid arthritis (RA). However, not all patients treated with these nonbiologic and biologic DMARDs respond satisfactorily and few predictors of treatment efficacy have been identified, despite the fact that these therapies have now been available for many years. Many studies have investigated genetic factors that might predict patient responsiveness to therapies used to treat RA, and epigenetic studies regarding response to treatment are expected to accumulate in the literature in the near future. Herein, we review the advances in identifying genetic and epigenetic predictors of therapeutic responses to methotrexate and/or TNF inhibitors in RA that have been made to date, and highlight important considerations for future studies, such as the need for an improved, preferably biological, outcome measure reflecting response to treatment. © 2014 Macmillan Publishers Limited.


Huo P.,Boston University | Coker D.F.,Boston University | Coker D.F.,University College Dublin
Journal of Chemical Physics | Year: 2010

Rather than incoherent hopping between chromophores, experimental evidence suggests that the excitation energy transfer in some biological light harvesting systems initially occurs coherently, and involves coherent superposition states in which excitation spreads over multiple chromophores separated by several nanometers. Treating such delocalized coherent superposition states in the presence of decoherence and dissipation arising from coupling to an environment is a significant challenge for conventional theoretical tools that either use a perturbative approach or make the Markovian approximation. In this paper, we extend the recently developed iterative linearized density matrix (ILDM) propagation scheme [E. R. Dunkel, J. Chem. Phys. 129, 114106 (2008)] to study coherent excitation energy transfer in a model of the Fenna-Matthews-Olsen light harvesting complex from green sulfur bacteria. This approach is nonperturbative and uses a discrete path integral description employing a short time approximation to the density matrix propagator that accounts for interference between forward and backward paths of the quantum excitonic system while linearizing the phase in the difference between the forward and backward paths of the environmental degrees of freedom resulting in a classical-like treatment of these variables. The approach avoids making the Markovian approximation and we demonstrate that it successfully describes the coherent beating of the site populations on different chromophores and gives good agreement with other methods that have been developed recently for going beyond the usual approximations, thus providing a new reliable theoretical tool to study coherent exciton transfer in light harvesting systems. We conclude with a discussion of decoherence in independent bilinearly coupled harmonic chromophore baths. The ILDM propagation approach in principle can be applied to more general descriptions of the environment. © 2010 American Institute of Physics.


Laughlin J.M.,University College Dublin
Radiation Protection Dosimetry | Year: 2012

Since its discovery by Dorn in 1900, studies of radon and its progeny have contributed to such diverse scientific fields as meteorology, geophysics, mineral exploration and radiation health effects. In addition to terrestrial scientific studies of radon, NASA missions in recent decades have yielded data on the behaviour of radon and its progeny on the Moon and on Mars. Radon has been used therapeutically for ~100 y in the form of radon seeds for the irradiation of malignant tumours. It is, however, for its negative health effects that radon is better and more justifiably known. The causal role of radon and, in particular, its progeny in the elevated incidence of lung cancer in underground uranium miners was established in the 1950s. It is of historical interest to note that the fatal lung disease of silver miners in Saxony and Bohemia in the 16th century, was undoubtedly lung cancer caused by the high levels of radon in the mines. In recent decades there has been an ever-growing interest in the public health effects of exposure to radon in homes. Extensive radon epidemiological studies both of underground miners and of the general public in recent decades have quantified the lung cancer risks from radon exposure. Radon was classified in 1988 by International Agency for Research on Cancer as a human carcinogen and in 2009 the World Health Organization identified radon as the second cause of lung cancer globally after smoking. Radon control strategies are used by many governments to control and reduce the risk to public health from radon. © The Author 2012. Published by Oxford University Press. All rights reserved.


McGettigan P.A.,University College Dublin
Current Opinion in Chemical Biology | Year: 2013

The transcriptomics field has developed rapidly with the advent of next-generation sequencing technologies. RNA-seq has now displaced microarrays as the preferred method for gene expression profiling.The comprehensive nature of the data generated has been a boon in terms of transcript identification but analysis challenges remain. Key among these problems is the development of suitable expression metrics for expression level comparisons and methods for identification of differentially expressed genes (and exons). Several approaches have been developed but as yet no consensus exists on the best pipeline to use.De novo transcriptome approaches are increasingly viable for organisms lacking a sequenced genome. The reduction in starting RNA required has enabled the development of new applications such as single cell transcriptomics.The emerging picture of mammalian transcription is complex with further refinement expected with the integration of epigenomic data generated by projects such as ENCODE. © 2013 Elsevier Ltd.


Holland C.V.,Trinity College Dublin | Hamilton C.M.,University College Dublin
Journal of Experimental Biology | Year: 2013

Toxocara canis is a parasitic nematode that infects canines worldwide, and as a consequence of the widespread environmental dissemination of its ova in host faeces, other abnormal hosts including mice and humans are exposed to infection. In such abnormal or paratenic hosts, the immature third-stage larvae undergo a somatic migration through the organs of the body but fail to reach maturity as adult worms in the intestine. The presence of the migrating larvae contributes to pathology that is dependent upon the intensity of infection and the location of the larvae. A phenomenon of potential public health significance in humans and of ecological significance in mice is that T. canis larvae exhibit neurotrophic behaviour, which results in a greater concentration of parasites in the brain, as infection progresses. Toxocara larval burdens vary between individual outbred mice receiving the same inocula, suggesting a role for immunity in the establishment of cerebral infection. Although the systemic immune response to T. canis has been widely reported, the immune response in the brain has received little attention. Differential cytokine expression and other brain injury-associated biomarkers have been observed in infected versus uninfected outbred and inbred mice. Preliminary data have also suggested a possible link between significant memory impairment and cytokine production associated with T. canis infection. Mice provide a useful, replicable animal model with significant applicability and ease of manipulation. Understanding the cerebral host-parasite relationship may shed some light on the cryptic symptoms of human infection where patients often present with other CNS disorders such as epilepsy and mental retardation. © 2013 Published by The Company of Biologists Ltd.


Devlin G.,University College Dublin | Talbot B.,Norwegian Forest And Landscape Institute
Applied Energy | Year: 2014

The Irish government has undertaken to reduce national CO2 emissions through a range of measures put out in their Biomass Action Plan and the National Renewable Energy Action Plan. The conversion of peat fired power plants to co-fire with renewable biomass is one of these. This paper considers how the adoption of sweeping policies impact on other actors presently supplying or utilizing woody biomass resources. The SAWMILL sector (18 sawmills), BOARD sector, 3 board plants, and ENERGY sector (3 peat fired power stations) were included in a Linear Programming (LP) based transportation study. Specific transport costs between each residue producing sawmill and each board and energy plant were modeled and used in finding the minimum delivered cost for a number of scenarios. Scenario 2015 represented the status quo, while Scenario 2030 represented a situation with 30% co-firing with woody biomass equivalents in the energy plants. For each time horizon, the problem was solved from the perspective of society at large (GLOBAL), for the benefit of the board sector (BOARD) or with emphasis on minimizing the cost to the energy sector (ENERGY). The cost of transporting alternative sources of renewable energy was varied between €100 and €500TJ-1. Results showed how overall supply costs increase with increasing alternative energy cost, but also how the dynamics between sectors focus worked. The cost of transport to the Energy sector ranged from €306,043 to €996,842 in Scenario 2015, while the increased demand in 2030 led to a range of between €1,132,831 and €4,926,040, depending on the alternative cost selected. For the Board sector, whose absolute demand remained constant, the total transport cost ranged between €868,506 and €3,454,916 in Scenario 2015. The unchanged demand showed that the transport costs also remained the same for the 2030 Scenario, however, the optimization focusing on the Energy sector, increased the delivery cost to the Board sector by up to €693,730 per year by 2015 and €842,271 per year by 2030, indicating how intervention would be necessary if political ambitions of a 30% co-firing should happen without detriment to other important wood based industries. © 2013.


Kelly C.P.,Beth Israel Deaconess Medical Center | Kyne L.,University College Dublin
Journal of Medical Microbiology | Year: 2011

Clostridium difficile is the most common cause of nosocomial bacterial diarrhoea in the Western world. Diarrhoea and colitis are caused by the actions of toxins A and B released by pathogenic strains of C. difficile. Adaptive immune responses to these toxins influence the outcomes of C. difficile infection (CDI). Symptomless carriers of toxinogenic C. difficile and those with a single episode of CDI without recurrence show more robust antitoxin immune responses than those with symptomatic and recurrent disease. Immune-based approaches to CDI therapy and prevention have been developed using active vaccination or passive immunotherapy targeting C. difficile toxins. Innate immune responses to C. difficile and its toxins are also central to the pathophysiology of CDI. An acute intestinal inflammatory response with prominent neutrophil infiltration and associated tissue injury is characteristic of CDI. Furthermore, inhibiting this acute inflammatory response can protect against the intestinal injury that results from exposure to C. difficile toxins in animal models. Studies examining host risk factors for CDI have led to validated clinical prediction tools for risk of primary and of recurrent disease. Risk factors associated with severe CDI with poor clinical outcomes have also been identified and include marked elevation of the peripheral white blood cell count and elevated creatinine. However, further work is needed in this area to guide the clinical application of new approaches to disease prevention and treatment including new antimicrobials as well as passive and active immunization. © 2011 SGM.


Wang L.,University of Southern California | Wang L.,University of Rochester | Long R.,University College Dublin | Prezhdo O.V.,University of Southern California
Annual Review of Physical Chemistry | Year: 2015

Nonequilibrium processes involving electronic and vibrational degrees of freedom in nanoscale materials are under active experimental investigation. Corresponding theoretical studies are much scarcer. The review starts with the basics of time-dependent density functional theory, recent developments in nonadiabatic moleculardynamics, and the fusion of the two techniques. Ab initio simulations of this kind allow us to directly mimic a great variety of time-resolved experiments performed with pump-probe laser spectroscopies. The focus is on the ultrafast photoinduced charge and exciton dynamics at interfaces formed by two complementary materials. We consider purely inorganic materials, inorganic-organic hybrids, and all organic interfaces, involving bulk semiconductors, metallic and semiconducting nanoclusters, graphene, carbon nanotubes, fullerenes, polymers, molecular crystals, molecules, and solvent. The detailed atomistic insights available from time-domain ab initio studies provide a unique description and a comprehensive understanding of the competition between electron transfer, thermal relaxation, energy transfer, and charge recombination processes. These advances now make it possible to directly guide the development of organic and hybrid solar cells, as well as photocatalytic, electronic, spintronic, and other devices relying on complex interfacial dynamics. © 2015 by Annual Reviews. All rights reserved.


Costello F.,University College Dublin | Watts P.,National University of Ireland
Psychological Review | Year: 2014

The systematic biases seen in people's probability judgments are typically taken as evidence that people do not use the rules of probability theory when reasoning about probability but instead use heuristics, which sometimes yield reasonable judgments and sometimes yield systematic biases. This view has had a major impact in economics, law, medicine, and other fields; indeed, the idea that people cannot reason with probabilities has become a truism. We present a simple alternative to this view, where people reason about probability according to probability theory but are subject to random variation or noise in the reasoning process. In this account the effect of noise is canceled for some probabilistic expressions. Analyzing data from 2 experiments, we find that, for these expressions, people's probability judgments are strikingly close to those required by probability theory. For other expressions, this account produces systematic deviations in probability estimates. These deviations explain 4 reliable biases in human probabilistic reasoning (conservatism, subadditivity, conjunction, and disjunction fallacies). These results suggest that people's probability judgments embody the rules of probability theory and that biases in those judgments are due to the effects of random noise. © 2014 American Psychological Association.


O'Brien E.,University College Dublin
Journal of Hypertension | Year: 2011

If ambulatory blood pressure measurement is not possible because the upper-arm circumference is so great that even the largest cuff provided with the monitor will not encircle the arm, satisfactory measurements can be obtained by applying a cuff to the forearm. © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins.


Casey P.,University College Dublin | Doherty A.,St Jamess Hospital
British Journal of Psychiatry | Year: 2012

Adjustment disorder has been a recognised disorder for decades but has been the subject of little epidemiological research. Now researchers have identified the prevalence of adjustment disorder in primary care, and found general practitioner recognition very low but with high rates of antidepressant prescribing. Possible reasons for the seemingly low prevalence, recognition rate and inappropriate management include its recognition as a residual category in diagnostic instruments and poor delineation from other disorders or from normal stress responses. These problems could be rectified in ICD-11 and DSM-5 if changes according it full syndromal status, among others, were made. This would have an impact on future research.


Powderly W.G.,University College Dublin
Current HIV/AIDS Reports | Year: 2012

Patients with HIV can develop several complications that involve bone including low bone mineral density and osteoporosis, osteonecrosis, and rarely osteomalacia. Low bone mineral density leading to osteoporosis is the most common bone pathology. This may result from HIV infection (directly or indirectly), antiretroviral toxicity, or as a consequence of other co-morbidities. The clinical relevance of osteoporosis in HIV infection has been uncertain; however, fragility fractures are increasingly reported in HIV-infected patients. Further research is required to understand the pathogenesis of osteoporosis in HIV-infected patients and determine effective management; however, initiation of antiretroviral therapy seems to accelerate (in the short-term) bone demineralization. Tenofovir may be associated with a greater degree of short-term loss of bone density than other antiviral agents and the potential long-term bone dysfunction is unclear. As the HIV-infected population ages, screening for low bone mineral density will become increasingly important. © 2012 Springer Science+Business Media, LLC.


Komito L.,University College Dublin
Journal of the American Society for Information Science and Technology | Year: 2011

Research indicates that migrants' social media usage in Ireland enables a background awareness of friends and acquaintances that supports bonding capital and transnational communities in ways not previously reported. Interview data from 65 Polish and Filipino non-nationals in Ireland provide evidence that their social media practices enable a shared experience with friends and relations living outside Ireland that is not simply an elaboration of the social relations enabled by earlier Internet applications. Social media usage enables a passive monitoring of others, through the circulation of voice, video, text, and pictures, that maintains a low level mutual awareness and supports a dispersed community of affinity. This ambient, or background, awareness of others enhances and supports dispersed communities by contributing to bonding capital. This may lead to significant changes in the process of migration by slowing down the process of integration and participation in host societies while also encouraging continual movement of migrants from one society to another. © 2011 ASIS&T.


Kalinin S.V.,Oak Ridge National Laboratory | Morozovska A.N.,Ukrainian Academy of Sciences | Chen L.Q.,Pennsylvania State University | Rodriguez B.J.,University College Dublin
Reports on Progress in Physics | Year: 2010

Ferroelectrics and multiferroics have recently emerged as perspective materials for information technology and data storage applications. The combination of extremely narrow domain wall width and the capability to manipulate polarization by electric field opens the pathway toward ultrahigh (>10 TBit inch-2) storage densities and small (sub-10 nm) feature sizes. The coupling between polarization and chemical and transport properties enables applications in ferroelectric lithography and electroresistive devices. The progress in these applications, as well as fundamental studies of polarization dynamics and the role of defects and disorder on domain nucleation and wall motion, requires the capability to probe these effects on the nanometer scale. In this review, we summarize the recent progress in applications of piezoresponse force microscopy (PFM) for imaging, manipulation and spectroscopy of ferroelectric switching processes. We briefly introduce the principles and relevant instrumental aspects of PFM, with special emphasis on resolution and information limits. The local imaging studies of domain dynamics, including local switching and relaxation accessed through imaging experiments and spectroscopic studies of polarization switching, are discussed in detail. Finally, we review the recent progress on understanding and exploiting photochemical processes on ferroelectric surfaces, the role of surface adsorbates, and imaging and switching in liquids. Beyond classical applications, probing local bias-induced transition dynamics by PFM opens the pathway to studies of the influence of a single defect on electrochemical and solid state processes, thus providing model systems for batteries, fuel cells and supercapacitor applications. © 2010 IOP Publishing Ltd.


Unger T.,University College Dublin | Markin N.,Nanyang Technological University
IEEE Transactions on Information Theory | Year: 2011

In the context of space-time block codes (STBCs), the theory of generalized quaternion and biquaternion algebras (i.e., tensor products of two quaternion algebras) over arbitrary base fields is presented, as well as quadratic form theoretic criteria to check if such algebras are division algebras. For base fields relevant to STBCs, these criteria are exploited, via Springer's theorem, to construct several explicit infinite families of (bi-)quaternion division algebras. These are used to obtain new 2 × 2 and 4 × 4 STBCs. © 2011 IEEE.


Flowerdew M.J.,British Antarctic Survey | Tyrrell S.,University College Dublin | Peck V.L.,British Antarctic Survey
Geology | Year: 2013

The delivery of ice-rafted debris (IRD) from glaciated margins is a function of ice sheet dynamics. Shifts in supply and sourcing of IRD can therefore identify episodes of ice sheet instability; however, records can be difficult to correctly interpret because the subglacial geology of the catchment areas, which controls IRD composition, may be obscured. Importantly, variations can also result from shifts in erosion sites due to changes in the basal ice sheet conditions. This study evaluates where subglacial erosion has occurred in catchments that flow into the southern Weddell Sea, Antarctica, by determining the Pb isotopic compositions of individual ice-rafted feldspars from late Holocene marine sediments. Feldspar compositions match those of rock units inferred (through extrapolation of outcrop, magnetic, and gravity data) to compose areas where ice velocity, bed roughness, and shear stress are high. Significantly, signals from areas where ice velocities are high but bed roughness and shear stresses are low were not recorded, suggesting that there is reduced bedrock erosion in these regions. Major variations in IRD composition in the Weddell Sea can result from changing the loci of subglacial erosion, and do not necessarily correspond with major ice sheet instability. © 2012 Geological Society of America.


Reilly G.O'.,University College Dublin
Legal and Criminological Psychology | Year: 2013

Objectives. To document criminality, psychiatric difficulty, IQ, EQ, and EI amongst Irish, male juvenile detainees (Detainee Group). To compare their IQ, EQ, and EI to non-offending boys attending a child psychiatry clinic (Psychiatric Group) and boys without offending or psychiatric problems (Community Group). To compare psychiatric morbidity between the detainee and psychiatric groups. Method. Criminality levels of 30 detainees were evaluated using official court charge sheets. Psychiatric status was assessed through structured clinical interview (DISC-IV); IQ through an individually administered IQ-scale (WASI); EQ using the BarOn EQi:Youth Version (EQi:YV); and EI using the MSCEIT: Youth Version - Research Edition (MSCEIT:YV-RE). IQ, EQ, and EI levels in the psychiatric and community groups were compared. Psychiatric morbidity between detainee and psychiatric groups were compared. Results. A total of 335 crimes led to the detention of detainees. Eighty-three percent of detainees had a psychiatric disorder compared to 60% of young people in the psychiatric group. Detainees had 3.1 disorders each compared to 1.4 disorders in the psychiatric group. A total of 63.3% of detainees had an externalizing problem, 37.9% an internalizing problem, and 66.7% a substance dependency or use problem. A total of 21.4% of detainees had an IQ score below 70. The detainee and psychiatric groups had similar deficits in EI and significantly lower EI than the community groups. Conclusions. Serious levels of criminality and psychiatric disorder exist amongst Irish detainees. They have significantly lower IQ than young people attending a psychiatry clinic and both share deficits in the ability to accurately identify emotions, use emotions to guide thought processes and to prioritize thinking and to effectively regulate emotions. © 2011 The British Psychological Society.


Zhu A.,University College Dublin
IEEE Transactions on Microwave Theory and Techniques | Year: 2015

A new behavioral model for digital predistortion of radio frequency (RF) power amplifiers (PAs) is proposed in this paper. It is derived from a modified form of the canonical piecewise-linear (CPWL) functions using a decomposed vector rotation (DVR) technique. In this model, the nonlinear basis function is constructed from piecewise vector decomposition, which is completely different from that used in the conventional Volterra series. Theoretical analysis has shown that this model is much more flexible in modeling RF PAs with non-Volterra-like behavior, and experimental results confirmed that the new model can produce excellent performance with a relatively small number of coefficients when compared to conventional models. © 1963-2012 IEEE.


Ryan C.,Baylor University | Kirby B.,University College Dublin
Dermatologic Clinics | Year: 2015

There is evidence that patients with moderate to severe psoriasis have an increased risk of conditions such as cardiovascular disease, obesity, diabetes mellitus, and metabolic syndrome. The precise mechanisms underlying the observed increase in cardiovascular disease in psoriasis remain to be defined but inflammatory pathways mutual to both conditions are probably involved. Suppression of systemic inflammation in psoriasis could help reduce cardiovascular inflammation but robust evidence is still lacking evidence is lacking. This article summarizes the current literature on cardiovascular and metabolic comorbidities in psoriasis, identifies research gaps, and suggests management strategies to reduce cardiovascular risk in patients with moderate to severe psoriasis. © 2015 Elsevier Inc.


Warnock J.N.,University College Dublin
Methods in molecular biology (Clifton, N.J.) | Year: 2011

Viral vector is the most effective means of gene transfer to modify specific cell type or tissue and can be manipulated to express therapeutic genes. Several virus types are currently being investigated for use to deliver genes to cells to provide either transient or permanent transgene expression. These include adenoviruses (Ads), retroviruses (γ-retroviruses and lentiviruses), poxviruses, adeno-associated viruses, baculoviruses, and herpes simplex viruses. The choice of virus for routine clinical use will depend on the efficiency of transgene expression, ease of production, safety, toxicity, and stability. This chapter provides an introductory overview of the general characteristics of viral vectors commonly used in gene transfer and their advantages and disadvantages for gene therapy use.


English N.J.,University College Dublin | Tse J.S.,University of Saskatchewan
Journal of Physical Chemistry Letters | Year: 2014

The thermal conductivity of both supercooled and ambient-temperature water at atmospheric pressure has been computed over the 140-270 K temperature range for three popular water models via equilibrium molecular dynamics in the Green-Kubo setting. No strong temperature dependence of thermal conductivity was observed. The underlying phonon modes contributing to thermal conduction processes have been examined in the present work, and it has been established that (translational) acoustic modes dominate in supercooled water. (Graph Presented). © 2014 American Chemical Society.


McLaughlin J.,University College Dublin
Radiation Protection Dosimetry | Year: 2010

An account is given of the behaviour of thoron and its progeny in the indoor environment. Emphasis is placed on the spatial distribution of these radionuclides in room air and on their interactions with indoor aerosols. How these aspects of thoron and progeny behaviour give rise to special problems for measuring them and assessing their radiological impact are described. Descriptions and comparisons are given of a range of thoron and progeny measurement techniques both passive and active. Recent progress in thoron dosimetry is described as well as compared with radon dosimetry. The results of some indoor thoron and progeny surveys carried out in different countries in recent years are given. As an example of this a summary account is presented of a recently concluded survey of thoron and its airborne progeny in over 200 houses in Ireland. © The Author 2010. Published by Oxford University Press. All rights reserved.


Aksamitiene E.,Thomas Jefferson University | Kiyatkin A.,Thomas Jefferson University | Kholodenko B.N.,Thomas Jefferson University | Kholodenko B.N.,University College Dublin
Biochemical Society Transactions | Year: 2012

In the present paper, we describe multiple levels of cross-talk between the PI3K (phosphoinositide 3- kinase)/Akt and Ras/MAPK (mitogen-activated protein kinase) signalling pathways. Experimental data and computer simulations demonstrate that cross-talk is context-dependent and that both pathways can activate or inhibit each other. Positive influence of the PI3K pathway on the MAPK pathway is most effective at sufficiently low doses of growth factors, whereas negative influence of the MAPK pathway on the PI3K pathway is mostly pronounced at high doses of growth factors. Pathway cross-talk endows a cell with emerging capabilities for processing and decoding signals from multiple receptors activated by different combinations of extracellular cues. ©The Authors Journal compilation ©2012 Biochemical Society.


Cummins E.P.,University College Dublin
Stem Cell Research and Therapy | Year: 2012

Human embryonic stem cells (hESCs) have been reported to confer cytoprotection in the context of tissue injury. This is somewhat counterintuitive given that microenvironmental factors such as hypoxia and oxidative stress may activate p53 and result in death and differentiation of these hESCs. In this article, we discuss a novel mechanism through which hESCs can be re-programmed (through exposure to hypoxia/oxidative stress) to transiently suppress p53, enhance 'stemness', and exist in a highly cytoprotective and undifferentiated state. © 2012 BioMed Central Ltd.


Gonzalez A.,University College Dublin | Hester D.,Queens University of Belfast
Journal of Sound and Vibration | Year: 2013

In recent years there have been a growing number of publications on procedures for damage detection in beams from analysing their dynamic response to the passage of a moving force. Most of this research demonstrates their effectiveness by showing that a singularity that did not appear in the healthy structure is present in the response of the damaged structure. This paper elucidates from first principles how the acceleration response can be assumed to consist of 'static' and 'dynamic' components, and where the beam has experienced a localised loss in stiffness, an additional 'damage' component. The combination of these components establishes how the damage singularity will appear in the total response. For a given damage severity, the amplitude of the 'damage' component will depend on how close the damage location is to the sensor, and its frequency content will increase with higher velocities of the moving force. The latter has implications for damage detection because if the frequency content of the 'damage' component includes bridge and/or vehicle frequencies, it becomes more difficult to identify damage. The paper illustrates how a thorough understanding of the relationship between the 'static' and 'damage' components contributes to establish if damage has occurred and to provide an estimation of its location and severity. The findings are corroborated using accelerations from a planar finite element simulation model where the effects of force velocity and bridge span are examined. © 2013 Elsevier Ltd.


A fourth-order in space and second-order in time 3D staggered (SG) and rotated-staggered-grid (RSG) method for the solution of Biot's equation are presented. The numerical dispersion and stability conditions are derived using a von Neumann analysis. The exact stability condition is calculated from the roots of a 12th-order polynomial and therefore no nontrivial expression exists. To overcome this, a 1D stability condition is usually generalized to three dimensions. It is shown that in certain cases, the 1D approximate stability condition is violated by a 3D SG method. The RSG method obeys the approximate 1D stability condition for the material properties and spatiotemporal scales in the examples shown. Both methods have been verified against an analytical solution for an infinite homogeneous porous medium with a misfit error of less than 0.5%. A free surface has been implement-ed to test the accuracy of this boundary condition. It also serves as a test of the methods to include high material contrasts. The methods have been compared with a quasi-analytical solution. For the specific material properties, spatial grid scaling, and propagation distance used in the test, a maximum error of 3.5% for the SG and 4.1% for the RSG was found. These errors depend on the propagation distance, temporal and spatial scales, and accuracy of the quasi-analytical solution. No discernable difference was found between the two methods except for time steps comparable with the stability-criteria threshold time step, the SG was found to be unstable. However, the RSG remained stable for a homogeneous half-space. Time steps, comparable to the stability criteria, reduce the computational time at the cost of a reduction in accuracy. The methods allow wave propagation to be modeled in a porous medium with a free surface. © 2010 Society of Exploration Geophysicists.


Healy D.,University College Dublin
Theoretical Criminology | Year: 2013

There is a significant conceptual divide between criminological theories that treat offenders as rational agents who freely choose their actions and those that portray offenders as individuals whose behaviour is determined by external forces. Recently, research into desistance from crime has produced a more complex and nuanced account of crime causation which acknowledges the interplay between agency and structure. Yet, while the concept of agency is frequently invoked in contemporary discourse, the variety of definitions and measures employed by researchers makes it difficult to establish a clear and consistent picture of its role. This article attempts to address this deficit by evaluating the contributions of agency-centred theories of desistance. An integrated framework, which aims to consolidate existing knowledge about agency and provide additional insights into its role in desistance, is then proposed. © The Author(s) 2013.


James K.,Royal College of Surgeons in Ireland | Dolan E.,Royal College of Surgeons in Ireland | O'Brien E.,University College Dublin
Blood Pressure Monitoring | Year: 2014

OBJECTIVES: Ambulatory blood pressure measurement (ABPM), although recommended for the diagnosis and management of hypertension, has limited availability. The objective of this study was to show that if the characteristics of patients attending pharmacies for ABPM are similar to those attending primary care, the technique can be made more widely available to patients through pharmacies. PATIENTS AND METHODS: A comparative study using a software program that allowed central collection, analysis and comparison of ABPM data from patients attending primary care and pharmacies for assessment of hypertension in Ireland. RESULTS: ABPM data from 46 978 patients attending primary care were compared with 1698 attending pharmacies between 2007 and 2013. The age, sex and blood pressure characteristics of patients attending primary care and pharmacies were similar. The mean pressures in all categories, except for systolic blood pressure recorded in primary care, were higher in men. The first ABPM measurements recorded in pharmacies were slightly higher than those in primary care (150.8±19.5/88.7±13.7 vs. 149.6±20.7/88. 0±14.4 mmHg). More patients attending primary care were normotensive than those attending pharmacies (19.5 vs. 16.4%), whereas more patients attending pharmacies were hypertensive than those attending primary care (62.8 vs. 60.7%), particularly female patients (61.0 vs. 56.4%). White-coat hypertension was similar in patients attending primary care and pharmacies (19.8 vs. 20.8%), but it was more prevalent in men attending pharmacies (22.0 vs. 17.4%) and in women attending primary care (21.9 vs. 19.7%). There were more dippers in pharmacy then primary care ABPMs (84.7 vs. 79.4%). A preference for having ABPM on Fridays and Saturdays was evident in patients attending pharmacies (19.6 vs. 6.6%), whereas there was a preference for early morning recording in primary care (4.1 vs. 1.1%). CONCLUSION: This study, which is the first to report on ABPM data from the pharmacy setting, shows that the blood pressure characteristics of patients with ABPMs recorded in pharmacies are similar to those recorded in primary care practices. It is feasible, therefore, to perform ABPM in pharmacies, which can be utilized to make ABPM more accessible to the large number of patients in the population with hypertension. © 2014 Wolters Kluwer Health Lippincott Williams & Wilkins.


Bustamante M.D.,University College Dublin
Physica D: Nonlinear Phenomena | Year: 2011

We prove by an explicit construction that solutions to incompressible 3D Euler equations defined in the periodic cube Ω=[ 0,L]3 can be mapped bijectively to a new system of equations whose solutions are globally regular. We establish that the usual BealeKatoMajda criterion for finite-time singularity (or blowup) of a solution to the 3D Euler system is equivalent to a condition on the corresponding regular solution of the new system. In the hypothetical case of Euler finite-time singularity, we provide an explicit formula for the blowup time in terms of the regular solution of the new system. The new system is amenable to being integrated numerically using similar methods as in Euler equations. We propose a method to simulate numerically the new regular system and describe how to use this to draw robust and reliable conclusions on the finite-time singularity problem of Euler equations, based on the conservation of quantities directly related to energy and circulation. The method of mapping to a regular system can be extended to any fluid equation that admits a BealeKatoMajda type of theorem, e.g. 3D NavierStokes, 2D and 3D magnetohydrodynamics, and 1D inviscid Burgers. We discuss briefly the case of 2D ideal magnetohydrodynamics. In order to illustrate the usefulness of the mapping, we provide a thorough comparison of the analytical solution versus the numerical solution in the case of 1D inviscid Burgers equation. © 2011 Elsevier B.V. All rights reserved.


Zhang Y.,University College Dublin | Zhang Y.,Trinity College Dublin | Wang Q.,CAS Institute of Chemistry
Advanced Materials | Year: 2012

Ternary FePt-Au nanorods are synthesized as magnetic-plasmonic 1D nanostructures. Besides their widely tunable magnetic properties, their unique plasmonic response to the illumination polarization provides a powerful tool to optically image these sub-wavelength single nanorods. These nanoparticles also show the potential as a novel nano-bioprobe based on the demonstration of simultaneous magnetic manipulation and optical imaging of single particles inside live cells. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Gologlu F.,University College Dublin
IEEE Transactions on Information Theory | Year: 2012

Blondeau and colleagues recently conjectured a characterization of when x 2t-1 is an almost perfect nonlinear function on F 2 n. In this paper, we will prove the conjecture when n is even. The short proof uses a theorem of Hou and colleagues concerning reversed Dickson polynomials and a theorem of Payne. © 2012 IEEE.


Convery F.J.,University College Dublin
Review of Environmental Economics and Policy | Year: 2011

It is important for policy makers to understand the extent to which the purported benefits of energy efficiency are real, and how they can be achieved. This "reflections" aims to help the policy community understand how the literature can assist them in assessing the opportunities, challenges, and choices they face as they consider how to develop and implement an energy efficiency policy agenda. The article examines what is meant by energy efficiency, how energy performance is generally evaluated, and why energy efficiency is generally presented as such a great opportunity. This is followed by discussions of the importance of understanding market failures and addressing the external benefits of energy efficiency, and the importance of understanding prices and price expectations. The article concludes with some guidelines for designing coherent and effective energy efficiency policies. Because the article is aimed particularly at assisting policymakers, much of the discussion, especially the lessons for policy, are directed to "you," the reader as policymaker. © The Author 2011. Published by Oxford University Press on behalf of the Association of Environmental and Resource Economists. All rights reserved.


Begg J.G.,Institute of Geological & Nuclear Sciences | Mouslopoulou V.,University College Dublin
Journal of Volcanology and Geothermal Research | Year: 2010

High-quality Light Detection and Ranging (lidar) data collected across the Rangitaiki Plains, the fastest extending section of the onshore Taupo Rift, New Zealand, reveal 122 active fault traces and provide new constraints on displacements, displacement rates and paleoearthquakes of the normal faults in the rift. The identified lineaments are scarps that record vertical offset of geomorphic surfaces (e.g., beach ridges, meander channel floors, river terraces, etc.) and trend parallel or sub-parallel to other active faults in the rift; these lineaments are interpreted to be active faults. Active fault traces trend ∼ 060° and their lengths range from 0.25 to 6 km. They mainly traverse and displace a diachronous landscape of < 6.5 kyr age, with throws that vary from 0.05 to 7 m and form a graben. Historic, geometric and kinematic constraints have been used to aggregate individual traces into eight fault zones that range in length from 5 to 40 km. Displacement rates in the rift beneath the Rangitaiki Plains vary between and along individual faults by more than one and three orders of magnitude, respectively, over the last 0.64 and/or 1.72 kyr. Variability of displacement rates on individual faults arises from episodic slip accumulation during a minimum of 15 paleoearthquakes of variable slip and recurrence interval. Repeated fault movements have produced about 3 mm/yr of subsidence over the last ∼ 2 kyr within the rift (i.e. between the Edgecumbe and Matata faults) while relatively stable conditions have persisted (uplift/subsidence of 0-0.6 mm/yr) on the rift shoulders for the last ∼ 3.3 to ∼ 6.5 kyr. These plain-wide signals of vertical movement were interrupted by short-lived episodes of rapid uplift (0-1.72 kyr) and subsidence (1.72 to ∼ 2.1 kyr) at the western and eastern margins, respectively, which we infer to result from prehistoric earthquakes. © 2009 Elsevier B.V. All rights reserved.


Hildebrandt A.,Friedrich - Schiller University of Jena | Gray J.S.,University College Dublin | Hunfeld K.-P.,Institute of Laboratory Medicine
Infection | Year: 2013

Although best known as an animal disease, human babesiosis is attracting increasing attention as a worldwide emerging zoonosis. Humans are commonly infected by the bite of ixodid ticks. Rare ways of transmission are transplacental, perinatal and transfusion-associated. Infection of the human host can cause a very severe host-mediated pathology including fever, and hemolysis leading to anemia, hyperbilirubinuria, hemoglobinuria and possible organ failure. In recent years, apparently owing to increased medical awareness and better diagnostic methods, the number of reported cases in humans is rising steadily worldwide. Hitherto unknown zoonotic Babesia spp. are now being reported from geographic areas where babesiosis was not previously known to occur and the growing numbers of travelers and immunocompromised individuals suggest that the frequency of cases in Europe will also continue to rise. Our review is intended to provide clinicians with practical information on the clinical management of this rare, but potentially life-threatening zoonotic disease. It covers epidemiology, phylogeny, diagnostics and treatment of human babesiosis and the potential risk of transfusion-transmitted disease with a special focus on the European situation. © 2013 Springer-Verlag Berlin Heidelberg.


Wilm M.,University College Dublin
Molecular & cellular proteomics : MCP | Year: 2011

Electrospray ionization is today the most widely used ionization technique in chemical and biochemical analysis. Interfaced with a mass spectrometer it allows the investigation of the molecular composition of liquid samples. With electrospray a large variety of chemical substances can be ionized. There is no limitation in mass which thus enables even the investigation of large noncovalent protein complexes. Its high ionization efficiency profoundly changed biomolecular sciences because proteins can be identified and quantified on trace amounts in a high throughput fashion. This review article focuses mainly on the exploration of the underlying ionization mechanism. Some ionization characteristics are discussed that are related to this mechanism. Typical spectra of peptides, proteins, and noncovalent complexes are shown and the quantitative character of spectra is highlighted. Finally the possibilities and limitations in measuring the association constant of bivalent noncovalent complexes are described.


Lonergan P.,University College Dublin
Theriogenology | Year: 2011

In cattle, the majority of embryo loss occurs very early during pregnancy (approximately Day 16), around or prior to maternal recognition of pregnancy. The actions of P4 in controlling LH pulsatility and ovarian follicular development may impinge negatively on oocyte quality. A considerable proportion of embryo loss may be attributable to inadequate circulating progesterone (P4) concentrations and the subsequent downstream consequences on endometrial gene expression and histotroph secretion into the uterine lumen. Conceptus growth and development require the action of P4 on the uterus to regulate endometrial function, including conceptus-maternal interactions, pregnancy recognition, and uterine receptivity for implantation. This review summarizes recent data highlighting the role of progesterone in determining oocyte quality and embryo development in cattle. © 2011 Elsevier Inc.


Cowley C.,University College Dublin
Bioethics | Year: 2012

In a recent issue of Bioethics, Bernard Gesang asks whether a moral philosopher possesses greater moral expertise than a non-philosopher, and his answer is a qualified yes, based not so much on his infallible access to the truth, but on the quality of his theoretically-informed moral justifications. I reject Gesang's claim that there is such a thing as moral expertise, although the moral philosopher may well make a valid contribution to the ethics committee as a concerned and educated citizen. I suggest that wisdom is a lot more interesting to examine than moral expertise. Again, however, moral philosophers have no monopoly on wisdom, and the study of philosophy may even impede its cultivation. © 2011 Blackwell Publishing Ltd..


Smith W.J.,University College Dublin
Energy Policy | Year: 2010

Between 1990 and 2006, the primary energy requirement of the Irish transport sector increased by 166%. Associated greenhouse gas (GHG) emissions have followed a corresponding trajectory, and are responsible-at least in part-for Ireland's probable failure to meet its Kyoto targets. As in most countries, Ireland's transport sector is almost totally reliant on oil-a commodity for which Ireland is totally dependent on imports-and therefore vulnerable to supply and price shocks. Conversely, the efficiency and carbon intensity of the Irish electricity supply system have both improved dramatically over the same period, with significant further improvements projected over the coming decade. This paper analyses the prospects for leveraging these changes by increasing the electrification of the Irish transport sector. Specifically, the potential benefits of plug-in hybrid-electric vehicles (PHEV) are assessed, in terms of reducing primary energy requirement (PER) and CO2 emissions. It is shown that, on a per-km basis, PHEV offer the potential for reductions of 50% or more in passenger car PER and CO2 intensity. However, the time required to turn over the existing fleet means that a decade or more will be required to significantly impact PER and emissions of the PC fleet. © 2009 Elsevier Ltd.


Lanigan F.,Trinity College Dublin | Geraghty J.G.,University College Dublin | Bracken A.P.,Trinity College Dublin
Oncogene | Year: 2011

Cellular senescence is an irreversible arrest of proliferation. It is activated when a cell encounters stress such as DNA damage, telomere shortening or oncogene activation. Like apoptosis, it impedes tumour progression and acts as a barrier that pre-neoplastic cells must overcome during their evolution toward the full tumourigenic state. This review focuses on the role of transcriptional regulators in the control of cellular senescence, explores how their function is perturbed in cancer and discusses the potential to harness this knowledge for future cancer therapies. © 2011 Macmillan Publishers Limited All rights reserved.


Noailly J.,CPB Netherlands Bureau for Economic Policy Analysis | Batrakova S.,University College Dublin
Energy Policy | Year: 2010

In the Netherlands where the building sector accounts for 33% of carbon emissions, the government aims to halve the total energy use from buildings by 2030 compared to 1990 levels. To this end, the Dutch government has set specific goals in order to foster technological innovation related to energy efficiency in buildings. The objective of this paper is to explore the links between technological innovation and public policies in this sector over the last 30 years. The paper aims (1) to measure the evolution of innovations related to energy efficiency in buildings in the Netherlands using patent counts and (2) to provide a historical overview of the policy framework. Descriptive data on patenting activities show that the Netherlands have a clear comparative advantage in the field of energy-saving lighting technologies, mainly due to intensive patenting activities by Philips. High-efficiency boilers also represent a substantial share of Dutch innovation activities in this domain over the last decades. In many other fields (such as insulation, heat-pumps and cogeneration, solar boilers, etc.), however, Germany, Austria and Scandinavian countries rank much higher than the Netherlands. The descriptive analysis of Dutch energy policy shows an intensification of energy policy in the mid-1990s, followed by a slight decline after 2001. Overall, the simultaneous introduction of policy instruments makes it difficult to evaluate the effectiveness of policies. Also, the policy framework is characterized by the introduction of a large number of short-lived policy instruments and frequent policy changes. The lack of stability and continuity of energy policy may be damaging for innovation. © 2010 Elsevier Ltd.


Colgan S.P.,University of Colorado at Denver | Taylor C.T.,University College Dublin
Nature Reviews Gastroenterology and Hepatology | Year: 2010

Intestinal epithelial cells that line the mucosal surface of the gastrointestinal tract are positioned between an anaerobic lumen and a highly metabolic lamina propria. As a result of this unique anatomy, intestinal epithelial cells function within a steep physiologic oxygen gradient relative to other cell types. Furthermore, during active inflammatory disease such as IBD, metabolic shifts towards hypoxia are severe. Studies in vitro and in vivo have shown that the activation of hypoxia-inducible factor (HIF) serves as an alarm signal to promote the resolution of inflammation in various mouse models of disease. Amelioration of disease occurs, at least in part, through transcriptional upregulation of nonclassic epithelial barrier genes. There is much interest in harnessing hypoxia-inducible pathways, including stabilizing HIF directly or via inhibition of prolyl hydroxylase enzymes, for therapy of IBD. In this Review, we discuss the signaling pathways involved in the regulation of hypoxia and discuss how hypoxia may serve as an endogenous alarm signal for the presence of mucosal inflammatory disease. We also discuss the pros and cons of targeting these pathways to treat patients with IBD. © 2010 Macmillan Publishers Limited. All rights reserved.


Boreham C.A.G.,University College Dublin | McKay H.A.,University of British Columbia
British Journal of Sports Medicine | Year: 2011

The aim of this review is to provide a concise overview and update on recent advances in the fi eld of physical activity in childhood and its effects on bone growth with an emphasis on the potential to prevent fractures. In addition, the review poses several unresolved questions in the fi eld for future research.


Giacomello A.,University of Rome La Sapienza | Chinappi M.,University of Rome La Sapienza | Meloni S.,University College Dublin | Casciola C.M.,University of Rome La Sapienza
Physical Review Letters | Year: 2012

In this Letter, we develop a continuum theory for the Cassie-Baxter-Wenzel (CB-W) transition. The proposed model accounts for the metastabilities in the wetting of rough hydrophobic surfaces, allows us to reconstruct the transition mechanism, and identifies the free energy barriers separating the CB and W states as a function of the liquid pressure. This information is crucial in the context of superhydrophobic surfaces, where there is interest in extending the duration of the metastable superhydrophobic CB state. The model is validated against free energy atomistic simulations. © 2012 American Physical Society.


Ottewill A.C.,University College Dublin | Wardell B.,Max Planck Institute For Gravitationsphysik
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2011

Building on an insight due to Avramidi, we provide a system of transport equations for determining key fundamental bitensors, including derivatives of the world function, σ(x,x′), the square root of the Van Vleck determinant, Δ1/2(x,x′), and the tail term, V(x,x′), appearing in the Hadamard form of the Green function. These bitensors are central to a broad range of problems from radiation reaction to quantum field theory in curved spacetime and quantum gravity. Their transport equations may be used either in a semi-recursive approach to determining their covariant Taylor series expansions, or as the basis of numerical calculations. To illustrate the power of the semi-recursive approach, we present an implementation in Mathematica, which computes very high order covariant series expansions of these objects. Using this code, a moderate laptop can, for example, calculate the coincidence limit [a7(x,x)] and V(x,x′) to order (σa)20 in a matter of minutes. Results may be output in either a compact notation or in xTensor form. In a second application of the approach, we present a scheme for numerically integrating the transport equations as a system of coupled ordinary differential equations. As an example application of the scheme, we integrate along null geodesics to solve for V(x,x′) in Nariai and Schwarzschild spacetimes. © 2011 American Physical Society.


Brennan L.,University College Dublin
Biochemical Society Transactions | Year: 2013

Metabolomics is the study of metabolites present in biological samples such as biofluids, tissue/cellular extracts and culture media. Combining metabolomic data with multivariate data analysis tools allows us to study alterations in metabolic pathways following different perturbations. Examples of perturbations can be disease state, drug or nutritional interventions with successful applications in the fields of drug toxicology, biomarker development and nutrition research. Application of metabolomics to nutrition research is increasing and applications range from assessing novel biomarkers of dietary intake to application of metabolomics in intervention studies. The present review highlights the use of metabolomics in nutrition research. © 2013 Biochemical Society.


Duffy M.J.,St Vincents University Hospital | Duffy M.J.,University College Dublin
Tumor Biology | Year: 2013

Of all the diseases affecting humankind, cancer is one of the most difficult to treat and cure. One of the main reasons for this difficulty relates to the fact that cancer is not a single disease but consists of hundreds of different types. Furthermore, cancers exhibit considerable genetic complexity with more than 400 different genes implicated in their development. In addition, cancers display major inter- and intratumor heterogeneity. Despite these complexities, several successes have been achieved in recent years. Most of these successes relate to the specific targeting of driver genes involved in cancer development. These successes include imatinib for the treatment of chronic myeloid leukemia, anti-HER2 therapies (trastuzumab, pertuzumab, and lapatinib) to treat breast cancer, anti-EGFR tyrosine kinase inhibitors (gefitinib and erlotinib) to treat non-small cell lung cancer, and anti-BRAF agents (vemurafenib and dabrafenib) to treat melanoma. Although the war on cancer has not yet been won, neither has it been lost. With continued basic and clinical research, cancer is being transformed into a chronic disease in which patients have increased survival rates and better quality of life. © 2013 International Society of Oncology and BioMarkers (ISOBM).


Ela E.,National Renewable Energy Laboratory | O'Malley M.,University College Dublin
IEEE Transactions on Power Systems | Year: 2012

With increasing levels of variable renewable energy, there is a growing need to study its impacts on power system operation. Variable generation (VG) is variable and uncertain at multiple timescales, and it is important that system operators understand how each of these characteristics impact their systems since each may have different mitigation strategies. To date, many of the studies of VG integration are limited to studying at one time resolution and therefore cannot analyze the variability and uncertainty impacts across multiple timescales. Here we study the variability and uncertainty impacts across multiple operational timescales. A model is used which integrates multiple scheduling sub-models with different update frequencies, time resolutions, and decision horizons. Using metrics that describe reliability and costs with a methodology that describes the sensitivities and tradeoffs of variability and uncertainty impacts separately with respect to the conditions that cause those impacts, case studies are performed which display greater information on expectations of these impacts on future systems with high penetrations of VG. © 2012 IEEE.


Kennelly R.P.,Park University | Rogers A.C.,Park University | Winter D.C.,Park University | Winter D.C.,University College Dublin
British Journal of Surgery | Year: 2013

Background: Rectal cancer outcomes following abdominoperineal excision (APE) have been inferior to those for anterior resection, including more positive circumferential resection margins (CRMs). An erroneously conservative interpretation of APE (rather than a radical resection termed 'extralevator') has been proposed as the cause. In this multicentre study, factors contributing to CRM positivity were examined following APE according to its original description. Methods: Data were collected from five hospital databases up to June 2011 including small- and larger-volume units (3 hospitals had 5 or fewer and 2 hospitals had more than 5 APE procedures per year). Primary outcome measures were CRM status; secondary outcomes were local recurrence and death. Results: Of 327 patients, 302 patients had complete data for analysis. Some 50·0 per cent of patients had neoadjuvant chemoradiotherapy. Histopathological examination showed that 62·9 per cent had tumour category T3 or T4 cancers, 42·1 per cent had node-positive disease and the CRM positivity rate was 13·9 per cent. Multivariable analysis showed only pathological tumour category pT4 (odds ratio 19·92, 95 per cent confidence interval 6·48 to 68·61) and node positivity (odds ratio 3·04, 1·32 to 8·05) to be risk factors for a positive circumferential margin. CRM positivity was a risk factor for local recurrence (P = 0·022) and decreased overall survival (P = 0·001). Hospital volume had no impact on the likelihood of CRM positivity (P = 0·435). Conclusion: In patients undergoing APE by appropriately trained surgeons using a standardized approach, margin positivity was dictated by tumour stage, but not by centre or surgeon. Copyright © 2012 British Journal of Surgery Society Ltd. Published by John Wiley & Sons, Ltd.


O'Connor N.E.,Queens University of Belfast | O'Connor N.E.,University College Dublin | Donohue I.,Trinity College Dublin
Global Change Biology | Year: 2013

Loss of biodiversity and nutrient enrichment are two of the main human impacts on ecosystems globally, yet we understand very little about the interactive effects of multiple stressors on natural communities and how this relates to biodiversity and ecosystem functioning. Advancing our understanding requires the following: (1) incorporation of processes occurring within and among trophic levels in natural ecosystems and (2) tests of context-dependency of species loss effects. We examined the effects of loss of a key predator and two groups of its prey on algal assemblages at both ambient and enriched nutrient conditions in a marine benthic system and tested for interactions between the loss of functional diversity and nutrient enrichment on ecosystem functioning. We found that enrichment interacted with food web structure to alter the effects of species loss in natural communities. At ambient conditions, the loss of primary consumers led to an increase in biomass of algae, whereas predator loss caused a reduction in algal biomass (i.e. a trophic cascade). However, contrary to expectations, we found that nutrient enrichment negated the cascading effect of predators on algae. Moreover, algal assemblage structure varied in distinct ways in response to mussel loss, grazer loss, predator loss and with nutrient enrichment, with compensatory shifts in algal abundance driven by variation in responses of different algal species to different environmental conditions and the presence of different consumers. We identified and characterized several context-dependent mechanisms driving direct and indirect effects of consumers. Our findings highlight the need to consider environmental context when examining potential species redundancies in particular with regard to changing environmental conditions. Furthermore, non-trophic interactions based on empirical evidence must be incorporated into food web-based ecological models to improve understanding of community responses to global change. © 2012 Blackwell Publishing Ltd.


Duffy M.J.,University College Dublin
Clinical chemistry | Year: 2013

Companion biomarkers are biomarkers that are used in combination with specific therapies and that prospectively help predict likely response or severe toxicity. In this article we review the role of companion biomarkers in guiding treatment in patients with cancer. In addition to the established companion biomarkers such as estrogen receptors and HER2 (human epidermal growth factor receptor 2) in breast cancer, several new companion biomarkers have become available in recent years. These include v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations for the selection of patients with advanced colorectal cancer who are unlikely to benefit from anti-epidermal growth factor receptor antibodies (cetuximab or panitumumab), epidermal growth factor receptor (EGFR) mutations for selecting patients with advanced non-small cell lung cancer (NSCLC) for treatment with tyrosine kinase inhibitors (gefitinib or erlotinib), v-raf murine sarcoma viral oncogene homolog B1 (BRAF) mutations for selecting patients with advanced melanoma for treatment with anti-BRAF agents (vemurafenib and dabrafenib), and anaplastic lymphoma receptor tyrosine kinase (ALK) translocations for identifying patients with NSCLC likely to benefit from crizotinib. The availability of companion biomarkers should improve drug efficacy, decrease toxicity, and lead to a more individualized approach to cancer treatment.


Gavin K.G.,University College Dublin
European Journal of Engineering Education | Year: 2010

This paper describes the design of the curriculum for a Master of Engineering programme in civil engineering at University College Dublin. The revised programme was established to meet the requirements of the Bologna process and this paper specifically considers the design of a new, second-cycle master's component of the programme. In addition to considering the content required to meet the learning outcome specified by the professional accreditation body, the paper presents details of attempts to move from a traditional instructor-centred model to a student-centred model of education in order to promote reflective (deep) learning. Although the paper presents a model curriculum for a civil engineering programme, the holistic approach to curriculum design outlined, which considers the organisation, sequence and evaluation strategies adopted, is applicable to all subject areas in higher education. © 2010 SEFI.


Ahern A.A.,University College Dublin
European Journal of Engineering Education | Year: 2010

This paper describes two case studies where problem-based learning (PBL) has been introduced to under- graduate civil engineering students in University College Dublin. PBL has recently been put in place in the penultimate and final year transport engineering classes in the civil engineering degree in University College Dublin. In this case study, the paper describes how PBL was introduced, the impacts of its intro- duction and the feedback received by students regarding PBL. PBL was introduced in these years to help students to become deep and active learners and to help them in the transition from passive note taker to researcher and lifelong learner.


Kelly B.D.,University College Dublin
Advances in Psychiatric Treatment | Year: 2015

'Best interests' is a key principle of the Mental Capacity Act 2005 (England and Wales), Mental Capacity Bill (2014) (Northern Ireland) and Mental Health Act 2001 (Ireland), although there are currently proposals to remove 'best interests' from Irish legislation. Legislation in Scotland refers to 'benefit' resulting from interventions. Judicious use of 'best interests', in line with guidelines that prioritise the person's autonomy, will and preferences, is a powerful way to promote the values and rights that underpin the United Nations Convention on the Rights of Persons with Disabilities and to safeguard the dignity of individuals with mental disorder and/or reduced mental capacity. LEARNING OBJECTIVES: • Appreciate the relevance and meanings of the principle of best interests • Understand the implications of the Convention on the Rights of Persons with Disabilities for mental capacity legislation and related practice • Understand recent proposals to merge mental health and mental capacity legislation into a single legislative framework (e.g. in Northern Ireland).


Mahmoudi M.,Tehran University of Medical Sciences | Kalhor H.R.,Sharif University of Technology | Laurent S.,University of Mons | Lynch I.,University College Dublin
Nanoscale | Year: 2013

Due to their ultra-small size, nanoparticles (NPs) have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. NPs are recognized as promising and powerful tools to fight against the human brain diseases such as multiple sclerosis or Alzheimer's disease. In this review, after an introductory part on the nature of protein fibrillation and the existing approaches for its investigations, the effects of NPs on the fibrillation process have been considered. More specifically, the role of biophysicochemical properties of NPs, which define their affinity for protein monomers, unfolded monomers, oligomers, critical nuclei, and other prefibrillar states, together with their influence on protein fibrillation kinetics has been described in detail. In addition, current and possible-future strategies for controlling the desired effect of NPs and their corresponding effects on the conformational changes of the proteins, which have significant roles in the fibrillation process, have been presented. © The Royal Society of Chemistry 2013.


Williams E.,University College Dublin
Reproduction in Domestic Animals | Year: 2013

Contents: Post-partum uterine disease has a detrimental effect on dairy cow fertility; affected cows require more serves per conception, have reduced conception rates and are more likely to be culled for infertility. Furthermore, the detrimental effects on fertility remain even after clinical resolution of disease. There are many factors that influence a cow's resistance to or development of post-partum disease, and the key drivers determining disease outcome are uterine microbial load, regulation of inflammation and immune responses peripherally and at a local level, production pressure, and metabolic (energy) status. These factors are intricately interlinked, which makes assessment of their individual effects difficult. It is clear, however, that the period surrounding calving is a key transition phase and events during this time point will influence uterine disease outcome and subsequent fertility. Good peripartum management and accurate diagnosis are critical to facilitate the use of the most effective treatment and limit the negative impact of post-partum uterine disease on fertility. If we can improve our understanding of the underlying causes of disease, then we can identify 'at risk' animals and implement management and breeding strategies to prevent uterine disease or reduce its severity. Thus, this article aims to summarize the key factors that drive uterine disease in the post-partum dairy cow. © 2013 Blackwell Verlag GmbH.


Smyth P.P.A.,University College Dublin
Current Opinion in Endocrinology, Diabetes and Obesity | Year: 2016

PURPOSE OF REVIEW: The female predominance of diseases of the thyroid and breast makes difficult the separation of an expected association with a causal linkage. This review will examine recent reports on associations between thyroid disease and breast cancer, comparing them with previous studies, with a view to elucidating what pointers are available to suggest either a common pathogenesis or novel thyroid-related therapeutic approach, which might arise from this association. RECENT FINDINGS: Reports on thyroid–breast cancer associations are reviewed under the following headings: breast cancer prevalence in different thyroid disorders and their effect on risk and outcome; the possible role of thyroid autoimmunity, thyroid enlargement, effect of radioactive iodine treatment, role of stable iodine, possible joint antigens sodium iodide transporter and thyroid peroxidase and thyroid–breast cancer coincidence. SUMMARY: Current studies on thyroid and breast cancer associations confirm earlier findings of the lack of definitive evidence of a causal relationship. The predominant relationship continues to be hypothyroidism or autoimmune thyroid disease perhaps contributing to increased breast cancer risk or outcomes. However, despite many studies and the findings of meta-analyses, elucidating the mechanisms underlying the association remains elusive. At present, there is little justification for utilizing thyroid insights as a possible therapeutic intervention in breast cancer. Copyright © 2016 Wolters Kluwer Health, Inc. All rights reserved.


Kennedy P.,University College Dublin
Health Policy | Year: 2010

The objective of this article is to explore recent and proposed future developments in maternity service provision in Ireland in the context of health policy reform. Ireland is experiencing an unprecedented demand for maternity services with in excess of 75,000 births in 2009, the highest since the 1970s when Ireland experienced a 'baby boom'. A further 10% rise is projected for 2010. This demographic change has placed increased demands on an already over-stretched maternity service. Despite more than a decade of economic success the health service has remained in constant crisis with many commentators arguing it has worsened rather than improved since the reform process was instigated in 2001 [1].Reform of maternity services has begun and this article presents two case studies to demonstrate the regional variations in maternity provision in a country which has a national health service and a national Maternity and Infant Care Scheme. It shows what developments have occurred and what direction maternity services are likely to go in the next decade. The two regions under scrutiny are the North East Health Services Executive (NEHSE) and the Greater Dublin Area (GDA). The former illustrates important developments which have occurred in the NEHSE as a result of the Maternity Services Task Force (2002-2010) and argues that there are important learning outcomes not only for the GDA which is the subject of the latter case study but also for the development of maternity services nationally. © 2010 Elsevier Ireland Ltd.


More S.J.,University College Dublin | Good M.,Food and the Marine
Veterinary Microbiology | Year: 2015

There is substantial variation in herd risk for bovine tuberculosis (bTB) in Ireland, with most herds playing little to no role in the ongoing endemic. In infected areas, bTB persistence (affecting one or a group of herds) is a key feature of the infection. In this paper, we present our current understanding and management of bTB risk in Ireland, based on a detailed review of research and policy. There is close interaction between science and policy in Ireland, seeking both to understand and effectively manage bTB risk. Detailed research on bTB persistence is presented, including current understanding of the relative importance of different infection sources, which can include residual infection in cattle and/or re-infection, either from local sources or following cattle introduction. In recent years, there have been three primary drivers for policy change, including scientific advances, ongoing improvements to programme supports, and ongoing programme review. In this review, three key future programme challenges are identified. Although good progress is being made, eradication has not yet been achieved. Firstly, a key question concerns the additional effort that will be required, to move towards final eradication. Secondly, a percentage of non-infected animals are falsely positive to current testing methods. This is an ongoing challenge, given the imperfect specificity of test methods but will become more so, as the positive predictive value falls with reducing bTB prevalence. Finally, there is a need to re-engage with the farming community, so that they play a much greater role in programme ownership. © 2015 The Authors.


Brazil T.J.,University College Dublin
IET Microwaves, Antennas and Propagation | Year: 2013

Microwave circuit simulation has always posed particular difficulties especially in highly non-linear applications because of the presence of distributed or electromagnetic structures, which are usually passive and linear, but difficult to incorporate effectively in time-domain analysis. A variety of specialised techniques has evolved to cope with this situation with reasonable success. In recent years, microwave systems are becoming more integrated and complex and often involve 'mixed-signals' that may operate over a very wide range of time scales, creating new simulation challenges. This study reviews the issues involved and suggests a practical paradigm for generalised time-domain simulation of microwave circuits. © The Institution of Engineering and Technology 2013.


Murphy C.D.,University College Dublin | Sandford G.,Durham University
Expert Opinion on Drug Metabolism and Toxicology | Year: 2015

Introduction: Fluorine's unique physicochemical properties make it a key element for incorporation into pharmacologically active compounds. Its presence in a drug can alter a number of characteristics that affect ADME-Tox, which has prompted efforts at improving synthetic fluorination procedures.Areas covered: This review describes the influence of fluorine on attributes such as potency, lipophilicity, metabolic stability and bioavailablility and how the effects observed are related to the physicochemical characteristics of the element. Examples of more recently used larger scale synthetic methods for introduction of fluorine into drug leads are detailed and the potential for using biological systems for fluorinated drug production is discussed.Expert opinion: The synthetic procedures for carbon-fluorine bond formation largely still rely on decades-old technology for the manufacturing scale and new reagents and methods are required to meet the demands for the preparation of structurally more complex drugs. The improvement of in vitro and computational methods should make fluorinated drug design more efficient and place less emphasis on approaches such as fluorine scanning and animal studies. The introduction of new fluorinated drugs, and in particular those that have novel fluorinated functional groups, should be accompanied by rigorous environmental assessment to determine the nature of transformation products that may cause ecological damage. © 2015 Informa UK, Ltd.


Scott M.,University College Dublin
Landscape Research | Year: 2012

The aim of this paper is to explore how collective memories of place have framed contemporary planning conflicts in a rural arena. Specifically, the paper charts the emergence of the Irish Rural Dwellers Association (IRDA) as a vocal campaigner for private property rights and a laissez-faire approach to accommodating new housing development in the open countryside. For the IRDA, postcolonial narratives and national(ist) identities provide an important vocabulary for protest and opposition to state regulation by: 1) providing a discursive device to create a shared storyline of rural struggle; 2) providing an exclusionary device, whereby drawing on 'memory' and representations of rurality creates an insider/outsider discourse where some voices are cast as illegitimate; and 3) providing a frame for placing emotional knowledge at the centre of planning and landscape policy-making. This paper questions the authenticity of this policy narrative and addresses the validity of self-acclaimed knowledge within the landscape and rural policy arena. More broadly, the paper attempts to enhance understanding of how memory shapes policy narratives in the (re)production of cultural landscapes. © 2012 Copyright Taylor and Francis Group, LLC.


McBean G.J.,University College Dublin
Amino Acids | Year: 2012

Astrocyte cells require cysteine as a substrate for glutamate cysteine ligase (γ-glutamylcysteine synthase; EC 6.3.2.2) catalyst of the rate-limiting step of the γ-glutamylcycle leading to formation of glutathione (L-γ-glutamyl- L-cysteinyl-glycine; GSH). In both astrocytes and glioblastoma/astrocytoma cells, the majority of cysteine originates from reduction of cystine imported by the x c - cystine-glutamate exchanger. However, the transsulfuration pathway, which supplies cysteine from the indispensable amino acid, methionine, has recently been identified as a significant contributor to GSH synthesis in astrocytes. The purpose of this review is to evaluate the importance of the transsulfuration pathway in these cells, particularly in the context of a reserve pathway that channels methionine towards cysteine when the demand for glutathione is high, or under conditions in which the supply of cystine by the x c - exchanger may be compromised. © Springer-Verlag 2011.


De Munari A.,University of Edinburgh | Semiao A.J.C.,University College Dublin | Antizar-Ladislao B.,University of Edinburgh
Water Research | Year: 2013

Nanofiltration (NF) is a well-established process used in drinking water production to effectively remove Natural Organic Matter (NOM) and organic micropollutants. The presence of NOM has been shown to have contrasting results on micropollutant retention by NF membranes and removal mechanisms are to date poorly understood. The permeate water quality can therefore vary during operation and its decrease would be an undesired outcome for potable water treatment. It is hence important to establish the mechanisms involved in the removal of organic micropollutants by NF membranes in the presence of NOM. In this study, the retention mechanisms of pesticide Endosulfan (ES) in the presence of humic acids (HA) by two NF membranes, TFC-SR2 and TFC-SR3, a "loose" and a "tight" membrane, respectively, were elucidated. The results showed that two mechanisms were involved: (1) the formation of ES-HA complexes (solute-solute interactions), determined from solid-phase micro-extraction (SPME), increased ES retention, and (2) the interactions between HA and the membrane (solute-membrane interactions) increased membrane molecular weight cut-off (MWCO) and decreased ES retention. HA concentration, pH, and the ratio between micropollutant molecular weight (MW) and membrane MWCO were shown to influence ES retention mechanisms. In the absence of HA-membrane interactions at pH 4, an increase of HA concentration increased ES retention from 60% to 80% for the TFC-SR2 and from 80% to 95% for the TFC-SR3 due to ES-HA complex formation. At pH 8, interactions between HA and the loose TFC-SR2 increased the membrane MWCO from 460 to 496g/mol and ES retention decreased from 55% to 30%, as HA-membrane interactions were the dominant mechanism for ES retention. In contrast, for the "tight" TFC-SR3 membrane the increase in the MWCO (from 165 to 179g/mol), was not sufficient to decrease ES retention which was dominated by ES-HA interactions. Quantification of the contribution of both solute-solute interactions and solute-membrane interactions is hence fundamental in understanding the removal mechanisms of micropollutant by NF membranes in the presence of NOM in order to optimize the treatment process. © 2013 Elsevier Ltd.


Knowles C.H.,Queen Mary, University of London | Horrocks E.J.,Queen Mary, University of London | Bremner S.A.,Queen Mary, University of London | Stevens N.,Queen Mary, University of London | And 3 more authors.
The Lancet | Year: 2015

Background Percutaneous tibial nerve stimulation (PTNS) is a new ambulatory therapy for faecal incontinence. Data from case series suggest it has beneficial outcomes in 50-80% patients; however its effectiveness against sham electrical stimulation has not been investigated. We therefore aimed to assess the short-term efficacy of PTNS against sham electrical stimulation in adults with faecal incontinence. Methods We did a double-blind, multicentre, pragmatic, parallel-group, randomised controlled trial (CONtrol of Faecal Incontinence using Distal NeuromodulaTion [CONFIDeNT]) in 17 specialist hospital units in the UK that had the skills to manage patients with faecal incontinence. Eligible participants aged 18 years or older with substantial faecal incontinence for whom conservative treatments (such as dietary changes and pelvic floor exercises) had not worked, were randomly assigned (1:1) to receive either PTNS (via the Urgent PC neuromodulation system) or sham stimulation (via a transcutaneous electrical nerve stimulation machine to the lateral forefoot) once per week for 12 weeks. Randomisation was done with permuted block sizes of two, four, and six, and was stratified by sex and then by centre for women. Patients and outcome assessors were both masked to treatment allocation for the 14-week duration of the trial (but investigators giving the treatment were not masked). The primary outcome was a clinical response to treatment, which we defined as a 50% or greater reduction in episodes of faecal incontinence per week. We assessed this outcome after 12 treatment sessions, using data from patients' bowel diaries. Analysis was by intention to treat, and missing data were multiply imputed. This trial is registered with the ISRCTN registry, number 88559475, and is closed to new participants. Findings Between Jan 23, 2012, and Oct 31, 2013, we randomly assigned 227 eligible patients (of 373 screened) to receive either PTNS (n=115) or sham stimulation (n=112). 12 patients withdrew from the trial: seven from the PTNS group and five from the sham group (mainly because they could not commit to receiving treatment every week). Two patients (one in each group) withdrew because of an adverse event that was unrelated to treatment (exacerbation of fibromyalgia and rectal bleeding). 39 (38%) of 103 patients with full data from bowel diaries in the PTNS group had a 50% or greater reduction in the number of episodes of faecal incontinence per week compared with 32 (31%) of 102 patients in the sham group (adjusted odds ratio 1·28, 95% CI 0·72-2·28; p=0·396). No serious adverse events related to treatment were reported in the trial. Seven mild, related adverse events were reported in each treatment group, mainly pain at the needle site (four in PTNS, three in sham). Interpretation PTNS given for 12 weeks did not confer significant clinical benefit over sham electrical stimulation in the treatment of adults with faecal incontinence. Further studies are warranted to determine its efficacy in the long term, and in patient subgroups (ie, those with urgency). © 2015 Elsevier Ltd.


Fitzpatrick J.M.,University College Dublin
World Journal of Urology | Year: 2011

Introduction: An evidence-based approach to the practice of urology relies on the accumulation of a body of evidence from clinical research. Ethical publishing has a major role to play in building confidence in the compiled evidence, which can lead to the development of clinical practice guidelines and new treatment paradigms. Methods: The literature on the recent developments in ethical publishing was reviewed to highlight how this supported the promotion of the evidence-based practice of urology. Conclusion: The requirements for complete and transparent reporting of results, the honest and full declaration of conflicts of interest, and the correct assignment of authorship are essential to build up confidence in the evidence-based practice of urology. Increasing the quality of the reporting of trials allows the evidence base to be scrutinized and validated. Reporting the experience and expertise of authors in compiling, analysing and interpreting evidence also helps to develop this trust. A great deal of progress has been made in the recent years, but there is a lot more work to be done. © 2011 Springer-Verlag.


Persu A.,Catholic University of Louvain | O'Brien E.,University College Dublin | Verdecchia P.,Hospital of Assisi
Hypertension research : official journal of the Japanese Society of Hypertension | Year: 2014

Resistant hypertension as defined by the European Society of Hypertension and American Heart Association is a blood pressure that remains uncontrolled despite concomitant intake of at least three antihypertensive drugs (one of them preferably being a diuretic) at full doses. This definition is still based on office rather than out-of-office blood pressure measurement. In this review we propose a new, stricter definition of resistant hypertension based on ambulatory blood pressure measurement. The main arguments in favor of this are: (1) in patients with resistant hypertension, ambulatory blood pressure is an independent predictor of cardiovascular morbidity whereas, after adjustment for conventional risk factors, conventional blood pressure has little added value; (2) white-coat resistant hypertension (uncontrolled office with normal ambulatory blood pressure) is frequent (30-40% of patients with apparently resistant hypertension) carrying a prognosis similar to that of controlled hypertension, and intensification of blood pressure lowering treatment, or the use of nondrug treatment strategies such as renal denervation or carotid baroreceptor stimulation, is not justified; (3) masked resistant hypertension (controlled office with elevated ambulatory blood pressure) is frequent (approximately one-third of patients with controlled office blood pressure on triple antihypertensive therapy) and associated with an increased risk of cardiovascular events; in such patients, treatment intensification should be considered; (4) the current definition of resistant hypertension (office blood pressure ⩾ 140/90 mm Hg on triple antihypertensive therapy) allows a substantial proportion of patients with spurious or white-coat resistant hypertension to undergo renal denervation in the absence of proven long-term benefits.


Akcay S.,University College Dublin | Van De Meent M.,University of Southampton
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2016

The effective-one-body theory (EOB) describes the conservative dynamics of compact binary systems in terms of an effective Hamiltonian approach. The Hamiltonian for moderately eccentric motion of two nonspinning compact objects in the extreme mass-ratio limit is given in terms of three potentials: a(v), d(v), q(v). By generalizing the first law of mechanics for (nonspinning) black hole binaries to eccentric orbits, [A. Le Tiec, Phys. Rev. D 92, 084021 (2015).] recently obtained new expressions for d(v) and q(v) in terms of quantities that can be readily computed using the gravitational self-force approach. Using these expressions we present a new computation of the EOB potential q(v) by combining results from two independent numerical self-force codes. We determine q(v) for inverse binary separations in the range 1/1200≤v1/6. Our computation thus provides the first-ever strong-field results for q(v). We also obtain d(v) in our entire domain to a fractional accuracy of 10-8. We find that our results are compatible with the known post-Newtonian expansions for d(v) and q(v) in the weak field, and agree with previous (less accurate) numerical results for d(v) in the strong field. © 2016 American Physical Society.


Equilibrium Born-Oppenheimer molecular dynamics simulations have been performed in the canonical ensemble to investigate the structural properties of liquid water and ice Ih (hexagonal ice) at 298 and 273 K, respectively, using a state-of-the-art non-local correlation functional, whilst size effects have been examined explicitly in the case of liquid water. This has led to improved agreement with experiments for pair distribution functions, in addition to molecular dipole moments, vis-à-vis previous flavours of ab-initio molecular dynamics simulation of water, highlighting the importance of appropriate dispersion. Intramolecular geometry has also been examined, in addition to hydrogen-bonding interactions; it was found that an improved description of dispersion via non-local correlation helps to reduce over-structuring associated with the Perdew-Becke-Ernzerhof (PBE) and other commonly-used functionals. © 2015 by the authors.


Smolka A.J.,Medical University of South Carolina | Backert S.,University College Dublin
Journal of Gastroenterology | Year: 2012

Infection of the human stomach mucosa by Helicobacter pylori induces strong inflammatory responses and a transitory hypochlorhydria which can progress in ∼2 % of patients to atrophic gastritis, dysplasia, or gastric adenocarcinoma. H. pylori infection of gastric biopsies or cultured gastric epithelial cells in vitro represses the activity of endogenous or transfected promoter of the alpha-subunit (HKα) of gastric H,K-adenosine triphosphatase (H,K-ATPase), the parietal cell enzyme mediating acid secretion. Some mechanistic details of H. pylori-mediated repression of HKα and ensuing hypochlorhydria have been recently elucidated. H. pylori strains expressing a type IV secretion system (T4SS) encoded by the cag pathogenicity island are known to upregulate the transcription factor nuclear factor (NF)-κB. The NF-κB-binding regions in the HKα promoter were identified and shown to repress its transcriptional activity. Interaction studies have indicated that although active phosphorylated NF-κB p65 is present in infected cells, an NF-κB p50/p65 heterodimeric complex fails to bind to the HKα promoter. Point mutations at-159 and-161 bp in the HKα promoter NF-κB binding sequence prevent the binding of NF-κB p50 and prevent H. pylori repression of point-mutated HKα promoter activity. The T4SS factors CagL, CagE, CagM, and possibly CagA and the lytic transglycosylase Slt, are mechanistically involved in NF-κB activation and repression of HKα transcription. CagL, a T4SS pilus component, binds to the integrin α 5β 1 to mediate translocation of virulence factors into the host cell and initiate signaling. During acute H. pylori infection, CagL dissociates ADAM 17 (a disintegrin and a metalloprotease 17) from the integrin α 5β 1 complex and stimulates ADAM17-dependent release of heparin-binding epidermal growth factor (HB-EGF), EGF receptor (EGFR) stimulation, ERK1/2 kinase activation, and NF-κB-mediated repression of HKα. These studies suggest that H. pylori inhibits HKα gene expression by an integrin α 5β 1 → ADAM17 → HBEGF → EGFR → ERK1/2 → NF-κB pathway mediating NF-κB p50 homodimer binding to the HKα promoter. Here we review the molecular basis and recent progress of this novel pathogen-dependent mechanism of H,K-ATPase inhibition, which contributes significantly to our current understanding of H. pylori pathophysiology. © 2012 Springer.


Kelly B.D.,University College Dublin
Irish journal of medical science | Year: 2015

BACKGROUND: Ireland's Assisted Decision-Making (Capacity) Bill (2013) aims to reform the law relating to persons who require assistance exercising their decision-making capacity. When finalised, the Bill will replace Ireland's outdated Ward of Court system which has an all-or-nothing approach to capacity; does not adequately define capacity; is poorly responsive to change; makes unwieldy provision for appointing decision-makers; and has insufficient provision for review.AIMS: To explore the content and implications of the Assisted Decision-Making (Capacity) Bill.METHODS: Review of the content of the Assisted Decision-Making (Capacity) Bill and related literature.RESULTS: The new Bill includes a presumption of capacity and defines lack of capacity. All interventions must minimise restriction of rights and freedom, and have due regard for "dignity, bodily integrity, privacy and autonomy". The Bill proposes legal frameworks for "assisted decision-making" (where an individual voluntarily appoints someone to assist with specific decisions relating to personal welfare or property and affairs, by, among other measures, assisting the individual to communicate his or her "will and preferences"); "co-decision-making" (where the Circuit Court declares the individual's capacity is reduced but he or she can make specific decisions with a co-decision-maker to share authority); "decision-making representatives" (substitute decision-making); "enduring power of attorney"; and "informal decision-making on personal welfare matters" (without apparent oversight).CONCLUSIONS: These measures, if implemented, will shift Ireland's capacity laws away from an approach based on "best interests" to one based on "will and preferences", and increase compliance with the United Nations' Convention on the Rights of Persons with Disabilities.


Hone D.W.E.,University College Dublin | Naish D.,University of Portsmouth | Cuthill I.C.,University of Bristol
Lethaia | Year: 2012

Cranial ornamentation is widespread throughout the extinct non-avialian Ornithodira, being present throughout Pterosauria, Ornithischia and Saurischia. Ornaments take many forms, and can be composed of at least a dozen different skull bones, indicating multiple origins. Many of these crests serve no clear survival function and it has been suggested that their primary use was for species recognition or sexual display. The distribution within Ornithodira and the form and position of these crests suggest sexual selection as a key factor, although the role of the latter has often been rejected on the grounds of an apparent lack of sexual dimorphism in many species. Surprisingly, the phenomenon of mutual sexual selection - where both males and females are ornamented and both select mates - has been ignored in research on fossil ornithodirans, despite a rich history of research and frequent expression in modern birds. Here, we review the available evidence for the functions of ornithodiran cranial crests and conclude that mutual sexual selection presents a valid hypothesis for their presence and distribution. The integration of mutual sexual selection into future studies is critical to our understanding of ornithodiran ecology, evolution and particularly questions regarding sexual dimorphism. © 2011 The Authors, Lethaia © 2011 The Lethaia Foundation.


Fitzgerald D.J.,University College Dublin
Circulation research | Year: 2013

The development of drugs that inhibit platelets has been driven by a combination of clinical insights, fundamental science, and sheer luck. The process has evolved as the days of stumbling on therapeutic gems, such as aspirin, have long passed and have been replaced by an arduous process in which a drug is designed to target a specific protein implicated in a well-characterized pathophysiological process, or so we would like to believe. The development of antiplatelet therapy illustrates the importance of understanding the mechanisms of disease and the pharmacology of the compounds we develop, coupled with careful clinical experimentation and observation and, yes, still, a fair bit of luck.


Kilbane D.,University College Dublin
Journal of Physics B: Atomic, Molecular and Optical Physics | Year: 2011

Potential extreme ultraviolet and soft x-ray radiation sources have been identified, using the flexible atomic code (FAC), as emission peaks arising from the 4d-4f and 4p-4d transitions in Pd-like to Rb-like ions of hafnium through actinium. The effects of configuration interaction are investigated and for increasing nuclear charge, these strong emitters are seen to separate and move to shorter wavelengths. Each source is characterized using the unresolved transition array model. They are proposed to complement the currently used nitrogen and argon sources in the 'water window', and as possible successors to tin in next-generation lithography. © 2011 IOP Publishing Ltd.


Harvey D.J.,University of Oxford | Rudd P.M.,University College Dublin
International Journal of Mass Spectrometry | Year: 2011

The negative ion CID spectra of singly ([M-H] -) and doubly ([M-2H] 2-) charged sialylated bi-, tri- and tetra-sialylated N-glycans are described with particular reference to ions that define the linkage of the sialic acids. The singly charged ions generally gave prominent deprotonated molecular ions but, because the proton mainly arose from the sialic acid moieties, the fragmentation was not as diagnostic as that of neutral glycans where deprotonation occurs from one of several hydroxyl groups. Nevertheless, ions defining most structural features such as the location of fucose residues and differentiation between triantennary isomers were still present. Ions in the high mass end of the spectra of glycans with α2 → 6-linked-sialic acids were generally dominated by 0,2A 7 cleavage products rather than the 2,4A 7 ions that dominate the spectra of the neutral glycans. The ion at m/z 306 ( 0,4A 2-CO 2) was most useful in defining the α2 → 6-linkage. The antenna-specific D and [D-18] - ions were usually present but of low intensity. Glycans with α2 → 3-linked-sialic acids produced spectra that more closely resembled those of the neutral compounds. Doubly charged ions fragmented mainly to singly charged products following loss of sialic acids. Neutralization by linkage-specific derivatization and consequent formation of [M+anion] - ions generally restored the abundant antenna-specific fragments. Singly charged sulfated glycans fragmented in a similar manner to the sialylated compounds but the lower end of the spectra were dominated by B 1 (sulfated GalNAc) and B 2 fragments rather than the cross-ring fragments common to the corresponding spectra of the sialylated compounds. © 2010 Elsevier B.V.


O'Brien E.,University College Dublin | Turner J.R.,Quintiles
Journal of Clinical Hypertension | Year: 2013

It has become apparent that noncardiovascular drugs can affect blood pressure (BP) in an off-target manner, either by raising or lowering pressure or by negating the beneficial hypotensive effect of concomitantly prescribed antihypertensives. This paper presents compelling evidence that ambulatory blood pressure monitoring (ABPM) should be used to detect BP effects during the development of noncardiovascular drugs. The requirements for standardizing ABPM to obtain the most information from the least number of participants and the many advantages of obtaining a 24-hour BP profile are discussed. The use of ABPM in trials of antihypertensive agents, though differing in purpose (the demonstration of BP-lowering efficacy) from the use of ABPM in trials of noncardiovascular drugs (the demonstration of any off-target effect on BP) nonetheless provides methodological similarities that can be applied in both contexts with advantage. The paper also considers whether there are lessons to be learned from a regulatory science approach that is designed to prospectively identify unacceptable off-target cardiac effects of noncardiac drugs and offers some thoughts on how a future paradigm of standardized use of ABPM to assess off-target BP effects during the development of noncardiovascular drugs might benefit patient safety. © 2012 Wiley Periodicals, Inc.


De Gascun C.F.,University College Dublin
AIDS research and human retroviruses | Year: 2012

HIV genetic diversity may have an impact on viral pathogenesis, transmission, response to treatment, and vaccine development. Public health surveillance that monitors the frequency and variety of HIV subtypes in a particular region or patient group is vital to successfully control the pandemic. We present the first comprehensive report on HIV diversity in Ireland. This study comprised all new HIV-1 diagnoses that were confirmed in the National Virus Reference Laboratory, University College Dublin, from January 2004 to December 2008. HIV 1 protease and reverse transcriptase sequences were generated using the Siemens Trugene HIV 1 Genotyping System. Subtypes were determined using web-based genotyping tools. There were 1579 new diagnoses [615 (39%) female and 964 (61%) male], of which 1060 had HIV-1 RNA specimens available for sequencing. Of sequenced samples, HIV-1 subtype B accounted for 50% overall, decreasing from 55.1% in 2004 to 49.5% in 2008. In addition, subtype B accounted for more than 80% of Irish-born individuals and more than 90% of Irish-born injection drug users and men who have sex with men. Subtype C was the second most prevalent in the overall cohort, accounting for 25%, although it accounted for only 6.1% of Irish-born individuals, with no evidence of in country transmission. The prevalence of non-subtype B HIV-1 infection in Ireland is increasing. However, these appear primarily to be imported infections not yet circulating within traditional Irish risk groups. Enhanced HIV-1 molecular epidemiology surveillance is required to monitor the spread of HIV-1, to inform future public health policy, and to ultimately control the HIV-1 epidemic in Ireland.


Milano F.,University College Dublin | Zarate-Minano R.,University of Castilla - La Mancha
IEEE Transactions on Power Systems | Year: 2013

This paper proposes a systematic and general approach to model power systems as continuous stochastic differential-algebraic equations. With this aim, the paper provides a theoretical background on stochastic differential-algebraic equations and justifies the need for stochastic models in power system analysis. Then, the paper describes a general procedure to define stochastic dynamic models. Practical issues related to the numerical integration of the resulting power system model are also discussed. A case study illustrating the proposed approach is provided based on the IEEE 145-bus 50-machine system. The case study also illustrates and compares the reliability of the results obtained using stochastic and conventional probabilistic models. © 2013 IEEE.


Walter S.,University of Aarhus | Nicholson P.,John Innes Center | Doohan F.M.,University College Dublin
New Phytologist | Year: 2010

TheFusarium species Fusarium graminearum and Fusarium culmorum, which are responsible for Fusarium head blight (FHB) disease, reduce world-wide cereal crop yield and, as a consequence of their mycotoxin production in cereal grain, impact on both human and animal health. Their study is greatly promoted by the availability of the genomic sequence of F. graminearum and transcriptomic resources for both F. graminearum and its cereal hosts. Functional genomic, proteomic and metabolomic studies, in combination with targeted mutagenesis or transgenic studies, are unravelling the complex mechanisms involved in Fusarium infection, penetration and colonization of host tissues, and host avoidance thereof. This review illuminates and integrates emerging knowledge regarding the molecular crosstalk between Fusarium and its small-grain cereal hosts. An understanding of the complexity of the host-pathogen interactions will be instrumental in designing new efficient strategies for the control of FHB disease. © 2009 New Phytologist.


Jackson S.,Vanderbilt University | Jackson S.,University College Dublin | Blake R.,Vanderbilt University | Blake R.,Seoul National University
Journal of Neuroscience | Year: 2010

Recent computational models of biological motion perception operate on ambiguous two-dimensional representations of the body (e.g., snapshots, posture templates) and contain no explicit means for disambiguating the three-dimensional orientation of a perceived human figure. Are there neural mechanisms in the visual system that represent a moving human figure's orientation in three dimensions? To isolate and characterize the neural mechanisms mediating perception of biological motion, we used an adaptation paradigm together with bistable point-light (PL) animations whose perceived direction of heading fluctuates over time. After exposure to a PL walker with a particular stereoscopically defined heading direction, observers experienced a consistent aftereffect: a bistable PL walker, which could be perceived in the adapted orientation or reversed in depth, was perceived predominantly reversed in depth.A phase-scrambled adaptor produced no aftereffect, yet when adapting and test walkers differed in size or appeared on opposite sides of fixation aftereffects did occur. Thus, this heading direction aftereffect cannot be explained by local, disparity-specific motion adaptation, and the properties of scale and position invariance imply higher-level origins of neural adaptation. Nor is disparity essential for producing adaptation: when suspended on top of a stereoscopically defined, rotating globe, a context-disambiguated "globetrotter" was sufficient to bias the bistable walker's direction, as were full-body adaptors. In sum, these results imply that the neural signals supporting biomotion perception integrate information on the form, motion, and three-dimensional depth orientation of the moving human figure. Models of biomotion perception should incorporate mechanisms to disambiguate depth ambiguities in two-dimensional body representations. Copyright © 2010 the authors.


Tukovic Z.,University of Zagreb | Ivankovic A.,University College Dublin | Karac A.,University of Zenica
International Journal for Numerical Methods in Engineering | Year: 2013

Correct calculation of stresses at the interface of bonded or otherwise joined materials plays a significant role in many applications. It is therefore important that traction at the material interface is calculated as accurately as possible. This paper describes procedures that can be employed to achieve this goal by using centre-based finite-volume method. Total traction at the interface is calculated by decomposing it into normal and tangential components, both being calculated at each side of the interface, and applying the continuity assumption. The way in which the traction approximation is achieved depends on calculation of tangential gradient of displacement at the interface. To this end, three different methods are proposed and validated against problems with known solutions. It was shown that all methods can be successfully used to simulate problems with multi-material domains, with the procedure based on finite area method being most accurate. © 2012 John Wiley & Sons, Ltd.


Kelly B.D.,University College Dublin
Irish Journal of Medical Science | Year: 2010

Background: The history of institutional care for individuals with intellectual disability is under-researched, complex and troubling. Aims: To explore the experiences of women who may have had intellectual disability and/or mental illness and were admitted to forensic psychiatric care in early twentieth-century Ireland. Methods: All female case records at the Central Mental Hospital, Dublin from 1910 to 1948 (n = 42) were studied for evidence of possible intellectual disability and a series of five cases is presented in detail. Results: These committals occurred in the context of adverse social conditions, over-crowding in asylums and a belief that rates of mental illness were rising. Particular challenges included diagnostic issues (especially in relation to intellectual disability), adjustment to asylum environments, mental illness and physical ill-health. Conclusions: The institutional experiences of individuals with intellectual disability represents an important area for further historical research, using larger and more varied forensic populations. © 2008 Royal Academy of Medicine in Ireland.


Hacariz O.,TUBITAK - Marmara Research Center | Sayers G.,University College Dublin | Baykal A.T.,TUBITAK - Marmara Research Center
Journal of Proteome Research | Year: 2012

Fasciola hepatica, a trematode helminth, causes an economically important disease (fasciolosis) in ruminants worldwide. Proteomic analysis of the parasite provides valuable information to understand the relationship between the parasite and its host. Previous studies have identified various parasite proteins, some of which are considered as vaccine candidates or important drug targets. However, the approximate distribution and abundance of the proteins on the surface and within internal parts of the liver fluke are unknown. In this study, two fractions including surface protein fraction (representing surface part of the parasite, near subplasma membrane of the tegument and above the basal membrane of the tegument) and internal protein fraction (representing internal part of the parasite, mainly deeper sides of the tegument including subbasal membrane and other further internal elements of the parasite) were obtained. Components of these two fractions were investigated by an advanced proteomics approach using a high-definition mass spectrometer with nano electrospray ionization source coupled to a high-performance liquid chromatography system (nanoUPLC-ESI-qTOF-MS). FABP1 was found highly abundant in the SPF fraction. Potentially novel F. hepatica proteins showing homology with AKT interacting protein (Xenopus tropicalis), sterol O-acyltransferase 2 (Homo sapiens), and integrin beta 7 (Mus musculus) were identified with high quantities in only the surface fraction of the parasite and may be possible candidates for future control strategies. © 2012 American Chemical Society.


Corcoran P.,University College Dublin | Mooney P.,National University of Ireland, Maynooth
European Physical Journal: Special Topics | Year: 2013

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. © 2013 EDP Sciences and Springer.


Giacomello A.,University of Rome La Sapienza | Meloni S.,University College Dublin | Chinappi M.,University of Rome La Sapienza | Casciola C.M.,University of Rome La Sapienza
Langmuir | Year: 2012

In this work, we study the wetting of a surface decorated with one nanogroove by a bulk Lennard-Jones liquid at various temperatures and densities. We used atomistic simulations aimed at computing the free energy of the stable and metastable states of the system, as well as the intermediate states separating them. We found that the usual description in terms of Cassie-Baxter and Wenzel states is insufficient, as the system presents two states of the Cassie-Baxter type. These states are characterized by different curvatures of the meniscus. The measured free energy barrier separating the Cassie-Baxter from the Wenzel state (and vice versa) largely exceeds the thermal energy, attesting the existence of Cassie-Baxter/Wenzel metastabilities. Finally, we found that the Cassie-Baxter/Wenzel transition follows an asymmetric path, with the formation of a liquid finger on one side of the groove and a vapor bubble on the opposite side. © 2012 American Chemical Society.


Ottewill A.C.,University College Dublin | Taylor P.,Trinity College Dublin
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2012

We derive a closed-form solution for the Green's function for the wave equation of a static (with respect to an undragged, static observer at infinity) scalar charge in the Kerr space-time. We employ our solution to obtain an analytic expression for the self-force on such a charge, comparing our results to those of L.M. Burko and Y.T. Liu, Phys. Rev. DPRVDAQ0556-2821 64, 024006 (2001)10.1103/PhysRevD.64.024006. © 2012 American Physical Society.


Caprani C.C.,Dublin Institute of Technology | OBrien E.J.,University College Dublin
Structural Safety | Year: 2010

To assess the safety of an existing bridge, the loads to which it may be subject in its lifetime are required. Statistical analysis is used to extrapolate a sample of load effect values from the simulation period to the required design period. Complex statistical methods are often used and the end result is usually a single value of characteristic load effect. Such a deterministic result is at odds with the underlying stochastic nature of the problem. In this paper, predictive likelihood is shown to be a method by which the distribution of the lifetime extreme load effect may be determined. An estimate of the distribution of lifetime-maximum load effect facilitates the reliability approach to bridge assessment. Results are presented for some cases of bridge loading, compared to a return period approach and significant differences identified. The implications for the assessment of existing bridges are discussed. © 2009 Elsevier Ltd. All rights reserved.


Smith W.J.,University College Dublin
Energy | Year: 2010

In the period 1990-2007, CO2 emissions from Ireland's Transport sector increased by 181%. It has been proposed that a transition to EV (electrically-powered vehicles) - either BEV (battery-powered) or PHEV (plug-in hybrids) - offers the potential for significant reductions in these emissions. However, the benefits of PHEV - and of plug-in vehicles generally - accrue because some fraction of the fossil fuel normally consumed by the vehicle is displaced by electricity extracted from the national grid. The net benefit therefore depends on many factors, including the characteristics of the electricity generation and distribution system, and the proportion of vkm (vehicle-kilometres) completed under electric power.This paper examines these factors in an Irish context. On the basis of individual vehicles, it is found that electrification yields substantial and immediate reductions in GHG (greenhouse gas) emissions for urban-type driving cycles. For inter-city travel, however, the percentage reduction attainable is much smaller, and the technical difficulty of achieving this capability is much greater. Unless that challenge can be overcome, it is shown, 50-75% of CO2 emissions from private cars will remain beyond the reach of electrification. © 2010 Elsevier Ltd.


Egan B.,University College Dublin | Egan B.,Karolinska Institutet | Zierath J.R.,Karolinska Institutet | Zierath J.R.,Novo Nordisk AS
Cell Metabolism | Year: 2013

Preservation of aerobic fitness and skeletal muscle strength through exercise training can ameliorate metabolic dysfunction and prevent chronic disease. These benefits are mediated in part by extensive metabolic and molecular remodeling of skeletal muscle by exercise. Aerobic and resistance exercise represent extremes on the exercise continuum and elicit markedly different training responses that are mediated by a complex interplay between a myriad of signaling pathways coupled to downstream regulators of transcription and translation. Here, we review the metabolic responses and molecular mechanisms that underpin the adaptatation of skeletal muscle to acute exercise and exercise training. © 2013 Elsevier Inc.


Acute kidney injury (AKI) is a syndrome that is associated with a major burden of morbidity and mortality in a variety of high risk patient populations, many of them cared for by intensivists. Following renal transplantation, delayed graft function (DGF) caused by severe acute tubular necrosis (ATN), defined by a requirement for dialysis during the initial post-transplant week, complicates postoperative management, and if prolonged (>14 days), adversely affects allograft survival. Neutrophil gelatinase-associated lipocalin (NGAL) and other novel biomarkers can detect AKI earlier than serum creatinine, and can predict AKI severity in high risk patient populations, including kidney transplant recipients. Hollmen and colleagues now demonstrate that elevated urine NGAL in deceased kidney donors is a significant risk factor for prolonged post-transplant DGF in recipients. These findings have clear implications with regard to potentially improved assessment of deceased donor suitability for potential renal allograft donation. These findings are also consistent with the growing evidence that severe ATN diagnosed by markedly elevated levels of AKI biomarkers is a useful predictor of the requirement for acute renal replacement therapy in AKI patients. © 2011 BioMed Central Ltd.


Phelan A.,University College Dublin
Journal of Elder Abuse and Neglect | Year: 2014

Until recent years, Ireland has not formally responded to elder abuse. This article considers the recent developments in Ireland through an ecological framework, which focuses on the multidimensional progress of Irish policy, practice, and legislation related to protecting older people. Although significant progress has been made, the discussion highlights areas for continued development and improvement. © 2014 Copyright Taylor and Francis Group, LLC.


Kelly B.D.,University College Dublin
International Journal of Law and Psychiatry | Year: 2011

In 2005, the World Health Organization (WHO) published its Resource Book on Mental Health, Human Rights and Legislation (Geneva: WHO) presenting a detailed statement of human rights issues which need to be addressed in national legislation relating to mental health. The purpose of this paper is to determine the extent to which revised mental health legislation in England, Wales (2007) and Ireland (2001) accords with these standards (excluding standards relating solely to children or mentally-ill offenders).Legislation in England and Wales meets 90 (54.2%) of the 166 WHO standards examined, while legislation in Ireland meets 80 standards (48.2%). Areas of high compliance include definitions of mental disorder, relatively robust procedures for involuntary admission and treatment (although provision of information remains suboptimal) and clarity regarding offences and penalties Areas of medium compliance relate to competence, capacity and consent (with a particular deficit in capacity legislation in Ireland), oversight and review (which exclude long-term voluntary patients and require more robust complaints procedures), and rules governing special treatments, seclusion and restraint. Areas of low compliance relate to promoting rights (impacting on other areas within legislation, such as information management), voluntary patients (especially non-protesting, incapacitated patients), protection of vulnerable groups and emergency treatment. The greatest single deficit in both jurisdictions relates to economic and social rights. There are four key areas in need of rectification and clarification in relation to mental health legislation in England, Wales and Ireland; these relate to (1) measures to protect and promote the rights of voluntary patients; (2) issues relating to competence, capacity and consent (especially in Ireland); (3) the role of "common law" in relation to mental health law (especially in England and Wales); and (4) the extent to which each jurisdiction wishes to protect the economic and social rights of the mentally ill through mental health legislation rather than general legislation. It is hoped that this preliminary analysis of mental health legislation will prompt deeper national audits of mental health and general law as it relates to the mentally ill, performed by multi-disciplinary committees, as recommended by the WHO. © 2011 Elsevier Ltd.


English N.J.,University College Dublin
Energies | Year: 2013

Massively-parallel classical equilibrium molecular dynamics (MD) simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC) model and single-particle model of Molinero et al. applied to simulation of methane hydrates, using systems consisting of several million particles, on a variety of Blue Gene/L, P and Q platforms. It was found that the newer Blue Gene/Q platform offers attractive performance for massively-parallel simulation. © 2013 by the author.


Wilm M.,University College Dublin
Molecular and Cellular Proteomics | Year: 2011

Electrospray ionization is today the most widely used ionization technique in chemical and biochemical analysis. Interfaced with a mass spectrometer it allows the investigation of the molecular composition of liquid samples. With electrospray a large variety of chemical substances can be ionized. There is no limitation in mass which thus enables even the investigation of large noncovalent protein complexes. Its high ionization efficiency profoundly changed biomolecular sciences because proteins can be identified and quantified on trace amounts in a high throughput fashion. This review article focuses mainly on the exploration of the underlying ionization mechanism. Some ionization characteristics are discussed that are related to this mechanism. Typical spectra of peptides, proteins, and noncovalent complexes are shown and the quantitative character of spectra is highlighted. Finally the possibilities and limitations in measuring the association constant of bivalent noncovalent complexes are described. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.


McMahon H.E.M.,University College Dublin
Biochemical Society Transactions | Year: 2012

The events leading to the degradation of the endogenous PrPC (normal cellular prion protein) have been the subject of numerous studies. Two cleavage processes, α-cleavage and β-cleavage, are responsible for the main C- and N-terminal fragments produced from PrPC. Both cleavage processes occur within the N-terminus of PrPC, a region that is significant in terms of function. α-Cleavage, an enzymatic event that occurs at amino acid residues 110 and 111 on PrPC, interferes with the conversion of PrPC into the prion disease-associated isoform, PrPSc (abnormal disease-specific conformation of prion protein). This processing is seen as a positive event in terms of disease development. The study of β-cleavage has taken some surprising turns. β-Cleavage is brought about by ROS (reactive oxygen species). The C-terminal fragment produced, C2, may provide the seed for the abnormal conversion process, as it resembles in size the fragments isolated from prion-infected brains. There is, however, strong evidence that β-cleavage provides an essential process to reduce oxidative stress. β-Cleavage may act as a double-edged sword. By β-cleavage, PrPC may try to balance the ROS levels produced during prion infection, but the C2 produced may provide a PrPSc seed that maintains the prion conversion process. © The Authors Journal compilation © 2012 Biochemical Society.


Maduar S.R.,RAS Frumkin Institute of Physical Chemistry and Electrochemistry | Belyaev A.V.,Moscow State University | Lobaskin V.,University College Dublin | Vinogradova O.I.,RWTH Aachen
Physical Review Letters | Year: 2015

We show that an electro-osmotic flow near the slippery hydrophobic surface depends strongly on the mobility of surface charges, which are balanced by counterions of the electrostatic diffuse layer. For a hydrophobic surface with immobile charges, the fluid transport is considerably amplified by the existence of a hydrodynamic slippage. In contrast, near the hydrophobic surface with mobile adsorbed charges, it is also controlled by an additional electric force, which increases the shear stress at the slipping interface. To account for this, we formulate electrohydrodynamic boundary conditions at the slipping interface, which should be applied to quantify electro-osmotic flows instead of hydrodynamic boundary conditions. Our theoretical predictions are fully supported by dissipative particle dynamics simulations with explicit charges. These results lead to a new interpretation of zeta potential of hydrophobic surfaces. © 2015 American Physical Society.


Babaie M.,Technical University of Delft | Staszewski R.B.,Technical University of Delft | Staszewski R.B.,University College Dublin
IEEE Journal of Solid-State Circuits | Year: 2015

In this paper, we propose a new class of operation of an RF oscillator that minimizes its phase noise. The main idea is to enforce a clipped voltage waveform around the LC tank by increasing the second-harmonic of fundamental oscillation voltage through an additional impedance peak, thus giving rise to a class-F2 operation. As a result, the noise contribution of the tail current transistor on the total phase noise can be significantly decreased without sacrificing the oscillator's voltage and current efficiencies. Furthermore, its special impulse sensitivity function (ISF) reduces the phase sensitivity to thermal circuit noise. The prototype of the class-F2 oscillator is implemented in standard TSMC 65 nm CMOS occupying 0.2 mm2. It draws 32-38 mA from 1.3 V supply. Its tuning range is 19% covering 7.2-8.8 GHz. It exhibits phase noise of -139 dBc/Hz at 3 MHz offset from 8.7 GHz carrier, translated to an average figure-of-merit of 191 dBc/Hz with less than 2 dB variation across the tuning range. The long term reliability is also investigated with estimated >10 year lifetime. © 1966-2012 IEEE.


Nolan B.,University College Dublin
Journal of European Social Policy | Year: 2013

The notion of 'social investment' has come to play a major part in debates about the role of social spending and the future of welfare states in Europe. This paper argues that social investment can be seen as a more or less detailed orientation or paradigm for social policies and spending or as a conceptual base and framework for analysis, and that it is also increasingly employed for political or rhetorical as well as academic purposes. It then sets out some serious issues and concerns in that regard, including whether social investment can credibly be presented as the paradigm most likely to underpin economic growth per se or indeed employment-friendly growth, whether the distinction between social 'investment' and other social spending is robust conceptually and the difficulties faced in seeking to make such a distinction empirically, and whether focusing on that distinction and on a narrowly economic rationale is the most useful way to frame the debate about the future of social spending. © The Author(s) 2013.


Long R.,University College Dublin | Dai Y.,Shandong University | Huang B.,Shandong University
Journal of Physical Chemistry Letters | Year: 2013

Electronic structures of C60 fullerenes interfaced with TiO 2(110) surfaces, on several types of hybrid organic/inorganic composites, have been investigated using density functional theory. For the C60/TiO2 surface, a type-II heterojunction can form but it could be inefficient because a small driving force cannot lead to efficient charge separation due to weak donor-acceptor coupling. The charge transfer from C60 to TiO2 can be enhanced by doping; however, a photoexcited electron-hole pair is expected to occur via rapid recombination. Interestingly, charge transfer can take place for both directions across an organic/inorganic interface with either a high or medium value when C 60 is covalently linked to the TiO2 surface with and without hydrogen termination. It is because a hydrogen atom alters the work function of the surface in the former case. In both cases, the strong hybridization between C 2p and Ti 3d leads to energy-level mismatch between organic and inorganic species. These observations indicate that, in a photovoltaic heterojunction based on a fullerene, the interfaces are inefficient due to either a small built-in potential or unfavorable energy band alignment. © 2013 American Chemical Society.


Dudley J.M.,University of Franche Comte | Dias F.,University College Dublin | Erkintalo M.,University of Auckland | Genty G.,Tampere University of Technology
Nature Photonics | Year: 2014

Optical rogue waves are rare, extreme fluctuations in the value of an optical field. The term 'optical rogue wave' was first used in the context of an analogy between pulse propagation in an optical fibre and wave group propagation on deep water, but has since been generalized to describe many other processes in optics. This Review provides an overview of the field, concentrating primarily on propagation in optical fibre systems that exhibit nonlinear breather and soliton dynamics, but also discussing other optical systems in which extreme events have been reported. Although statistical features such as long-tailed probability distributions are often considered to be the defining feature of rogue waves, we emphasize the underlying physical processes that drive the appearance of extreme optical structures. © 2014 Macmillan Publishers Limited. All rights reserved.


Lynch K.,University College Dublin
Ethics in Science and Environmental Politics | Year: 2013

This paper analyses the ranking of universities within the socio-political context of neoliberalism and the organisational context of new managerialism. It examines the forces that have facilitated the emergence of the ranking industry and the ideologies underpinning the so-called 'global' university rankings. What the paper shows is that rankings are a politically inspired mode of governance; they are designed to ensure that universities are regulated and controlled in accordance with market values. The seemingly objective character of rankings, in particular the use of numbers, creates an impression that what is of value in education can be simply counted, hierarchically ordered and uncontrovertibly judged. The simplicity and accessibility of rankings deflects attention from their political and moral purposes. Rankings are reconstituting the academy, for both academics and students; they are a new mode of external governance through which market values are reframing the social relations of education. They have altered the cognitive and moral frames through which university education is being appraised. The paper calls for a debate on the public interest objectives of universities in the context of growing market regulation. © Inter-Research 2013.


Collier M.J.,University College Dublin
Landscape Research | Year: 2013

In some parts of Europe, stone wall field boundaries pervade agricultural landscapes, yet despite their prominence there has been very little research into field boundary walls anywhere. However, these anthropogenic features within cultural landscapes may offer insights into current debates on 'novel' ecosystems because of their artifice, their longevity in the landscape particularly in remote or exposed regions, and their morphology. In a review of the available, published literature in Europe, it was found that no publications exist that examine or illustrate specific ecological characteristics of field boundary stone walls, despite this longevity. Using examples from Ireland, where these structures are locally abundant, this paper aims first to draw attention to the poorly representative literature on this topic, and thus stimulate research that will detail the potential ecological characteristics of these ancient forms of field boundary. It then briefly explores the potential for these walls to be considered as 'novel' ecosystems within current debates on the issue. © 2013 Copyright Taylor and Francis Group, LLC.


Riemer K.,University of Sydney | Johnston R.B.,University College Dublin
European Journal of Information Systems | Year: 2014

The IT artefact, conceived as a bundle of features or properties, is frequently seen as the core object of interest in IS. We argue that this view of IT derives from a worldview that stresses a duality between the individual and the external world. Using a stylized account of an IT implementation project, we show how this worldview conditions the phenomena that show up as most central in the IS discipline and the way mainstream theories and research approaches make sense of these phenomena. Retelling the same story through the lens of Heidegger's analysis of equipment in Being and Time (1927/1962), we present an alternative conception of IT as equipment holistically interwoven with other equipment, user practices, and individual identities. This allows rethinking what are central and peripheral concepts and phenomena in the IS discipline, and outline implications of such a shift for IS theorising, research practice and design. © 2014 Operational Research Society Ltd. All rights reserved.


Scott M.,University College Dublin
Geography Compass | Year: 2013

This paper examines the concept of resilience and its increasing application within rural studies in the face of both economic uncertainty and ecological crisis. Two approaches to resilience are firstly explored: an equilibrium (or bounce-back) approach, based on 'return to normal' assumptions, and an evolutionary (or bounce-forward) approach characterised by an emphasis on adaptive capacity and transformation. While resilience overlaps with the existing literature within rural studies and rural development, the paper argues that resilience thinking opens up new perspectives and provides the potential to 're-frame' rural studies debates, provides a bridging concept. Two key contributions of resilience are identified: Firstly, resilience offers alternative analytical methods and insights for rural studies, particularly when drawing on evolutionary economic geography ideas of path dependencies and path creation, a relational perspective of rural space, and identification of place attributes which may enhance or undermine resilience. Secondly, resilience provides an alternative policy narrative for rural development practice. This includes an emphasis on adaptive networked governance, embedding ecological concerns into rural development practices and a call for blending the local and global in rural development processes. The paper concludes by identifying future research directions for rural resilience. © 2013 The Author(s) Geography Compass © 2013 John Wiley & Sons Ltd.


Healy D.,University College Dublin
British Journal of Criminology | Year: 2014

It is thought that agency plays an important role in the transition from the identity of 'offender' to 'ex-offender'. Yet, despite a growing theoretical literature, little is known about how people use agency in their interactions with the social world to achieve valued goals. This article aims to (1) establish whether agentic action is facilitated by the ability to imagine a credible new self and (2) investigate the situational coping mechanisms that desisters use to overcome barriers to change and achieve meaningful lives. It presents the results of an exploratory study which involved in-depth interviews with a sample of adult men who were in the process of desisting from crime. The results suggested that the ability to imagine a credible future self was associated with agency, coping and well-being. © The Author 2014.


Fair T.,University College Dublin
Reproduction, Fertility and Development | Year: 2010

During the lifespan of the female, biochemical changes occur in the ovarian environment. These changes are brought about by numerous endogenous and exogenous factors, including husbandry practices, production demands and disease, and can have a profound effect on ovarian oocyte quality and subsequent embryo development. Despite many investigations, there is no consensus regarding the time or period of follicular oocyte development that is particularly sensitive to insult. Here, the key molecular and morphological events that occur during oocyte and follicle growth are reviewed, with a specific focus on identifying critical checkpoints in oocyte development. The secondary follicle stage appears to be a key phase in follicular oocyte development because major events such as activation of the oocyte transcriptome, sequestration of the zona pellucida, establishment of bidirectional communication between the granulosa cells and the oocyte and cortical granule synthesis occur during this period of development. Several months later, the periovulatory period is also characterised by the occurrence of critical events, including appropriate degradation or polyadenylation of mRNA transcripts, resumption of meiosis, spindle formation, chromosome alignment and segregation, and so should also be considered as a potential checkpoint of oocyte development. © 2010 IETS.


Murphy B.A.,University College Dublin
Veterinary Journal | Year: 2010

The circadian system provides animals with a means to adapt their internal physiology to the constantly changing environmental stimuli that exist on a rotating planet. Light information is translated into molecular timing mechanisms within pacemaker cells of the mammalian hypothalamic suprachiasmatic nucleus (SCN) via transcriptional-translational feedback loops. Humoral and neural outputs from this 'master' clock result in circadian rhythms of physiology and behaviour. The larger circadian system involves SCN synchronisation of cellular clocks throughout the organism such that individual organs can adapt their specific function to the time of day. In the short history of this scientific field, the vast majority of mammalian chronobiological research has been conducted using small laboratory animals. This review examines what these studies have revealed, discusses how recent chronobiological findings in the horse compare to what is known and highlights how the principles of circadian biology are applicable to equine husbandry and veterinary care. © 2009 Elsevier Ltd.


Irwin J.A.,University College Dublin
Environmental Technology | Year: 2010

Extremophiles can be defined as organisms that can survive in extreme environments that cannot support mammalian life. They include microorganisms that can tolerate temperature extremes, extremes of pH, salinity, hydrostatic pressure and ionizing radiation, as well as low oxygen tension, desiccation and the presence of heavy metals. Psychrophilic organisms also include fish in polar waters and animals that withstand freezing. Rare examples of thermophilic pathogens exist, and the main category of extremophilic animal pathogens comprises psychrophilic and psychrotrophic microorganisms that cause fish diseases, e.g. Flavobacterium psychrophilum, Moritella viscosa, Aliivibrio wodanis and Aliivibrio salmonicida. The most widely known application of an extremophile product in veterinary medicine is DNA polymerase from thermophiles, which is a mainstay of PCR-based diagnostics for an extensive range of animal pathogens. DNA polymerases and other extremophile enzymes are also used in many molecular biology applications and animal genomics. Other extremophile products may find application in veterinary medicine in the future. These include enzymes in biosensors, compatible solutes in skin care products, drug excipients, treatments for respiratory disease, radioprotectants, peptide antibiotics, archaeal lipids for drug delivery and anti-cancer therapeutics. © 2010 Taylor & Francis.


Toner J.,Sports Coach UK | Moran A.,University College Dublin
Journal of Sports Sciences | Year: 2011

Researchers have suggested that skill performance deteriorates when people try to exert conscious control over automatic actions. Unfortunately, little is known about the effects of different types of conscious processing on skilled performance by expert athletes. We conducted two experiments to address this issue. Experiment 1 investigated the influence of a specific form of conscious control (making technical adjustments to a stroke) on the putting skills of expert golfers. The expert golfers maintained putting proficiency (i.e. number of putts holed) when making technical adjustments. However, this form of conscious processing altered the timing and consistency of golfers' putting strokes. Experiment 2 compared the influence of technical adjustments and conscious monitoring (paying attention to the execution of the stroke) on expert golfers' putting skills. Technical adjustments had no disruptive influence on expert golfers' putting proficiency but did reduce the consistency of their strokes. However, conscious monitoring was found to impair putting proficiency. The implications of the work for theory and future work are discussed. © 2011 Taylor & Francis.


Hanson J.R.,Dr Mackinnon Memorial Hospital | Carlin B.,University College Dublin
British Journal of Sports Medicine | Year: 2012

The prehospital management of serious injury is a key skill required of pitch-side medical staff. Previously, specific training in sports prehospital-immediate care was lacking or not of a comparable standard to other aspects of emergency care. Many principles have been drawn from general prehospital care or in-hospital training courses. This article discusses sports prehospitalimmediate care as a niche of general prehospital care, using spinal injury management as an illustration of the major differences. It highlights the need to develop the sport-specific prehospital evidence base, rather than relying exclusively on considerations relevant to prolonged immobilisation of multiply injured casualties from motor vehicle accidents, falls from height or burns.


Rice J.H.,University College Dublin
Nanoscale | Year: 2010

This review outlines progress in atomic force infrared microscopy, reviewing the methodology and its application in nanoscale infrared absorption imaging of both biological and functional materials, including an outline of where this emerging method has been applied to image cellular systems in aqueous environments. © 2010 The Royal Society of Chemistry.


Dias F.,University College Dublin
Journal of Fluid Mechanics | Year: 2014

Ship wakes are fascinating. They can be observed by the human eye and appear to have a V shape when the ship is advancing at constant speed along a straight trajectory. Under idealized conditions, Kelvin found that the angle between the two branches of the V is ∼39°. However, in a number of cases, this angle appears to be smaller. This phenomenon has been studied by various authors, and several explanations have been suggested. The most elegant one, which is based on the amplitude of the ship waves rather than their phase, has recently been revisited by Darmon, Benzaquen & Raphaël (J. Fluid Mech., vol. 738, 2014, R3). © 2014 Cambridge University Press.


Murphy C.D.,University College Dublin
Applied Microbiology and Biotechnology | Year: 2016

Since the discovery over 60 years ago of fluorocortisone’s biological properties (9-α-Fluoro derivatives of cortisone and hydrocortisone; Fried J and Sabo EF, J Am Chem Soc 76: 1455–1456, 1954), the number of fluorinated drugs has steadily increased. With the improvement in synthetic methodologies, this trend is likely to continue and will lead to the introduction of new fluorinated substituents into pharmaceutical compounds. Although the biotransformation of organofluorine compounds by microorganisms has been well studied, specific investigations on fluorinated drugs are relatively few, despite the increase in the number and variety of fluorinated drugs that are available. The strength of the carbon-fluorine bond conveys stability to fluorinated drugs; thus, they are likely to be recalcitrant in the environment or may be partially metabolized to a more toxic metabolite. This review examines the research done on microbial biotransformation and biodegradation of fluorinated drugs and highlights the importance of understanding how microorganisms interact with this class of compound from environmental, clinical and biotechnological perspectives. © 2016 Springer-Verlag Berlin Heidelberg


Kirby R.,Prostate Center | Fitzpatrick J.M.,University College Dublin
BJU International | Year: 2012

What's known on the subject? and What does the study add? Due to the fear of missing clinically significant cancer, it is often uncertain whether a repeat biopsy should be performed in men with ≥1 prior negative prostate biopsies but persistent suspicion of prostate cancer. However, the repeat biopsy may again be negative and a biopsy may be associated with anxiety, discomfort and complications (resulting in hospitalisation in 4.1% of men). This review discusses strategies to optimise repeat biopsy procedures in order to better predict the biopsy outcome. Optimising repeat biopsy procedures include adjusting the location and number of cores and the use of MRI to detect suspicious areas. The use of diagnostic markers, e.g. (Prostate CAncer) gene 3, which is predictive of biopsy outcome, can aid in guiding repeat biopsy decisions and reduce the number of unnecessary and uncomfortable biopsies. To review strategies to optimise repeat biopsy procedures and to better predict the biopsy outcome. As it is often uncertain whether a repeat biopsy should be performed in men with ≥1 previous negative prostate biopsies but persistent suspicion of prostate cancer. The repeat biopsy may also be negative and a biopsy may be associated with anxiety, discomfort and occasionally (severe) complications. A search in PubMed was performed to find English language original and review articles related to repeat prostate biopsies. Strategies to optimise repeat biopsy procedures include applying the appropriate indications and adjusting the location and number of biopsy cores. The PROGENSA™ Prostate CAncer gene 3 (PCA3) Assay is a highly prostate cancer-specific test. A higher PCA3 Score corresponds with an increased probability of a positive repeat biopsy and including the PCA3 Score in multivariate models significantly increased their predictive accuracy for predicting repeat biopsy outcome. The PCA3 Score seems also to be predictive of future biopsy outcome. In clinical practice it is often uncertain whether a prostate biopsy should be repeated or not. Optimising repeat biopsy procedures and the use of diagnostic markers, such as PCA3, can increase the probability of a positive repeat biopsy and reduce the number of unnecessary and uncomfortable biopsies © 2011 BJU INTERNATIONAL.


Largely a disease of older men, prostate cancer is likely to become a growing burden in the developed world as the population ages and overall life expectancy increases. Furthermore, prostate cancer management in older men is not optimal, reflecting the lack of training dedicated to senior adults in fellowship programs and the lack of specific guidelines to manage senior adults. The International Society of Geriatric Oncology (SIOG) convened a multidisciplinary Prostate Cancer Working Group to review the evidence base and provide advice on the management of the disease in senior age groups. The Working Group reported that advancing age, by itself, is not a reliable guide to treatment decision making for men with either localized or advanced prostate cancer. Instead, the SIOG guidelines advise health care teams to assess the patient's underlying health status, which is largely dictated by associated comorbid conditions, but also by dependency in activities of daily living and nutritional status, and to use the findings to categorize the individual into one of four groups: healthy, vulnerable, frail, or terminally ill. The guidelines recommend that a patient categorized as healthy or vulnerable (i.e., with reversible problems following geriatric intervention) should receive the same approach to treatment as a younger patient. Frail patients should be managed using adapted treatment strategies, and the terminally ill should receive symptomatic/palliative care only. The guidelines may have ongoing relevance as the treatment options for prostate cancer expand.


A 2 × 2 factorial experiment was conducted to investigate the interactions between laminarin (LAM; 0 and 300 parts per million (ppm)) and fucoidan (FUC; 0 and 240 ppm) levels on intestinal morphology, selected microbiota and inflammatory cytokine gene expression in the weaned pig. There was an interaction between LAM and FUC supplementation on the Enterobacteriaceae population (P< 0·05) and the abundance of attaching and effacing Escherichia coli (AEEC) strains (P< 0·05) in the colon. Pigs offered the FUC diet had a reduced Enterobacteriaceae population compared with pigs offered the basal diet. However, the effect of FUC on the Enterobacteriaceae population was not observed when combined with LAM. Pigs offered the LAM diet had reduced abundance of AEEC strains compared with pigs offered the basal diet. However, there was no effect of LAM on the abundance of AEEC strains when combined with FUC. There was an interaction between LAM and FUC supplementation on villous height (P< 0·01) and the villous height:crypt depth ratio (P< 0·01) in the duodenum. Pigs offered the LAM or FUC diet had an increased villous height and villous height:crypt depth ratio compared with pigs offered the basal diet. However, there was no effect of the LAM and FUC combination diet on intestinal morphology. Pigs offered the LAM-supplemented diets had a lower IL-6 (P< 0·05), IL-17A (P< 0·01) and IL-1β (P< 0·01) mRNA expression in the colon compared with pigs offered the diets without LAM. In conclusion, supplementation with either LAM or FUC alone modified intestinal morphology and selected intestinal microbiota, but these effects were lost when offered in combination.


Balado F.,University College Dublin
ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings | Year: 2010

This paper firstly gives a brief overview of information embedding in deoxyribonucleic acid (DNA) sequences and its applications. DNA data embedding can be considered as a particular case of communications with or without side information, depending on the use of coding or noncoding DNA sequences, respectively. Although several DNA data embedding methods have been proposed over the last decade, it is still an open question to determine the maximum amount of information that can theoretically be embedded - that is, its Shannon capacity. This is the main question tackled in this paper. ©2010 IEEE.


English N.J.,University College Dublin | Tse J.S.,University of Saskatchewan
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

The relationship between structure, thermal conductivity, and phonon propagation in low-, high- and very-high-density amorphous ices (LDA, HDA, and VHDA) at 30-180 K and over the pressure range from 0.1 to 1.1 GPa has been investigated with equilibrium molecular dynamics simulations employing the Green-Kubo approach and the TIP4P-ice potential model. HDA and VHDA were shown to have weak, amorphouslike temperature dependence, while a more crystal-like temperature dependence of LDA was predicted. The weak temperature effect on the thermal conductivity in HDA and VHDA is attributed to strong hybridization of acoustic and optic modes. The calculated dynamical structure factors confirm the observed phononlike collective excitations sustained to high frequencies and momentum transfer for all of the amorphous ices. This behavior differs fundamentally from liquid and rapidly quenched water. Apart from having structural similarity to crystalline ice, LDA was found to have a negative average Grüneisen parameter with acousticlike phonons softening under compression. This observation is consistent with the suggested negative Bridgman parameter, where the thermal conductivity decreases with increasing pressure. The existence of phonon instability and intermediate ordering in amorphous ices indicates that the conversion of LDA to HDA is due to mechanical instabilities of the ice lattice. However, care should be taken when extrapolating the conclusions to liquid water owing to limitations in the potential model. © 2011 American Physical Society.


O'Brien P.J.,University College Dublin | O'Brien P.J.,Park West Enterprise Center
Basic and Clinical Pharmacology and Toxicology | Year: 2014

High-content analysis (HCA) of in vitro biochemical and morphological effects of classic (small molecule) drugs and chemicals is concordant with potential for human toxicity. For hepatotoxicity, concordance is greater for cytotoxic effects assessed by HCA than for conventional cytotoxicity tests and for regulatory animal toxicity studies. Additionally, HCA identifies chronic toxicity potential, and drugs producing idiosyncratic adverse reactions and/or toxic metabolites are also identified by HCA. Mechanistic information on the subcellular basis for the toxicity is frequently identified, including various mitochondrial effects, oxidative stress, calcium dyshomeostasis, phospholipidosis, apoptosis and antiproliferative effects, and a fingerprinting of the sequence and pattern of subcellular events. As these effects are frequently non-specific and affect many cell types, some toxicities may be detected and monitored by HCA of peripheral blood cells, such as for anticancer and anti-infective drugs. Critical methodological and interpretive features are identified that are critical to the effectiveness of the HCA cytotoxicity assessment, including the need for multiple days of exposure of cells to drug, use of a human hepatocyte cell line with metabolic competence, assessment of multiple pre-lethal effects in individual live cells, consideration of hormesis, the need for interpretation of relevance of cytotoxicity concentration compared to efficacy concentration and quality management. Limitations of the HCA include assessment of drugs that act on receptors, transporters or processes not found in hepatocytes. HCA may be used in a) screening lead candidates for potential human toxicity in drug discovery alongside of in vitro assessment of efficacy and pharmacokinetics, b) elucidating mechanisms of toxicity and c) monitoring in vivo toxicity of drugs with known toxicity of known mechanism. © 2014 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).


Parnell A.C.,University College Dublin | Buck C.E.,University of Sheffield | Doan T.K.,Trinity College Dublin
Quaternary Science Reviews | Year: 2011

In this paper we explain the background, workings, and results obtained from three recently developed statistical age-depth models implemented in freely available, general purpose software packages (Bpeat, OxCal and Bchron). These models aim to reconstruct the sedimentation rate in a single core (typically lake, peat or ocean) given a limited number of scientific date estimates (usually radiocarbon) and fixed depths. Most importantly, they provide a suitably qualified estimate of the uncertainty in the age-depth chronology and thus can be used in a variety of applications. We perform a large data-driven study of the three models and discuss their general utility in chronology construction for palaeoenvironmental research. © 2011 Elsevier Ltd.


Murphy E.,University College Dublin | Killen J.E.,Trinity College Dublin
Urban Studies | Year: 2011

This paper revisits the notion of random commuting within the excess commuting framework. In doing so, it argues that the average random commute, is a more appropriate basis for measuring the efficiency of urban commuting patterns. Using this as a base, the paper introduces two new measures of commuting efficiency based on measuring the collective commuting economy of individuals for the journey to work: commuting economy and normalised commuting economy. It is argued that because the average random comute has an intrinsically behavioural interpretation, the measures introduced yield more explicit explanations of the overall nature of travel behaviour within the constraints set by land use geography and the spatial distribution of the transport network. The framework is applied for two different years, 1991 and 2001, and for different modes of transport. The results show that the average actual commute has moved further away from the average random comute, implying that greater intermixing of residential and employment functions has led to more efficient commuting behaviour. © 2010 Urban Studies Journal Limited.


Ochoa L.F.,University of Manchester | Keane A.,University College Dublin | Harrison G.P.,University of Edinburgh
IEEE Transactions on Power Systems | Year: 2011

Renewable distributed generation (DG), primarily wind power, will represent the lion's share of the new generation capacity that will be connected to distribution systems. However, while both firm and variable generation present our traditionally passive distribution networks with well-established technical challenges, the requirements and practices related to the power factor operation of these generation plants might lead to undesirable effects at the transmission level with the reactive power support needed by high penetrations of DG capacity potentially impacting on weak areas of the transmission grid. In this work, this problem is formulated as the minimization of the reactive support for DG and is investigated using two different operational perspectives: adopting passive but enhanced power factor and substation settings, and implementing Smart Grid control schemes. These two approaches are modeled using a tailored multi-period AC optimal power flow technique that caters for the variability of demand and generation, and considers N-1 contingencies. The results demonstrate that the enhanced passive approach is able to achieve a performance almost as good as Smart Grid control without the need for any additional investment. © 2006 IEEE.


Ippolito M.,Consorzio Interuniversitario Per Le Applicazioni Of Supercalcolo Per University cerca | Meloni S.,University College Dublin
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

By means of molecular dynamics simulations based on the Billeter environment-dependent classical force field we studied the structural features of SiN x samples at various stoichiometries. Our results are in good agreement with experimental data and are able to reproduce some features which so far were not reproduced by simulations. In particular, we identified units containing N-N bonds, which are thought to be responsible for an unassigned peak in the radial distribution function obtained from neutron diffraction data and signals observed in electron spin resonance, x-ray photoemission spectroscopy, electron-energy-loss spectroscopy, and optical absorption experiments. We have identified defects which are thought to be responsible for the high concentration of charge traps that makes this material suitable for building nonvolatile memory devices. We analyzed the dependency of the concentration of these defects with the stoichiometry of the sample. © 2011 American Physical Society.


Sartor A.O.,Tulane University | Fitzpatrick J.M.,University College Dublin
BJU International | Year: 2012

What's known on the subject? and What does the study add? The interplay between urologists and oncologists in the treatment of prostate cancer has been long standing. Recent paradigm shifts in treatment are reviewed with an emphasis on how these treatments may eventually alter the dynamic equilibrium between urology and oncology specialists. The treatment landscape for men with castration-resistant prostate cancer (CRPC) is undergoing significant changes; a redefinition of the respective roles of oncologists and urologists will probably occur. In addition, the advent of the multidisciplinary team or coordinated-care approach, which has been gathering momentum over the last decade, will become not simply a preference but a clear necessity. In the present review, we explore the current wave of new treatments and describe the possibility of more complex approaches to combined therapy. New treatment options include abiraterone acetate, cabazitaxel, MDV3100 (in development), radium-223 (in development) and sipuleucel-T. We also present the traditional roles of the urologist and oncologist in caring for patients with CRPC and discuss how these may change. Compounding the new potential for treatment success, as well as the complexity of therapeutic strategies, is the emergence of novel biomarkers to evaluate treatment efficacy and to assist in patient prognosis. The prospects for successful treatment of patients with CRPC have developed considerably so that these patients may soon have a reasonable expectation of therapeutic efficacy and meaningful extension of their lives. © 2012 BJU INTERNATIONAL.


Mehta J.P.,University College Dublin
Methods in Molecular Biology | Year: 2014

Small RNAs are important transcriptional regulators within cells. With the advent of powerful Next Generation Sequencing platforms, sequencing small RNAs seems to be an obvious choice to understand their expression and its downstream effect. Additionally, sequencing provides an opportunity to identify novel and polymorphic miRNA. However, the biggest challenge is the appropriate data analysis pipeline, which is still in phase of active development by various academic groups. This chapter describes basic and advanced steps for small RNA sequencing analysis including quality control, small RNA alignment and quantification, differential expression analysis, novel small RNA identification, target prediction, and downstream analysis. We also provide a list of various resources for small RNA analysis. © Springer Science+Business Media New York 2014.


Albrecht M.,University College Dublin
Chemical Reviews | Year: 2010

A study was conducted some of the fundamental aspects and the latest trends in the field of cyclometalation using d-block transition metals. It was revealed that cyclometalation had emerged as one of the most popular organometallic reactions, providing a simple entry to organometallic compounds. It allowed for the investigation of the essential aspects governing the metal-mediated activation of unreactive bonds, such as the C-H bond. The study covered seminal fundamental literature and the latest highlights and the trends that emerged till early 2009. Cyclometalation gained significance due to the reaction representing the mildest route for achieving strong C-H and C-R bonds. It had also emerged as an attractive and versatile synthetic method for creating organometallic entities with significantly wide application potential.


Higgins M.,University College Dublin
Current Diabetes Reviews | Year: 2010

Diabetes mellitus complicates 1-2% of all pregnancies but is associated with high a perinatal morbidity and mortality. Gestational diabetes affects up to 4% of pregnancies and is associated with foetal macrosomia (large for dates). Foetal growth is a complex process influenced by genetics, maternal factors, uterine environment and maternal and foetal hormonal status. Infants of pregestational diabetic mothers have an additional influence of maternal fluctuations in glycaemia. The purpose of this paper is to review maternal and foetal growth factors, including insulin, in the aetiology of macrosomia in diabetic pregnancy. Placental Growth Hormone is the major growth hormone secreted during human pregnancy. Leptin may have a role in satiety. Resistin was originally proposed as the link between obesity and diabetes but is now thought to have a more complex role. These hormones and their actions on human foetal growth are reviewed in depth with particular reference to both pre-gestational (type 1 and type 2 diabetes) and gestational diabetes. Previously, increased foetal weight in infants of diabetic mothers was thought to be as a result of maternal hyperglycaemia. It is now evident that the control of foetal growth, in normal as well as diabetic pregnancies, is far more complex than previously understood. © 2010 Bentham Science Publishers Ltd.


Smolenski A.,University College Dublin
Journal of Thrombosis and Haemostasis | Year: 2012

Endothelial prostacyclin and nitric oxide potently inhibit platelet functions. Prostacyclin and nitric oxide actions are mediated by platelet adenylyl and guanylyl cyclases, which synthesize cyclic AMP (cAMP) and cyclic GMP (cGMP), respectively. Cyclic nucleotides stimulate cAMP-dependent protein kinase (protein kinase A [PKA]I and PKAII) and cGMP-dependent protein kinase (protein kinase G [PKG]I) to phosphorylate a broad panel of substrate proteins. Substrate phosphorylation results in the inactivation of small G-proteins of the Ras and Rho families, inhibition of the release of Ca 2+ from intracellular stores, and modulation of actin cytoskeleton dynamics. Thus, PKA/PKG substrates translate prostacyclin and nitric oxide signals into a block of platelet adhesion, granule release, and aggregation. cAMP and cGMP are degraded by phosphodiesterases, which might restrict signaling to specific subcellular compartments. An emerging principle of cyclic nucleotide signaling in platelets is the high degree of interconnection between activating and cAMP/cGMP-dependent inhibitory signaling pathways at all levels, including cAMP/cGMP synthesis and breakdown, and PKA/PKG-mediated substrate phosphorylation. Furthermore, defects in cAMP/cGMP pathways might contribute to platelet hyperreactivity in cardiovascular disease. This article focuses on recent insights into the regulation of the cAMP/cGMP signaling network and on new targets of PKA and PKG in platelets. © 2011 International Society on Thrombosis and Haemostasis.


Play, laughter and theatrical forms of activism have been recently documented by scholars interested in the politics and spatiality of resistance. This article focuses on the playful techniques of resistance deployed by street vendors and artisans in Mexico City as a result of the displacement generated by a recently implemented policy popularly called Plazas Limpias (clean plazas). Through a case study Coyoacan, a tourist-oriented neighbourhood known for its historical richness and aestheti