2022-01-23T14:51:14Z
http://ulir.ul.ie/oai/request
oai:ulir.ul.ie:10344/349
2017-01-26T14:57:31Z
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Transport in randomly-fluctuating spatially-periodic potentials
Gleeson, James P.
SFI
random transport
colored noise
peer-reviewed
The motion of overdamped particles in a one-dimensional spatially-periodic potential is considered. The potential is also randomly-fluctuating in time, due to multiplicative colored noise terms, and has a deterministic tilt. Numerical simulations show two distinct parameter regimes, corresponding to free-running near-deterministic particles, and particles which are trapped in local minima of the potential with intermittent escape flights. Perturbation and asymptotic methods are developed to understand the drift velocity and diffusion coefficient in each parameter regime.
Science Foundation Ireland: 06/IN.1/366 and 05/RFP/MAT0016.
2010-01-08T11:01:33Z
2010-01-08T11:01:33Z
2009
Journal Article
all_ul_research
ul_published_reviewed
none
Gleeson, J.P. (2009) 'Transport in randomly-fluctuating spatially-periodic potentials' Physica A, 388 (4), pp 277-287
http://hdl.handle.net/10344/349
10.1016/j.physa.2008.10.013
eng
Physica A;388/4
http://dx.doi.org/10.1016/j.physa.2008.10.013
05/RFP/MAT0016
oai:ulir.ul.ie:10344/350
2015-04-30T14:31:10Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_73
hdl_10344_20
Diffusion coefficient in periodic and random potentials
Khoury, Maria
Gleeson, James P.
Sancho, J. M.
Lacasta, A. M.
Lindenberg, Katja
SFI
perturbation theory
surface diffusion
peer-reviewed
Transport and diffusion of particles on modulated surfaces is a nonequilibrium problem which is receiving a great deal of attention due to its technological applications, but analytical calculations are scarce. In earlier work, we developed a perturbative approach to begin to provide an analytic platform for predictions about particle trajectories over such surfaces. In some temperature and forcing regimes, we successfully reproduced results for average particle velocities obtained from numerical simulations. In this paper, we extend the perturbation theory to the calculation of higher moments, in particular the diffusion tensor and the skewness. Numerical simulations are used to check the domain of validity of the perturbative approach.
2010-01-08T11:02:48Z
2010-01-08T11:02:48Z
2009
Journal Article
all_ul_research
ul_published_reviewed
none
Khoury, M., Gleeson, J.P., Sancho1, J. M., Lacasta, A. M. and Lindenberg, K. (2009) 'Diffusion coefficient in periodic and random potentials', Physical Review E 80, 021123
http://hdl.handle.net/10344/350
en_US
Physical Review E;80 Art No. 021123
http://dx.doi.org/10.1103/PhysRevE.80.021123
06/IN.1/I366
MACSI
American Physical Society
oai:ulir.ul.ie:10344/347
2015-05-18T11:02:42Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_73
hdl_10344_20
Bond percolation on a class of clustered random networks
Gleeson, James P.
networks
percolation
peer-reviewed
Analytical results are derived for the bond percolation threshold and the size of the giant connected component in a class of random networks with nonzero clustering. The network's degree distribution and clustering spectrum may be prescribed and theoretical results match well with numerical simulations on both synthetic and real-world networks.
Science Foundation Ireland: 06/IN.1/I366 and MACSI 06/MI/005
2010-01-08T11:00:22Z
2010-01-08T11:00:22Z
2009
Journal Article
all_ul_research
ul_published_reviewed
none
Gleeson, J.P. (2009) 'Bond percolation on a class of clustered random networks', Phys. Rev. E 80, 036107 (2009)
http://hdl.handle.net/10344/347
en_US
Physical Review E;80 Art No. 036107
http://dx.doi.org/10.1103/PhysRevE.80.036107
American Physical Society
oai:ulir.ul.ie:10344/348
2020-12-02T12:55:22Z
hdl_10344_10
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Analytical results for bond percolation and k-core sizes on clustered networks
Gleeson, James P.
Melnik, Sergey
network theory
percolation
peer-reviewed
An analytical approach to calculating bond percolation thresholds, sizes of k-cores, and sizes of giant connected components on structured random networks with nonzero clustering is presented. The networks are generated using a generalization of Trapman's [P. Trapman, Theor. Popul. Biol. 71, 160 (2007)] model of cliques embedded in treelike random graphs. The resulting networks have arbitrary degree distributions and tunable degree-dependent clustering. The effect of clustering on the bond percolation thresholds for networks of this type is examined and contrasted with some recent results in the literature. For very high levels of clustering the percolation threshold in these generalized Trapman networks is increased above the value it takes in a randomly wired (unclustered) network of the same degree distribution. In assortative scale-free networks, where the variance of the degree distribution is infinite, this clustering effect can lead to a nonzero percolation (epidemic) threshold.
SFI
2010-01-08T11:01:20Z
2010-01-08T11:01:20Z
2009
Journal Article
all_ul_research
ul_published_reviewed
none
Gleeson, J.P. and (Melnik, S. 2009) 'Analytical results for bond percolation and k-core sizes on clustered networks' Phys. Rev. E 80, 046121
http://hdl.handle.net/10344/348
10.1103/PhysRevE.80.046121
http://dx.doi.org/10.1103/PhysRevE.80.046121
Physical Review E;80 Art No. 046121
05/RFP/MAT0016
06/IN.1/I366
MACSI
05/RFP/MAT0016
American Physical Society
oai:ulir.ul.ie:10344/1645
2014-09-12T00:29:28Z
hdl_10344_10
hdl_10344_9
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High frequency elastic wave inversion
Ryan, Niall C
Nolan, Clifford J.
IRCSET
high frequency
elastic wave conversion
peer-reviewed
This thesis is concerned with the problem of high frequency elastic wave inversion. This is the problem of determining sharp, localised changes in the properties of materials beneath the surface of the earth using only measurements of reflected seismic waves taken at or near the surface.
The central objective of this thesis is to construct multiparameter inversion operators
which map data from surface wave measurements into accurate estimates for the high frequency perturbations in the density, ρ, and in the 21 independent Hooke’s tensor components, cijkl, of subsurface anisotropic inclusions. Using results from the field of microlocal analysis of Fourier Integral Operators, it is shown that asymptotically valid inversion operators exist which can invert all 22 independent elastic parameter perturbations directly, without relying on statistical estimates. To gather the required data, the technique of using ensembles of linked seismic experiments
is introduced and extensively analysed in the context of a standard linearised
single scattering model for elastic waves based on the Born approximation. This technique builds on work by Burridge and others in [10:Burridge R. ; De Hoop M. V. ; Miller D. ; Spencer C. ; 1998], and by Nolan in [17:Clifford J. Nolan 1997][49:Nolan and Ryan 2007]. In addition, a fundamental theoretical analysis of the seismic inversion problem is carried out. By analysing important components of the seismic forward problem, a theoretical
framework is introduced which allows the determination of whether or not multiparameter inversion is possible, and specifically with what types of seismic ensembles and elastic wave modes. In particular, this framework will show under which circumstances multiparameter
inversion is not possible, both for the case of point anisotropic inclusions, and in
particular for larger volume inclusions. It is shown that these results can be extended to inversion in multiple type of seismic backgrounds. To complement the theoretical results, an application of evolutionary algorithm is presented which is used to find practical invertible seismic ensembles which allow inversion to be carried out feasibly.
The thesis also presents a introductory overview of the techniques of Fourier Integral Operators and microlocal analysis, which are used to construct later inversion models. Other more elaborate mathematical techniques used in the thesis are also introduced or expanded on in the appendices for the benefit of the general reader.
Finally, supporting lemmas in the appendices introduce a new method for determining
the component dependencies of linear elastic materials.
2011-12-02T12:55:41Z
2011-12-02T12:55:41Z
2010
Doctoral thesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
none
http://hdl.handle.net/10344/1645
eng
University of Limerick
oai:ulir.ul.ie:10344/1686
2014-09-12T00:33:27Z
hdl_10344_10
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Promoting student interest in mathematics : a framework for effective teaching of algebra at junior cycle
Prendergast, Mark
O'Donoghue, John
junior cycle
algebra
teaching
peer-reviewed
In 2010, figures show that only 45 per cent of Irish students took Higher Level
mathematics for the Junior Certificate examination and only 16 per cent took Higher
Level mathematics for the Leaving Certificate examination www.examinations.ie).
Research suggests that there are two major reasons for such low numbers, namely;
ineffective teaching (NCCA, 2006) and a subsequent lack of student interest in the
subject (PISA, 2003). Traditional styles of teaching make it difficult for students to
take an interest in a confusing topic in which they can see no immediate relevance
(MacGregor, 2004). This is particularly true regarding the topic of algebra and its
teaching in school (Herscovics and Linchevski, 1994). Taking steps to enhance
student interest in the mathematics classroom is one of the most direct ways to
approach the problem of ineffective mathematics teaching (Mitchell, 1993).
This thesis describes a pedagogical framework designed by the author for the
purpose of promoting student interest in mathematics through effective teaching
using the topic of algebra as an exemplar. The framework identifies and integrates
three theoretical perspectives, one for each of the main issues highlighted in italic.
These theoretical perspectives include pedagogical principles, a model for
conceptualising algebraic activity and a model for interest development. Once the
design of the framework is complete it is field-tested through the development,
implementation and evaluation of a teaching intervention. This intervention takes the
form of an algebra revision package for 1st year (12 -14 year old) students. It was
implemented in five Irish Second level schools between September 2009 and June
2010. Its evaluation reached a successful conclusion showing that an appropriately
designed pedagogical framework supported theoretically can bring about positive
changes in student attitude.
2011-12-09T12:16:14Z
2011-12-09T12:16:14Z
2011
Doctoral thesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
none
http://hdl.handle.net/10344/1686
eng
University of Limerick
oai:ulir.ul.ie:10344/1689
2021-02-24T15:58:24Z
hdl_10344_10
hdl_10344_9
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hdl_10344_20
hdl_10344_505
hdl_10344_244
Pricing models for collateralized debt obligations
Hurley, Julie
Gleeson, James P.
debt obligations
mathematical
peer-reviewed
One of the most controversial and innovative finnancial products in recent years has been collateralised debt obligations (CDOs). Much of the blame for the current credit crisis is being attributed to the mathematical
models and quantitative methods associated with these credit derivatives.
In recent years, there has been rapidly growing research on credit derivatives
and correlated defaults and in this thesis we examine the possible replacement of current copula based approaches with intuitive contagion models for percolation on nite networks. We propose that modelling the probability of default in a correlated portfolio is similar to modelling the
probability of default of contagion spreading in a network.
In the rst part of our thesis we review current models from the literature
that have been suggested to price CDOs. From the literature review we noted that the critical input in the pricing of a CDO is an estimate of the default dependence (default correlation) between the underlying names
in a portfolio. Dependency modelling with copula functions, introduced by Li (2000), has become a market standard in the pricing of CDOs. We compute the default distribution for both the Gaussian and student t4
copulas by implementing both a Monte Carlo and theoretical approach.
We then compare these copulas ability to t market data.
In the second part of our thesis we begin by introducing some of the earliest network models proposed by Paul Erd}os and Alfr ed R enyi. We show how similar to component sizes on a network being related to contagion
on a network, it is possible then to compute the probability of default for a portfolio of names using network percolation. We present the nite and in nite network models used to model the default dependency between
names in a portfolio and thus extend the in nite network model to compute the probability of default for a CDO portfolio. We nally compare the percolation model, Gaussian and Student t4 copulas to market
data and from our results determine that the percolation model provides a better t to market data than the Gaussian and Student t4 copulas.
2011-12-09T13:33:37Z
2011-12-09T13:33:37Z
2011
info:eu-repo/semantics/masterThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
none
http://hdl.handle.net/10344/1689
eng
University of Limerick
oai:ulir.ul.ie:10344/1959
2012-10-05T09:12:27Z
hdl_10344_10
hdl_10344_9
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hdl_10344_243
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Bubble formation in selected industrial problems
Devereux, Michael
Lee, William T.
bubble nucleation
industry
peer-reviewed
Foam and bubbles are ubiquitous in industry and nature. They have a wide range of applications but are also an undesirable product of certain processes. This thesis considers two individual industrial problems with the common phenomenon of bubble and foam formation.
Bubble nucleation is a phenomenon observed in many different physical situations from decompression sickness to champagne effervescence. It is of vital importance to the formation of a creamy head that is
distinctive to stout beers. I present experimental work that demonstrates
that cellulose fibres can be used to initiate stout beers and could serve
as an alternative to widget technology. I derive mathematical models for
the various gas pocket geometries I observed in cellulose fibres that produce
bubbles when submerged in stout beer. These models are solved and compared to experimental results where possible to give the first quantitative evaluation of the current models of bubble nucleation.
I present the work done to model a novel design for accurate volume measurement of milk. The new design proposes a modification of the air elimination vessel used in current milk pumping systems to increase
accuracy by preventing air bubbles being pumped with milk. We consider the operation of the entire system to pump milk, the flow of milk inside the air elimination vessel, the entrainment of air bubbles into a pool of
milk and the drainage of foam.
2012-02-10T13:38:04Z
2012-02-10T13:38:04Z
2011
Doctoral thesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
none
http://hdl.handle.net/10344/1959
eng
University of Limerick
oai:ulir.ul.ie:10344/1965
2012-02-14T10:44:55Z
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Resonant over-reflection of waves by jets.
Lapin, Vladimir Nikolaevich
Benilov, Eugene
linear equations
resonant over-reflection
waves
peer-reviewed
The present thesis studies the problem of scattering of large-scale waves by surface currents in the ocean. It has been known for more than a century that corresponding linear
equations governing propagation of small amplitude waves across the shear flow contain
critical layer singularities (Rayleigh [74]). And more than 40 years ago it was established that propagating waves can effectively interact with the mean flow at such points. As the result, the waves can be partly absorbed (Booker & Bretherton [8]) or over-reflected (i.e. amplified) (Jones [40]). A special case of this phenomenon, when amplification is infinitely strong, is traditionally referred to as resonant over-reflection. Physically the latter corresponds
to spontaneous emission of waves by the current. Resonant over-reflection was
poorly studied in the past with only a few cases reported in the literature. The aim of
this study is to fill this gap and clarify the nature of the phenomenon.
We examine scattering of inertia-gravity gravity waves by zonal currents within the
reduced gravity rotating shallow water model and Rossby-wave scattering by “two-jet”
currents on the quasi-geostrophic β-plane. In both cases reflection and transmission coefficients were calculated numerically for the case when mean flow velocity profiles are
approximated by Bickley jets.
Resonant over-reflection was found to occur within these two models. We proposed a
plausible physical interpretation of the phenomenon as a “resonance” of a wave trapped
between two containing potential barriers. It is further demonstrated that, generally,
resonantly over-reflected waves are always marginal to radiating instabilities, and hence, indicate when unstable shear flows can generate temporally growing propagating waves that carry energy into the far field. The importance of the obtained results is connected to investigation of sources and distribution of waves in the ocean and atmosphere.
SFI grant 08/RFP/MTH1476
MACSI
2012-02-13T12:09:08Z
2012-02-13T12:09:08Z
2011
Doctoral thesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
none
http://hdl.handle.net/10344/1965
eng
University of Limerick
oai:ulir.ul.ie:10344/1979
2012-02-15T10:49:49Z
hdl_10344_10
hdl_10344_9
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Diapiric ascent : asymptotics and numerics of slow flow with strongly temperature-dependent viscosity.
O'Brien, Michael Anthony
Vynnycky, Michael
geophysics
magma
Earth's crust
peer-reviewed
In the field of geophysics, it has long been accepted that the bodies of igneous rock, known as intrusions, that are often found at shallow levels of the Earth’s continental crust are a result of the solidification of granitic magma that was generated in the deep lithosphere. This raises the question
of how the magma is transported a distance of tens of kilometres through the lithosphere before being emplaced. One possibility is that large volumes of hot buoyant magma - or diapirs - are transported en masse from their point of origin to the shallow crust. In this thesis we
investigate, through mathematical modelling, the viability of magmatic diapirism as an ascent mechanism. Whilst the problem has been tackled by earlier authors, a literature review indicates a litany of algebraic errors and unwarranted assumptions in earlier work, which requires us to begin
from scratch. A moving boundary problem for an ascending diapir, modelled as a hot, buoyant sphere rising through a lithosphere that behaves as a thermoviscous, power-law fluid, is formulated. Numerically, this turns
out to be very difficult to solve, and an alternative asymptotics-based approach
is adopted. This centres on the non-isothermal, thermoviscous, analogue of the Hadamard-Rybczinski problem for a light and relatively inviscid fluid rising in a denser, more viscous fluid, and is governed by two dimensionless parameters: the P´eclet number, Pe, and a viscosity variation
parameter, ǫ. Significant analytical progress is found to be possible in
four asymptotic regimes; furthermore, it is possible to recover all of these
numerically. The asymptotic analysis is then extended to the case of a power-law fluid. Again, significant progress is possible in four regimes. These asymptotic results are then used to construct a zero-dimensional
model for a rising diapir. The results of this model are compared to those
of earlier formulations of the problem. It is concluded that the diapir rises through a considerably smaller distance than was predicted previously, and that the role of thermal softening, whereby the diapir’s heat
is able to decrease the local crust viscosity allowing it to rise further, has
been overstated.
2012-02-14T14:53:44Z
2012-02-14T14:53:44Z
2011
Doctoral thesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
none
http://hdl.handle.net/10344/1979
eng
University of Limerick
oai:ulir.ul.ie:10344/2025
2021-02-22T15:59:32Z
hdl_10344_10
hdl_10344_9
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An investigation into the teaching and learning of probability at senior cycle
Murphy, Conor
O'Donoghue, John
Ní Ríordáin, Máire
probability
probability and statistics
peer-reviewed
In Ireland at present, the National Council for Curriculum and Assessment is comprehensively overhauling the Second Level Mathematics curriculum. This reformed curriculum is known as Project Maths and is a response to concerns about how Irish students are taught and learn mathematics. These concerns are based around the achievement of Irish student’s in international studies (Close and Oldham 2005; Cosgrove, Shiel, Sofroniou, Zastrutzki and Shortt 2005; Perkins, Moran, Cosgrove and Shiel 2010; Oldham 2002, 2006) as well as domestic and international literature which, highlights the problems associated with the behaviourist methodology favoured by Irish teachers (Conway and Sloane 2006; English, O’Donoghue and Bajpai 1992; Lyons, Lynch, Close, Sheerin and Boland 2003; NCCA 2005). The aim of the study was to improve the teaching and learning of Probability through the development of a resource pack. probability was chosen as the focus of the intervention due to the author’s experiences in the classroom, international literature highlighting its pedagogical difficulties (Shaughnessy 1992; Fischbein, Nello and Marino 1991; Ahlgren and Garfield 1988; Hawkins and Kapadia 1984) and its lack of popularity among Irish Leaving Certificate students (Chief Examiner 2000, 2005). The study was designed to examine the benefits of the active learning methodologies and contextualised questions promoted by the Project Maths curriculum, specifically with regards to students’ attitudes and understanding through the implementation and evaluation of a resource pack designed by the author.
The evaluation process produced data, which was inconclusive in establishing a link between the promoted methodologies and students’ attitudes and understanding. The
only significant shift in students’ attitude was a negative one in response to the statement “I know I can do well in Maths”. A dip in students’ confidence however is not unusual in studies involving changes in pedagogical style (Carpenter, Franke, Jacobs, Fennema and Epsom 1998; Cobb, Wood, Yackel, Nicholls, Wheatley, Trigatti and Perlwitz, 1991; Vershaffel and De Corte 1997; Fauzan et al. 2002; Van Reeuwijk 1992) and though not significant, student scores did improve in the three sub-categories of ‘Perception of Usefulness’, ‘Anxiety’ and ‘Effective Motivation’. There were also indications that these methodologies had a positive effect on understanding. The data also suggested that the resource pack, designed and developed by the author to support the teaching and learning of probability, will be of use to teachers who embrace Project Maths and what it is trying to achieve in Irish classrooms.
2012-02-21T15:17:48Z
2012-02-21T15:17:48Z
2011
info:eu-repo/semantics/masterThesis
ul_published_reviewed
none
http://hdl.handle.net/10344/2025
eng
University of Limerick
oai:ulir.ul.ie:10344/1983
2012-02-16T10:38:11Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_504
hdl_10344_20
A transient model of the renal medulla.
Ceveron, Gonzalez Maria T.
Hegarty, Alan F.
Randall Thomas, S.
renal medullla
kidney
transient shunt model
peer-reviewed
The kidney is one of the most important organs in the body, responsible for regulating the volume and composition of the extracellular fluid; excreting metabolic waste (as urine) and foreign substances;
and also producing some hormones. Through its functional unit, the nephron, blood is filtered and along the course of the different segments reabsorption and secretion takes place until the final product
leaves the collecting duct as urine.
This thesis focuses on the urine concentrating mechanism, presenting
a transient shunt model of the renal medulla where a population of nephrons is merged into a common structure. The model, consisting of a coupled system of PDEs-ODEs describing concentrations and volume flows through the loop of Henle, collecting duct, and vasa recta, is solved by the numerical Method of Lines.
For the first time in the case of a shunt model, the prebend transition occurring at a fixed distance before the turn at the tip of the descending loop of Henle is included. The hypothesis considering glycolysis as a source of external osmoles is presented in a model of the vasa recta, where a new numerical approach based on the software package Chebfun is considered. Later, this process is included in a full model
of the renal medulla. Several results from the transient analysis are also presented, such as the time that it takes to wash out the gradient if an increase of blood flow occurs and the time that the gradient takes
to build up for the different solutes.
2012-02-15T12:06:40Z
2012-02-15T12:06:40Z
2011
Doctoral thesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
none
http://hdl.handle.net/10344/1983
eng
University of Limerick
oai:ulir.ul.ie:10344/1985
2019-05-01T14:55:46Z
hdl_10344_10
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Cascade dynamics on complex networks.
Hackett, Adam W.
Gleeson, James P.
network theory
network structure
cascade dynamics
peer-reviewed
The network topologies on which many natural and synthetic systems are built provide ideal settings for the emergence of complex phenomena. One well-studied manifestation of this, called a cascade or avalanche, is
observed when interactions between the components of a system allow an
initially localized effect to propagate globally. For example, the malfunction
of technological systems like email networks or electrical power grids is often attributable to a cascade of failures triggered by some isolated event. Similarly, the transmission of infectious diseases and the adoption of innovations or cultural fads may induce cascades among people in society.
In recent years, it has been extensively demonstrated that the dynamics of cascades depends sensitively on the patterns of interaction laid out in the underlying network. One of the goals of network theory is to provide a solid theoretical basis for this dependence. In order to do this it is necessary, first, to construct network models that are both mathematically sound and
capture the salient features of their real-world counterparts. So far, there
has been limited success in this direction. The primary shortcoming of most
existing network models in this regard is their lack of realistic structural
motifs, in particular the absence of significant levels of clustering, which
refers to the propensity of triples of connected vertices to form triangles,
and is a prominent feature of networked systems across multiple settings.
In this thesis we investigate the interplay between network structure and cascade dynamics. Beginning with dynamics, we consider an analytically tractable technique to determine the expected cascade size in a broad range of dynamical models on locally tree-like networks of arbitrary degree
distribution. We validate this approach by demonstrating its excellent agreement with the results of extensive numerical simulations, and closely examine its applicability to real socio-technological systems. Here we focus particularly on problems relating to social influence and opinion formation, and we develop a number of important modifications of the basic theory. Following this, we turn our attention to the structural characterization
of networks. We investigate the properties of a new generation of network
models that incorporate clustering by embedding cliques of fully connected
vertices within a locally tree-like topology, and that thus directly extend
the classical configuration model construction. In one such model, devised by
a member of our group, the sizes of these cliques may vary, allowing one to prescribe a clustering spectrum to match empirically measured values.
Finally, we significantly extend the theory of dynamics on tree-like networks
to these new, more structurally realistic ones. From this we uncover answers to some important questions, which have earned considerable recent attention, concerning the effects of increased clustering on cascades.
SFI grant 06/IN.1/I366
MACSI 06/MI/005
2012-02-15T13:31:08Z
2012-02-15T13:31:08Z
2011
Doctoral thesis
all_ul_research
ul_published_reviewed
none
http://hdl.handle.net/10344/1985
eng
University of Limerick
oai:ulir.ul.ie:10344/2054
2021-02-23T10:50:14Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
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On the valuation of cashflow CSOs without Monte Carlo simulation.
Villiers, Rory
Gleeson, James P.
cashflow collateralized debt oblication
Monte Carlo integration
peer-reviewed
The most common method of pricing a cashflow
collateralized debt obligation (cashflow
CDO) is to use Monte Carlo integration. However, Monte Carlo integration is computationally intensive and often faster methods of pricing are required. Gallagher et
al. (2009) proposed a semi-analytic approximation that allows fast pricing of cashflow CDOs.This thesis has two goals: (i) A self contained description of the mathematical background necessary for practical implementations of cash
ow CDO pricing and (ii) a critical examination of the semi-analytic cashflow
CDO pricing method proposed by
Gallagher et al. (2009). We examine one of the main arguments in their paper surrounding
the modality of the underlying probability distribution and suggest an alternative
explanation for the accuracy of their method. With this new understanding, we describe the conditions under which the approximation will be most accurate.
SFI grant 06/IN.1/I366
2012-02-27T17:27:26Z
2012-02-27T17:27:26Z
2011
info:eu-repo/semantics/masterThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
none
http://hdl.handle.net/10344/2054
eng
University of Limerick
oai:ulir.ul.ie:10344/2472
2012-09-12T13:44:50Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_20
hdl_10344_504
Generalised smoothing in functional data analysis
Carey, Michelle
Gath, Eugene
Hayes, Kevin
MACSI
functional data analysis
ordinary differential equation (ODE)
generalised smoothing
peer-reviewed
The incorporation of model-based penalties in a penalised regression frame-
work (generalised smoothing) has been the subject of many publications,
most notably: Cao and Ramsay (2007); Heckman and Ramsay (2000);
Ramsay and Silverman (2005); Ramsay et al. (2007). Generalised smooth-
ing facilitates the estimation of the parameters of an ordinary di erential
equation (ODE) from noisy data without the speci cation of an explicit
expression of the functional entity described by the ODE. This is a notable
consequence of the smoothing procedure however it is not its primary aim.
Generalised smoothing aims to obtain an estimated functional entity that
adheres to the data and incorporates domain speci c information de ned
by the ODE. The existing methodology for the estimation of the param-
eters in generalised smoothing is hindered by the absence of an explicit
expression in terms of the parameters of the ODE for the penalty within
penalised tting criterion. The aim of this research is to obtain this ex-
plicit expression for penalties de ned by B{spline basis functions in order
to facilitate the development of the estimation procedure.
The recursive algorithm developed by de Boor (2001) is the predominant
methodology for the evaluation of B-spline basis functions over a given in-
terval. While this algorithm is a fast and numerically stable method for
nding a point on a B-spline curve given the domain, it does not explicitly
provide knowledge of the internal structure of the B-spline functions. This
work introduces an alternative representation of B{spline basis functions
in terms of the underlying polynomials that comprise the B{spline. This
alterative representation of B{spline basis functions produces generalised
penalties which can be written explicitly in terms of the parameters of the
ODE. A joint estimation strategy in which the penalised least squares cri-
terion is minimised with respect to the parameters of the B-spline and the
parameters of the ODE is developed. Finally this joint estimation strat-
egy is shown to produce estimates of both parameters that have a higher
accuracy and are more computationally e cient than estimates developed
by existing methods.
2012-08-22T15:12:28Z
2012-08-22T15:12:28Z
2012
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/2472
eng
info:eu-repo/semantics/openAccess
University of Limericik
oai:ulir.ul.ie:10344/2474
2014-10-03T09:23:49Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_20
hdl_10344_504
An analysis of performance in mathematics for technology undergraduates and an investigation of teaching interventions for these students
Faulkner, Fiona
Gill, Olivia
Hannigan, Ailish
MACSI
NCE-MSTL
NAIRTL
mathematics education
technology undergraduates
numeracy skills
economists
educationalists
peer-reviewed
Declining standards in students’ mathematical competency levels has become a major issue in mathematics education both nationally and internationally (Smith 2004; Kajander and Lovric 2005; Gill et al 2010). This decline in standards, which has commonly become known as the ‘Mathematics Problem’, refers to issues such as poor numeracy skills in beginning undergraduates, difficulties with basic arithmetic and algebraic manipulations and an inability to cope with mathematics which is presented in unfamiliar formats (Hourigan and O’Donoghue 2007). Economists and educationalists agree that competent citizens in the area of mathematics and science are necessary for a successful economy (OECD 2006; Breen et al 2009; IBEC 2010). The need to try and overcome, or at least alleviate somewhat, the ‘Mathematics Problem’ has therefore been a priority of many third level institutions worldwide (Croft 2000; Tonkes et al 2005; Symonds et al 2008). Third level institutions have introduced a variety of different mathematical support structures in an attempt to support their mathematically less prepared students. One popular example of this is the introduction of diagnostic testing which aims to establish where students’ difficulties may lie and to identify the students within a particular cohort who are most ‘at risk’ of failing university mathematics courses. The University of Limerick (UL) introduced diagnostic testing in 1997. The same diagnostic test is still distributed today and so a large dataset has been created which currently consists of data on almost 8,000
students between 1997 and 2010. Diagnostic test data has been found to provide valuable
research opportunities such as the profiling of mathematics students over time (Kannemeyer 2005; Wilson and MacGillivary 2007; Faulkner et al 2010). Another popular use of diagnostic testing, which is prevalent in international education literature, is the prediction of students’ mathematical achievement (Simonite 2004; Barry and Chapman 2007; McDonald 2008). The wealth of data contained in the UL dataset and the examination of literature in the area of the ‘Mathematics Problem’ led the author to investigate the profile of third level mathematics students over time. An investigation into the profile of ‘at risk’ mathematics students over time enabled the author to create a predictive model of performance in mathematics. Finally the author used these research findings to inform a mathematics intervention which was implemented in UL. The intention of these investigations is to further quantify the ‘Mathematics Problem’ so as to inform and improve the teaching and learning of mathematics both nationally and internationally.
2012-08-23T10:34:49Z
2012-08-23T10:34:49Z
2012
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/2474
eng
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/2679
2014-07-01T08:01:34Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Non-traditional statistical process control for commercial irradiation
Donovan, J
Murphy, Eamonn
UK and European Panel on Gamma and Electron Irradiation
statistical process control
irradiation
standardized charts
non-peer-reviewed
Commercial irradiation typically involves applying electron beam or gamma
radiation to a product with a view to sterilizing the product and killing
any bacteria present. This is extremely important in the medical device
industry where packaged products or pallets require irradiation between
a minimum and maximum dose. As packaged product provides a level of
shielding it is difficult to monitor such processes to ensuring that all prod-
ucts on the pallet received a dose greater than the minimum and yet less
than the maximum. This di±culty was solved for both the gamma ray and
electron beam radiation facilities by the use of non-traditional Statistical
Process Control (SPC) techniques. By combining standardized charts and
group charts, a single control chart could accommodate both minimum and
maximum doses while e®ectively monitoring the entire process. In addition,
guidance tables were developed the allowed operations to determine a win-
dow of suitable dosages that would simultaneously satisfy the irradiation
requirements of di®erent groups of products.
2012-11-20T09:41:02Z
2012-11-20T09:41:02Z
2007
info:eu-repo/semantics/conferenceObject
all_ul_research
http://hdl.handle.net/10344/2679
eng
Conerence on Applied Statistics in Ireland (CASI);pp. 57-
http://www.istat.ie/casi.php?subLookup=26
info:eu-repo/semantics/openAccess
Irish Statistical Association
oai:ulir.ul.ie:10344/2757
2014-07-07T10:33:34Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Survival analysis for longitudinal data
MacKenzie, Gilbert
longitudinal data
survival analysis
model mis-specification
grouped likelihood
peer-reviewed
In longitudinal studies with a set of continuous or ordinal repeated response
variables it may be convenient to summarise the outcome as a threshold
event. Then, the time to this event becomes of interest. This is particularly
true of recent Ophthalmological trials evaluating the effect of treatment
on the loss of visual acuity over time. However, the practice of employing
conventional survival analysis methods for testing the null hypothesis of
no treatment effect in these types of studies is intrinsically flawed as the
exact time to the threshold event is not measured. In this paper we obtain
a general likelihood for the unknown parameters when the underlying sur-
vival model is parametric. We also recover the actual information available
in repeated measures data for a variety of models and compare the results
with those obtained using a mis-specified model, which assumes the time
to the event is one of the possibly irregularly spaced inspection times.
2012-12-19T16:30:30Z
2012-12-19T16:30:30Z
1999
info:eu-repo/semantics/conferenceObject
all_ul_research
http://hdl.handle.net/10344/2757
eng
Proceedings of the 14th International Workshop on Statistical Modelling
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2773
2016-10-03T15:05:49Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Modelling marginal covariance structures in linear mixed models
MacKenzie, Gilbert
Pan, Jianxin
Cholesky decomposition
covariate dependent covariance
linear mixed models
longitudinal data
peer-reviewed
Pourahmadi (1999) provided a convenient reparameterisation of the marginal
covariance matrix arising in longitudinal studies. We exploit his work to
model the dependence of this covariance structure on baseline covariates,
time and their interaction. The rationale for this approach is the realisation
that in linear mixed models (LMMs) the assumption of a homogeneous covariance
structure with respect to the covariate space is a testable model
choice. Accordingly, we provide methods for testing this assumption and
re-analyse Kenward’s (1987) cattle data set using our new model.
2013-01-04T11:44:17Z
2013-01-04T11:44:17Z
2001
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2773
eng
Proceedings of the 16th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2774
2014-07-01T15:34:03Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Modelling conditional covariance structure in linear mixed models
Pan, Jianxin
MacKenzie, Gilbert
covariance structure
linear mixed models
polynominal fitting
maximum hierarchical likelihood
peer-reviewed
2013-01-04T12:14:38Z
2013-01-04T12:14:38Z
2001
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2774
eng
Proceedings of the 16th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2775
2016-10-03T15:03:22Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
A logistic regression model for survival data
MacKenzie, Gilbert
canonical model
Fisher' Z
gneralized time-dependent logistic
non-PH survival
peer-reviewed
The near non-identifiability of one of the parameters in the Generalized
Time-Dependent Logistic (GTDL) Survival Model (MacKenzie, 1996, 1997)
is discussed. A new canonical 3-parameter logistic model survival model,
in which all of the parameters are identifiable, is obtained. A direct connection
with Fisher’s Z distribution is established. The properties of this
non-PH model are contrasted briefly with Cox’s PH model. The new model
is used to investigate survival from lung cancer in a population study.
2013-01-04T12:45:54Z
2013-01-04T12:45:54Z
2002
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2775
eng
Proceedings of the 17th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2776
2018-07-26T14:55:34Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
A logistic PH regression model for interval censored survival data
Al-tawarah, Yasin
MacKenzie, Gilbert
interval censoring
logistic survival
proportional hazards
mis-specification likelihood
peer-reviewed
The survival function of the logistic proportional hazards (PH) regression
model, MacKenzie (1996), is obtained. A general likelihood for interval
censored survival data which depends only on various closed forms of the
survival function of a continuous underlying failure time distribution is introduced.
The use of the logistic PH survival distribution is proposed for
the analysis of interval censored data following a PH distribution. The corresponding
interval censored likelihood is developed and compared with a
mis-specified likelihood which treats the interval censored data as if they
were exact. A simulation study is used to compare the two likelihoods.
2013-01-04T14:21:48Z
2013-01-04T14:21:48Z
2002
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2776
eng
Proceedings of the 17th International Workshop on Statistical Modelling.;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2777
2014-07-01T15:31:26Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
A comparison of non-PH and PH gamma frailty models
Blagojevic, Milica
MacKenzie, Gilbert
Do Ha, II
PH
non-PH models
gamma frailty
canonical logistics
peer-reviewed
The non-PH Canonical Time Dependent Logistic survival regression model
described by MacKenzie (1996, 2002), is extended by incorporating a multiplicative
Gamma frailty component into the hazard function. The resulting
model is obtained in closed form and its properties are compared with
the classical PH, Weibull frailty regression model described by (Hougaard,
1994). The performance of the models, with and without frailty, is investigated
by re-analyzing some data from the NI lung cancer study (MacKenzie,
1996).
2013-01-04T14:38:42Z
2013-01-04T14:38:42Z
2003
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2777
eng
Proceedings of the 18th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2778
2014-07-01T15:40:58Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Non-PH multivariate survival models based on the GTDL
MacKenzie, Gilbert
Do Ha, II
Lee, Youngjo
frailty models
generalized time-dependent logistic
non-PH model
random effect
peer-reviewed
Correlated survival times may be modelled by introducing a random effect,
or frailty, component into the hazard function. For multivariate survival
data we extend a non-PH model, the generalized time-dependent logistic
(GTDL) survival model (MacKenzie, 1996, 1997), to include random effects.
The extension leads to two different, but related, non-PH models according
to the method of incorporating the random effects. The h-likelihood
procedures of Ha, Lee and Song (2001) and Ha and Lee (2003), which obviate
the need for marginalization (over the random effect distribution), are
derived for these extended models and their properties discussed. The new
models are used to analyze two practical examples in the survival literature
and the results are compared with those obtained from fitting the PH and
PH frailty models.
2013-01-04T15:09:29Z
2013-01-04T15:09:29Z
2003
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2778
eng
Proceedings of the 18th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2779
2018-07-26T14:56:23Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
A non-PH accelerated hazard model for analyzing clinical trial data
Al-tawarah, Yasin
MacKenzie, Gilbert
interval censoring
logistic survival
non-PH model
accelerated hazard
mis-specified likelihood
peer-reviewed
In longitudinal studies with a set of continuous or ordinal repeated response
variables it may be convenient to summarize the outcome as a threshold
event. Then, the time to this event becomes of interest. In this paper we obtain
the general likelihood for the unknown parameters when the underlying
survival model is parametric and the survival times are interval-censored.
We investigate the use of a member of the Generalized Time Dependent
Logistic family of survival distributions (MacKenzie, 1996) which is a non-
PH Accelerated Hazard Model and has a logistic baseline hazard function.
We use simulation to investigate how inference on the treatment parameter
is compromised by using the mis-specified likelihood, which treats the
interval-censored survival times as if they were exact.
2013-01-04T15:28:25Z
2013-01-04T15:28:25Z
2003
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2779
eng
Proceedings of the 18th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2780
2016-10-03T14:58:07Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Advances in covariance modelling
MacKenzie, Gilbert
Cholesky decomposition
covariance modelling
joint model space
longitudinal studies
GEE
GLMMs
peer-reviewed
Conventionally, in longitudinal studies, the mean structure has been thought
to be more important than the covariance structure between the repeated
measures on the same individual. Often, it has been argued that, with re-
spect to the mean, the covariance was merely a `nuisance parameter' and,
consequently, was not of `scientific interest'. Today, however, one can see
that from a formal statistical standpoint, the inferential problem is entirely
symmetric in both parameters. In recent years there has been a steady
stream of new results and we pause to review some key advances in the expanding field of covariance modelling, In particular, developments since the
seminal work by Pourahmadi (1999, 2000) are traced. While the main focus
is on longitudinal data with continuous responses, emerging approaches to
joint mean-covariance modelling in the GEE, and GLMM arenas are also
considered briefly.
2013-01-04T16:15:26Z
2013-01-04T16:15:26Z
2004
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2780
eng
Proceedings of the 19th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2781
2014-07-01T15:43:08Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
PH and non-PH frailty models for multivariate survival data
Blagojevic, Milica
MacKenzie, Gilbert
frailty models
EM
finite mixtures
correlated survival model
peer-reviewed
We generalize the previously developed Non-PH CTDL-Gamma and
the PH Weibull-Gamma frailty models to correlated survival data. In particular,
we seek analytical results using the marginal approach, to determine whether the
univariate results generalize to the multivariate context. We consider both the
shared and correlated frailty cases.We also develop non-parametric frailty models
which enable us to check the appropriateness of the assumed distributional form
of the random effect.
2013-01-04T16:25:51Z
2013-01-04T16:25:51Z
2004
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2781
eng
Proceedings of the 19th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2786
2016-10-03T14:54:03Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Model selection for frailty structures
MacKenzie, Gilbert
Lee, Youngjo
model selection
AIC
DIC
frailty models
h-likelihood
peer-reviewed
Frailty models are now widely used for analyzing multivariate survival data. An open question is how best to determine how to select the most
appropriate frailty structure supported by the data. Herein, we develop a proce-
dure for selecting the optimal frailty structure from a set of (possibly) non-nested
frailty models. Our focus is on the dispersion parameters which define the frailty
structure. We propose two new AIC criteria: one based on the deviance for goodness of fit and the other on the extended restricted likelihood (ERL) of Lee and
Nelder (1996). A simulation study shows that the AIC based on the extended
restricted likelihood is better when attention is focussed on selecting the frailty
structure.
2013-01-07T15:27:28Z
2013-01-07T15:27:28Z
2006
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2786
eng
Proceedings of the 21st International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2787
2016-10-03T14:49:43Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Modelling survival data with crossing hazards
MacKenzie, Gilbert
Do Ha, II
crossing hazards
GTDL family
non-PH survival modeling
peer-reviewed
We revisit the crossing hazards problem in survival analysis and compare the use of Cox's semi-parametric model with a parametric non-PH model
from the generalised time-dependent logistic family(GTDL). A set of gastric can-
cer data is analysed and a GTDL gamma-frailty model is shown to explain the
observed data well. The role of heterogeneity in the crossing hazards problem is
discussed.
2013-01-07T15:48:40Z
2013-01-07T15:48:40Z
2007
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2787
eng
Proceedings of the 22nd International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2788
2016-10-03T13:59:00Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Analysis of breast cancer survival in local health authorities
Lynch, Joseph
MacKenzie, Gilbert
Kaplan-Meier
cause-specific
all-cause
PH/non-PH
peer-reviewed
Kaplan-Meier analysis of a large breast cancer dataset is carried
out under all-cause and cause-specific survival. The results are compared with
a variety of model-based analyses, including Cox's Proportional Hazard (PH)
model and its Gamma frailty variant, along with the non-PH Generalised Time-
Dependent Logistic Model (GTDL) and its Gamma frailty variant.
2013-01-07T16:21:58Z
2013-01-07T16:21:58Z
2007
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2788
eng
Proceedings of the 22nd International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2789
2014-07-01T15:31:57Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
CTDL-positive stable frailty model
Blagojevic, Milica
MacKenzie, Gilbert
canonical logistic
frailty models
positive stable
non-PH
ration-of-uniforms
peer-reviewed
The non-PH Canonical Time Dependent Logistic (CTDL) survival re-
gression model is extended by incorporating a positive stable frailty component
into the hazard function within the Bayesian framework. The resulting model is
compared numerically with the Weibull-positive stable frailty model, using data
from a placebo controlled randomized trial of gamma interferon in chronic gran-
ulotomous disease (CGD). Moreover, supremum bounds of the ratio-of-uniforms
(ROU) algorithm, used for sampling from complete conditional distributions, are
obtained analytically thus yielding a more efficient form of the algorithm.
2013-01-07T16:44:05Z
2013-01-07T16:44:05Z
2007
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2789
eng
Proceedings of the 22nd International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2790
2016-10-03T14:47:02Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
On the analysis of censored reliability data
Peng, Defen
MacKenzie, Gilbert
reliability
censoring types I & II
interim analysis
designed experiment
peer-reviewed
We develop an analysis of the reliability of reliability data following
a negative exponential distribution and subject to type I censoring. Our main
focus is to determine the role of the particular analytical approach in interim
analysis. Accordingly, in this preliminary study, we aim to investigate, by means
of a detailed simulation study, the effects of early stopping on decision-making in
a comparative two group reliability study (eg, a two group randomised controlled
clinical trial). In passing, we extend previous results to inverse parametrizations
and type II censoring.
2013-01-08T14:43:33Z
2013-01-08T14:43:33Z
2007
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2790
eng
Proceedings of the 22nd International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2791
2016-10-03T14:51:21Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Modelling high dimensional sets of binary co-morbidities
Conde, Susana
MacKenzie, Gilbert
co-morbidity index
binary data
hierarchical long-linear model
peer-reviewed
The construction of classical co-morbidity indices is described. When
the co-morbidities are binary we advocate the use of log-linear models which
better capture the dependence structure in the data. We use R to implement new
search strategies which enable us to analyse, sparse, high dimensional contingency
tables rapidly and hence identify the best fitting models. We apply our new
algorithms to a set of real medical data.
2013-01-08T15:00:39Z
2013-01-08T15:00:39Z
2007
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2791
eng
Proceedings of the 22nd International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2792
2019-05-01T12:11:17Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_20
hdl_10344_2626
Space -time clustering revisited
MacKenzie, Gilbert
Xu, Jing
SFI
space-time clustering
exact distribution
correlated outcomes
spatial data
covariance model
peer-reviewed
The history of space-time clustering concepts and methods are re-
viewed briefly. The space-time clustering model of Ederer et al is investigated in
detail. This method has been used extensively in the epidemiological literature,
but we show that the distribution of main test statistic involved does not follow the distribution proposed by the authors. We note, too, that the two indices
proposed are not statistically independent, leading to potential over-reporting
in the epidemiological literature. We obtain the correlation between the original
clustering indices and suggest a new combined test statistic which has the correct
null distribution. We develop a fuller spatial model and illustrate the methodology using data from a study of the incidence of childhood leukaemia in Northern
Ireland.
2013-01-08T15:13:21Z
2013-01-08T15:13:21Z
2009
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2792
eng
Proceedings of the 24th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
07/MI012
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2795
2019-05-01T12:10:55Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Modelling of covariance structure in constrained marginal models for longitudinal data
Xu, Jing
MacKenzie, Gilbert
longitudinal data
inequality constraints
marginal models
covariance modelling
Cholesky decomposition
peer-reviewed
A data-driven method for modelling intra-subject covariance matrix is introduced to constrained marginal models with longitudinal data. A constrained iteratively re-weighted least squares algorithm is presented consequently.
Asymptotic properties of the constrained ML estimates, including strong consistency, approximate representation and asymptotic distribution, are given. Real
data analysis and simulations are conducted to compare our new approach with
classical menu-selection-based modelling technique.
2013-01-09T10:07:18Z
2013-01-09T10:07:18Z
2009
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2795
eng
Proceedings of the 24th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2796
2021-02-01T14:18:45Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Interval censored PH survival models for longitudinal data: precision of estimators
MacKenzie, Gilbert
Peng, Defen
SFI
artificial precision
interval censoring
longitudinal RCTs
PH survival models
proxy likelihood
peer-reviewed
We present a general likelihood for interval censored survival data
arising in longitudinal studies such as longitudinal randomized controlled clinical
trials (RCTs) and give some general formulae for inference in parametric, interval
censored, proportional hazards, regression survival models. For the exponential
regression model we compare the performance of the general likelihood with a
commonly used proxy likelihood, which ignores the interval censoring by treating
the interval censored times to events as if they were exact. We show analytically
that use of the proxy likelihood leads to estimators (for example, of the treatment
effect) which are artificially precise and we quantify the extent of the resulting
biases in a simulation study.
2013-01-09T11:08:29Z
2013-01-09T11:08:29Z
2010
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2796
eng
Proceedings of the 25th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
07/MI/012
05/RF/MAT026
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2807
2019-05-01T12:10:34Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Modelling covariance structures for multivariate longitudinal data
Xu, Jing
MacKenzie, Gilbert
SFI
multivariate longitudinal data
marginal models
covariance modelling
block triangular factorization
matrix logarithm
peer-reviewed
2013-01-14T09:49:30Z
2013-01-14T09:49:30Z
2010
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2807
eng
Proceedings of the 25th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
07/MI012
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2797
2021-02-01T14:19:55Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Precision of estimators in interval censored parametric survival models
Peng, Defen
MacKenzie, Gilbert
SFI
artificial precision
interval censoring
longitudinal RCTs
PH & non-PH survival modelling
proxy liklihoods
peer-reviewed
Recently, several advances have been made in the analysis of interval
censored (IC) data mainly in relation to semi-parametric proportional hazard
(PH) models (Gómez et al., 2009, Lesaffre et al., 2005). It is arguable, however,
that the parametric case has been somewhat neglected, overall, and that more
can be learned, especially in relation to non-PH models. Accordingly, we focus on
simple parametric models for interval censored survival data arising in longitudinal RCTs. For the exponential regression model we compare the performance of
a general likelihood with commonly used proxy likelihoods, which ignore the interval censoring by treating the interval censored times to events as if they were
exact. We show analytically that use of proxy likelihoods leads to estimators
which are artificially precise and we quantify the extent of the resulting biases in
a simulation study and by analyzing real data. We also compare the likelihoods
using non-PH models and obtain different findings.
2013-01-09T14:41:18Z
2013-01-09T14:41:18Z
2011
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2797
eng
Proceedings of the 26th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
07/MI/012
05/RF/MAT/026
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2798
2016-10-03T14:28:18Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
On bivariate survival regression models
Lynch, Joseph
MacKenzie, Gilbert
SFI
Weibull
GTDL
frailty
dependence between times
peer-reviewed
We compare and contrast the properties of the bivariate Weibull
and GTDL regression survival models. An analytic expression for the correlation
between times is derived for the Weibull model and a modified Kullback-Leibler
distance is proposed for measuring the dependence between times in both models.
2013-01-09T15:04:12Z
2013-01-09T15:04:12Z
2011
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2798
eng
Proceedings of the 26th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
07/MI012
IRCSET
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2800
2019-09-25T10:46:44Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
LASSO penalised likelihood in high-dimensional contingency tables
Conde, Susana
MacKenzie, Gilbert
Glaxosmithkline (GSK)
SFI
LASSO
model selection
penalized likelihood
stepwise search algorithms
peer-reviewed
We consider several least absolute shrinkage and selection operator
(LASSO) penalized likelihood approaches in high dimensional contingency tables
and with hierarchical log-linear models. These include the proposal of a parametric,
analytic, convex, approximation to the LASSO. We compare them with "classical"
stepwise search algorithms. The results show that both backwards elimination
and forward selection algorithms select more parsimonious (i.e. sparser)
models which are always hierarchical, unlike the competing LASSO techniques.
2013-01-10T11:24:39Z
2013-01-10T11:24:39Z
2011
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2800
eng
Proceedings of the 26th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
07/MI/012
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2801
2014-07-01T15:39:49Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Multi-parameter regression survival models
Burke, Kevin
MacKenzie, Gilbert
SFI
IRCSET
crossing hazards
multi-parameter regression survival models
PH and non-PH models
peer-reviewed
It is well known that the proportional hazards (PH) assumption is a
simplifying assumption in survival analysis that may not always be appropriate.
However, PH models are routinely fitted and inference is made on the data based
on such models. A major flaw here is that if the data are non-PH then we will
reach incorrect conclusions by making this assumption. For example we may find
a covariate to be statistically insigni cant when in fact it is important, but the
model fails to pick this up. Even if a PH model does pick up the statistical
significance of a non-PH covariate, the nature of the effect of the covariate on
survival, as determined by this simplistic model, will clearly be incorrect. We
introduce a regression-based extension of PH modelling to try an account for
situations such as those described above and offer new, previously unavailable
insights, into the data.
2013-01-10T11:44:47Z
2013-01-10T11:44:47Z
2012
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2801
eng
Proceedings of the 27th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
07/MI012
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2802
2019-09-25T10:47:13Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Model selection in sparse contingency tables: LASSO penalties vs classical method
Conde, Susana
MacKenzie, Gilbert
SFI
contingency tables
model selection
regularisation
smooth LASSO
sparseness
peer-reviewed
We compare improved classical backward elimination and forward
selection methods of model selection in sparse contingency tables with methods
based on a regularisation approach involving the least absolute shrinkage and
selection operator (LASSO) and the Smooth LASSO. The results show that the
modified classical methods outperform the regularisation methods, by producing
sparser models which are always hierarchical. Curiously, models selected by the
regularisation methods often include effects which are known to be inestimable
in the classical paradigm. Our findings support the use of classical methodology.
2013-01-10T12:05:40Z
2013-01-10T12:05:40Z
2012
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2802
eng
Proceedings of the 27th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
07/MI012
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2805
2018-07-26T14:55:59Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
A Non-PH Weibull accelerated hazard model
Al-tawarah, Yasin
MacKenzie, Gilbert
Weibull model
non-PH model
accelerated hazard
peer-reviewed
In this paper we investigate the use of accelerated Weibull hazard
model. We compare it with Logistic Accelerated Hazard model. The models are
used to analyze survival data from the Northern Ireland lung cancer study and
the findings. Maximum likelihood method was used to estimate the parameters
of two factors: age and sex.
2013-01-11T11:29:01Z
2013-01-11T11:29:01Z
2005
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2805
eng
Proceedings of the 20th International Workshop on Statistical Modelling.;
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2806
2014-07-08T10:48:06Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Survival distributions based on the XD model class
Burke, Kevin
MacKenzie, Gilbert
SFI
IRCSET
extreme dispersion
survival
Morris class
quadratic slopes
peer-reviewed
We aim to explore the survival distributions based on the extreme
dispersion, XD, models proposed by Jørgensen (2010). It is suggested that survival times can be modelled within the XD framework by taking log T = Y ~
XD( µ,𝜆 ), where T is the survival time and Y is the extreme dispersion random
variable. We will show how these survival models can be generated using XD
and look at the distribution and properties of the survival time T = eY .
2013-01-11T12:50:15Z
2013-01-11T12:50:15Z
2011
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2806
eng
Proceedings of the 26th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
07/MI012
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2814
2014-07-01T15:30:51Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Comparison of infrared coagulation and rubber band ligation for first and second degree haemorrhoids: a randomised prospective clinical trial
Templeton, John L
Spence, R.A.J.
Kennedy, T.L.
Parks, T.G.
MacKenzie, Gilbert
Hanna, W.A
first and second degree haemorrhoids
clinical trial
peer-reviewed
One hundred and thirty seven previously untreated outpatients
with first and second degree haemorrhoids were
allocated at random to treatment by infrared coagulation
(n=66) or rubber band ligation (n= 71). Complete follow
up was obtained in 122 patients (60 who had undergone
infrared coagulation (group 1), and 62 rubber band
ligation (group 2)) at periods from three months to one
year after completion of treatment.
Infrared coagulation produced a satisfactory outcome
in 51 patients (85%): 34 were rendered asymptomatic and
17 improved. Rubber band ligation produced a satisfactory
outcome in 57 patients (92%): 33 were rendered
asymptomatic and 24 improved. Both methods were
equally effective in first and second degree haemorrhoids.
The incidence of side effects, particularly discomfort,
during and after treatment was significantly higher in
those treated by rubber band ligation (p <0 001). This
appeared to be an appreciable deterrent to future patient
compliance. The number of patients losing more than 24
hours from work was higher after rubber band ligation
than after infrared coagulation. The number of treatments
necessary to cure symptoms did not differ significantly
between the two methods. Infrared coagulation was significantly faster than rubber band ligation (p <0-001).
Infrared coagulation is a simple, fast, and effective
outpatient method for the treatment of first and second
degree haemorrhoids with fewer troublesome side effects
and higher patient acceptability than rubber band
ligation.
2013-01-17T09:04:13Z
2013-01-17T09:04:13Z
1983
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2814
eng
British Medical Journal;286(6375), pp. 1387-1389
http://group.bmj.com/group/advertising/portfolio/bmj-editions
info:eu-repo/semantics/openAccess
BMJ Group
oai:ulir.ul.ie:10344/2815
2018-07-10T07:57:59Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Sub-vastus approach is more effective than a medial parapatellar approach in primary total knee arthroplasty: a randomized controlled trial
Bridgman, Stephen A.
Walley, Gayle
MacKenzie, Gilbert
Clement, Darren
Griffiths, David
Maffulli, Nicola
total knee arthroplasty
sub-vastus approach
RCT
randomized
osteoarthritis
peer-reviewed
In a prospective single-centre longitudinal randomized controlled trial 116 patients were allocated to the sub-vastus approach, and 115 to the medial parapatellar approach. At one week follow-up, compared to baseline, range of motion, Knee Society (KS) global, KS knee, and KS pain scores were significantly better in the sub-vastus group. At the one year follow-up, WOMAC global and pain scores, SF36 physical function and
role-physical scores, and EuroQol utility and pain score were significantly better in the sub-vastus group. The ease of exposure in the sub-vastus approach was significantly worse. There was no significant difference in length of stay or analgesia intake. The sub-vastus approach to total knee arthroplasty was more effective than a medial parapatellar approach at both one week and one year post-operatively, but surgeons reported a less
easy exposure in the sub-vastus group.
2013-01-17T11:43:25Z
2013-01-17T11:43:25Z
2009
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2815
eng
The Knee;16(3), pp. 216-22
http://dx.doi.org/10.1016/j.knee.2008.11.012
This is the author’s version of a work that was accepted for publication in The Knee. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in The Knee, 16(3), pp. 216-222 doi:10.1016/j.knee.2008.11.012
info:eu-repo/semantics/openAccess
Elsevier
oai:ulir.ul.ie:10344/2816
2018-07-10T07:58:34Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Sub-vastus approach versus the medial parapatellar approach in primary total knee: a randomised controlled trial
Bridgman, Stephen A.
Walley, Gayle
MacKenzie, Gilbert
Clement, Darren
Griffiths, David
Maffulli, Nicola
knee replacements
knee arthroplasty
peer-reviewed
Background: Thirty thousand knee replacements are performed annually in the UK. There is uncertainty as to the best surgical approach to the knee joint for knee arthroplasty. We planned a randomised controlled trial to compare a standard medial parapatellar arthrotomy with sub-vastus arthrotomy for patients undergoing primary total knee arthroplasty in terms of short and long term knee function.
Methods: Patients undergoing primary total knee arthroplasty at the local NHS Trust are to be recruited into the study. Patients are to be randomised into either the subvastus or medial parapatellar approache to knee arthroplasty. The primary outcome measures will be the American Knee Society and WOMAC Scores. The secondary outcome measures will be patient based measures of EuroQol and SF-36. All outcomes will be measured pre-operatively, 1, 6, 12 and 52 weeks post-operatively. We will also review pain intensity using a pain and analgesia diary. Ease of surgical exposure and complications will also be analysed.
Discussion: Evidence is lacking concerning the best surgical approach to the knee joint for patients undergoing primary total knee replacement. This pragmatic randomised trial tests the hypothesis that the sub-vastus approach is significantly superior to the standard medial parapatellar approach in terms of short and long term knee function.
2013-01-17T12:05:21Z
2013-01-17T12:05:21Z
2006
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2816
eng
Trials;7(23)
http://dx.doi.org/10.1186/1745-6215-7-23
info:eu-repo/semantics/openAccess
BioMed Central Ltd.,
oai:ulir.ul.ie:10344/2817
2014-07-01T15:38:06Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Sampling-based inference for the generalized time-dependent logistic hazard model
Louzada-Neto, Francisco
Cremasco, Caroline Pires
MacKenzie, Gilbert
SFI
Bayesian modelling
GTDL
hazard modelling
MCMC
peer-reviewed
Lifetimes which satisfy a non-proportional hazard model may arise in several areas, such
as, Medicine, Biometrics, Criminology and Industrial Reliability. For these data it is reasonable to presume that the hazard function is time-dependent, thereby accommodating crossing hazards. Such dependency can be modelled directly by introducing a time-dependent term in the model for the hazard function. Accordingly, in this paper we utilize a generalized time-dependent logistic (GTDL) hazard model which can accommodate non-proportional hazards data. A sampling-based inference procedure based on Markov chain Monte Carlo Methods is developed and the methodology is used to investigate survival from advanced lung cancer in a well known dataset.
2013-01-17T14:41:30Z
2013-01-17T14:41:30Z
2010
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2817
eng
Journal of Statistical Theory and Applications;9(2), pp. 169-184
07/MI012
info:eu-repo/semantics/openAccess
Gowas Publishers
oai:ulir.ul.ie:10344/2818
2014-07-01T15:43:43Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Prototype modelling of body surface maps using tangent distance
Patterson, Richard
MacKenzie, Gilbert
classification
invariance dimension
prototype models
peer-reviewed
In recent years the tangent distance approach of Simard et al (1993) to
pattern recognition tasks such as handwritten character recognition has
proven successful. Simard's distance measure could be made locally invariant to any set of transformations of the input and when implemented in
one-nearest-neighbour classification of handwritten digits, outperformed all
other classification schemes.
Hastie et al (1996) propose prototype models which generalise the concept
of a centroid of a set of images in the Euclidian metric to a low-dimensional
hyperplane in the tangent metric, and these prototypes can be used to
reduce lookup time in classification.
We propose to apply and extend the tangent distance approach to classify
a set of body surface maps, which are recordings of the electrical activity
of the heart, of a large number of patients with various cardiac conditions.
Using a grid of p electrodes attached to the anterior chest, we calculate a
number of p-dimensional observation vectors for each patient and classify
input maps on the basis of overall distance of map to prototypes derived
from training set maps over all included observation vectors.
2013-01-17T16:48:45Z
2013-01-17T16:48:45Z
1999
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2818
eng
Proceedings of the 14th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/2836
2020-12-02T14:37:17Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_504
hdl_10344_20
Rolling optimisation, stochastic demand modelling and scenario reduction applied to the UK gas market
Devine, Mel T.
Gleeson, James P.
Kinsella, John
Ramsey, David
SFI
UK natural gas market
ROM
Ireland
peer-reviewed
In recent years the daily gas demand in the UK and Ireland has become increasingly
uncertain. This due to the changing nature of electricity markets, where intermittent
wind energy levels lead to variations in the demand for gas needed to produce electricity.
As a result, there is an increasing need for models of natural gas markets that
include stochastic demand. In this thesis, a Rolling Optimisation Model (ROM) of the
UK natural gas market is introduced. It takes as an input demand scenarios simulated
from a stochastic process of UK gas demand which is developed as a part of this work.
The model is informed by an analysis of the two main types of natural gas market models:
complementarity-based equilibrium models and cost minimisation models. This
analysis shows that when market power (i.e. Nash-Cournot competition) is removed
from complementarity-based equilibrium models the outputs are equivalent to those
from a corresponding cost minimisation model. The outputs of the Rolling Optimisation
Model are the ows of gas in the UK, i.e., how the different sources of supply
meet demand, as well as how gas ows in to and out of gas storage facilities, and the
daily System Average Price of gas in the UK. The model was found to t reasonably
well to historic data (from the UK National Grid) for the years starting on the 1st of
April for both 2010 and 2011. This work also investigates the bene t of using scenario
reduction techniques on the set of demand scenarios used in ROM. These techniques
allow the effects of large sets of stochastically-generated scenarios to be captured in
ROM, whilst maintaining a relatively low computational cost for solving the model.
In the nal chapter of this thesis, ROM is used to predict future ows and prices of gas
in the UK and investigate various `What-if' scenarios in the UK natural gas market.
2013-01-29T15:59:33Z
2013-01-29T15:59:33Z
2012
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/2836
eng
06/MI/005
06/IN.1/I366
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/2852
2019-09-24T08:16:50Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_504
hdl_10344_20
Spatial periodic solutions of the extended Cahn-Hilliard equation
Sedakov, Roman Olegovich
Benilov, Eugene
Lee, William T.
SFI
Mathematical Applications Consortium for Science and Industry
Cahn-Hillard equation
numerical studies
peer-reviewed
The present thesis studies the problem of existence and stability of spatial periodic
solutions of the extended Cahn–Hilliard equation. The extended Cahn–Hilliard
equation is a well-known model that describes the process of phase transition in
diblock copolymer melts and can be derived using the general Landau theory of
phase separations together with some approximations for a short range and long
range interactions in copolymer subchains [7], [31], [35].
In this thesis we will present studies of the existence of periodic steady states of
the extended Cahn–Hilliard equation in a full parameter space. We will analytically
describe steady states in the case of weak nonlinearity (solutions are close to trivial)
using perturbation theory. Besides single-wave solutions, described by Liu and
Goldenfeld in [32], we found regions where two-wave solutions coexist along with the
general type solutions. Numerical studies were done to find periodic steady states
in general situation without any assumptions regarding parameters.
We will also present linear stability analysis of described above steady states for
bounded disturbances using Floquet boundary conditions. Stability diagram will be
shown and comparison with the results of [32] will be presented.
2013-01-31T16:11:18Z
2013-01-31T16:11:18Z
2012
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/2852
eng
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/2855
2018-04-03T13:41:48Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_504
hdl_10344_20
An investigation into the integration of mathematics and science at junior cycle in Irish mathematics and science at junior cycle in Irish post primary schools
Treacy, Páraic
O'Donoghue, John
McClelland, George
mathematics
second level education
teaching
peer-reviewed
Within the mathematics education community there have been calls for a greater
range of assessment practices as well as a more holistic approach to learning as
research has shown that the current approach to instruction that has generally been
adopted is producing students who struggle to solve problems and display large
gaps in their Mathematical knowledge and understanding. One of the main
necessities, according to research, is the need for mathematics to be placed in
context and, thus, linked with other subjects. As such, a range of international
education groups (NCTM, NRC, SSMA, Curriculum Corporation) have lent their
support to the drive to integrate mathematics with other subject areas, especially
science, within second level education.
Attempts at integrating mathematics and science have been made but no
definitive, widely adopted teaching model has been developed to date. Research
suggests that hands-on, practical, pupil-centred, authentic activities should form a
central element when designing an effective model for the integration of
mathematics and science. The ‘Authentic Instruction’ model, developed by Fred
Newmann and his associates in the early 1990’s, provides the basis for a model
for the integration of mathematics and science as it is integrative in its very
nature, and there is considerable empirical evidence backing up its merits. The
author has taken the key elements of ‘Authentic Instruction’ and modified them to
produce a new model entitled ‘Authentic Integration’ which caters for the specific
needs of integration of mathematics and science. This model requires that each
lesson be based around a rich task which relates to the real world and ensures that
hands-on group work, inquiry and discussion are central to the lesson.
This teaching model was tested through an intervention which was carried out in
four Irish post-primary schools. Six lessons which integrated mathematics and
science were created for 2nd year pupils using the Authentic Integration model,
three of these lessons were implemented in each school. Analysis of the
intervention was completed using teacher interviews, assessment of pupil work,
pupil focus groups, and teacher questionnaires. It was found that the approach
employed positively affected pupil understanding; integration of mathematics and
science can be incorporated into regular tuition in Irish post primary schools; and
the teachers that completed the intervention displayed a very positive attitude
towards the approach, intimating that they would continue to implement the
practice in their classrooms.
Furthermore, testing of this model led to the creation of explicit design principles
for the integration of mathematics and science which will guide mathematics and
science teachers in the development of their own lessons to integrate the subjects.
2013-02-01T12:49:23Z
2013-02-01T12:49:23Z
2012
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/2855
eng
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/2863
2013-02-05T10:16:57Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_505
hdl_10344_244
hdl_10344_20
An investigation into the effects of introducing algebra using a function-based approach
Sterritt, Nicola
O'Donoghue, John
Liston, Miriam
mathematics syllabus
algebra
Ireland
peer-reviewed
Ireland is currently witnessing a major overhaul of its mathematics syllabus for second level education. This syllabus is known as ‘Project Maths’ and came about as a results of concerns relating to the mathematics performance of students in Ireland in international comparative studies such as the PISA (Program for International Student Assessment) tests (Close & Oldham 2005; Cosgrove, Shiel, Sofroniou, Zastrutzki & Shortt 2005; Perkins, Moran, Cosgrove and Shiel 2010; Oldham 2002, 2006).
The author found inspiration for this research when she identified concerns in her own classroom. These concerns were two-fold; firstly the author found that first year students began secondary school with a poor attitude towards mathematics and secondly, the author found that first year students had a lot of difficulty grasping and retaining basic algebraic concepts. The author followed an action research approach to implementing an intervention in her classroom aimed at overcoming these problems. In the first phase of this research, the author carried out a comprehensive review of literature on affect pertaining to mathematics education and on the teaching and learning of algebra. As a result of this review, the author decided to use a function-based approach to teaching algebra as a means of improving students understanding of basic algebra. A collaborative peer learning environment was chosen as the main pedagogical tool for improving attitude towards mathematics. The second phase of this research saw the development and implementation of an intervention in the author’s classroom during which fourth year students tutored first year students. Quantitative and qualitative data was gathered during this phase. The third phase comprised of an analysis of data, presentation of results and discussion of findings.
The data gathered produced a lot of contradicting and conflicting results. There was no significant change (p > 0.05) in either first or fourth year students’ overall attitude towards mathematics. Results indicate, however, that there was a significant increase (p < 0.05) in first year students understanding of basic algebra. This result may have significance for the Project Maths Development Team as they advocate a function-based approach to the teaching and learning of algebra in the new syllabuses. Due to the limited amount of students involved in the study, however, the author does not believe that these results can be generalised in a national or global sense.
2013-02-04T14:22:20Z
2013-02-04T14:22:20Z
2012
info:eu-repo/semantics/masterThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/2863
eng
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/2877
2021-01-13T16:04:01Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Height and weight bias: the influence of time
Shiely, Frances
Hayes, Kevin
Perry, Ivan J.
Kelleher, Cecily C.
BMI
height
weight
influence
peer-reviewed
Background: We have previously identified in a study of both self-reported body mass index (BMI) and clinically measured
BMI that the sensitivity score in the obese category has declined over a 10-year period. It is known that self-reported weight
is significantly lower that measured weight and that self-reported height is significantly higher than measured height. The
purpose of this study is to establish if self-reported height bias or weight bias, or both, is responsible for the declining
sensitivity in the obese category between self-reported and clinically measured BMI.
Methods: We report on self-reported and clinically measured height and weight from three waves of the Surveys of Lifestyle
Attitudes and Nutrition (SLÁN) involving a nationally representative sample of Irish adults. Data were available from 66 men
and 142 women in 1998, 147 men and 184 women in 2002 and 909 men and 1128 women in 2007. Respondents were
classified into BMI categories normal (,25 kg/m2), overweight (25–,30 kg/m2) and obese ($30 kg/m2).
Results: Self-reported height bias has remained stable over time regardless of gender, age or clinical BMI category. Selfreported
weight bias increases over time for both genders and in all age groups. The increased weight bias is most notable
in the obese category.
Conclusions: BMI underestimation is increasing across time. Knowledge that the widening gap between self-reported BMI
and measured BMI is attributable to an increased weight bias brings us one step closer to accurately estimating true obesity
levels in the population using self-reported data.
2013-02-11T12:52:13Z
2013-02-11T12:52:13Z
2012
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/2877
eng
PLoS One;8(1), e54386
http://dx.doi.org10.1371/journal.pone.0054386
info:eu-repo/semantics/openAccess
Public Library of Science
oai:ulir.ul.ie:10344/3049
2019-09-13T09:23:21Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Large population evolutionary games played within a life history framework
Ramsey, David
SFI
evolutionary game theory
game against the field
evolutionarily stable strategy
neighbourhood invasion strategy
polymorphism
peer-reviewed
In many evolutionary games, such as parental care games, the length of time spent playing a realisation
of the game is dependent on the strategy of an individual. Also, the payoff of a deserting
male cannot be defined in isolation from the strategies used in the population as a whole. Such games
should be defined as games against the field (large population games) rather than two-player games.
Several examples are presented to illustrate the theory of such games against the field.
2013-04-18T14:49:19Z
2013-04-18T14:49:19Z
2009
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3049
eng
Operations Research and Decisions;7(2), pp. 51-74
07/MI012
info:eu-repo/semantics/openAccess
Politechnika Wroclawska * Oficyna Wydawnicza
oai:ulir.ul.ie:10344/3088
2019-09-13T09:23:45Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
A large population parental care game:polymorphisms and feedback between patterns of care and the operational sex ratio
Ramsey, David
SFI
evolutionarily stable strategy
cycle time
Fisher condition
polymorphism
mixed strategy
peer-reviewed
This article presents a game theoretic model of parental care which models the feedback between patterns of care and the operational sex ratio. It is assumed here that males can be in one of two states: searching for a mate or breeding (including caring for their offspring). Females can be in one of three states: receptive (searching), non-receptive or breeding. However, these sets of states can be adapted to the physiology of a particular species. The length of time that an individual remains in the breeding state depends on the level of care an individual gives. When in the searching state, individuals find partners at a rate dependent on the proportion of members of the opposite sex searching. These rates are defined to satisfy the Fisher condition that the total number of offspring of males equals the total number of offspring of females. The operational sex ratio is not defined exogenously, but can be derived from the adult sex ratio and the pattern of parental care. Pure strategy profiles and so-called single sex stable polymorphisms, in which behaviour is varied within one sex, are derived analytically. The difference between mixed evolutionarily stable strategies and stable polymorphisms within this framework is highlighted. The effects of various physiological and demographic parameters on patterns of care are considered
2013-05-13T08:59:59Z
2013-05-13T08:59:59Z
2010
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3088
eng
Journal of Theoretical Biology;266(4), pp. 675-690
http://dx.doi.org/10.1016/j.jtbi.2010.07.024
07/MI/012
This is the author’s version of a work that was accepted for publication in Journal of Theoretical Biology. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Journal of Theoretical Biology, 266(4), pp. 675-690 doi:10.1016/j.jtbi.2010.07.024
info:eu-repo/semantics/openAccess
Elsevier
oai:ulir.ul.ie:10344/3089
2019-09-13T09:28:17Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Strategy dependent mortality in life history games
Ramsey, David
SFI
game theory
parental care games
computers
peer-reviewed
In games such as the war of attrition and
parental care games the length of time spent in a
realisation of the game is dependent on the strategy
used. Hence, there is a trade off between the mean
reward obtained per realisation of the game and the
mean number of games played per unit time. Such a
game should not be modelled using the standard twoplayer
form, but should be defined as a game against
the field (a large population game). In parental care
games, such an approach also enables us to define a
more consistent model, which takes into account, for
example, the obvious fact that each individual has one
parent of both sexes and that the ease with which a
male deserter can find a new partner depends on the
strategy profile used in the population. If the mortality
rate is independent of strategy, then each individual
should simply maximise the rate of producing offspring.
However, if mortality rates depend on strategy, then at
equilibrium an individual should maximise the number
of offspring produced during their lifetime. This paper
considers pure equilibria in a parental care game, in
which the mortality rate depends on an individual's
strategy.
2013-05-13T11:03:50Z
2013-05-13T11:03:50Z
2009
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3089
eng
Game Theory for Networks, 2009. GameNets '09. International Conference;pp. 339-346
http://dx.doi.org/10.1109/GAMENETS.2009.5137419
07/MI012
“© 2009 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
info:eu-repo/semantics/openAccess
IEEE Computer Society
oai:ulir.ul.ie:10344/3095
2014-07-01T15:44:18Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_20
hdl_10344_2626
Robust frailty modelling using non-proportional hazards models
Do Ha, II
MacKenzie, Gilbert
Korea Research Foundation
SFI
frailty models
Generalized time-dependent logistic (GTDL)
hierarchical likelihood
non-PH model
random effect
peer-reviewed
Correlated survival times can be modelled by introducing a random
effect, or frailty component, into the hazard function. For multivariate survival data
we extend a non-PH model, the generalized time-dependent logistic survival model, to
include random effects. The hierarchical-likelihood procedure, which obviates the need
for marginalization over the random effect distribution, is derived for this extended
model and its properties discussed. The extended model leads to a robust estimation
result for the regression parameters against the mis-specification of the form of the
basic hazard function or frailty distribution compared to PH-based alternatives. The
proposed method is illustrated by two practical examples and a simulation study which
demonstrate the advantages of the new model.
2013-05-15T11:54:41Z
2013-05-15T11:54:41Z
2010
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3095
eng
Statistical Modelling;10(3), pp. 315-332
http://dx.doi.org/10.1177/1471082X0801000304
KRF-2006-013-C00092
07/MI/012
© SAGE Publications
info:eu-repo/semantics/openAccess
SAGE Publications
oai:ulir.ul.ie:10344/3101
2019-09-13T09:21:28Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
The C/A polymorphism in intron 11 of the XPC gene plays a crucial role in the modulation of an individual’s susceptibility to sporadic colorectal cancer
Gil, Justyna
Ramsey, David
Stembalska, Agnieszka
Karpinski, Pawel
Pesz, Karolina A
Laczmanska, Izabela
Leszczynski, Przemyslaw
Grzebieniak, Zygmunt
Sasiadek, Maria Malgorzata
State Committee for Scientific Research, Polish Ministry for Scientific Research and Information Technology
SFI
colorectal cancer (CRC)
gene polymorphism
individual’s susceptibility to cancer
peer-reviewed
Background: Epidemiological data show that colorectal cancer (CRC) is the second
most frequent malignancy worldwide. The involvement of “minor impact genes” such as
XME and DNA-repair genes in the etiology of sporadic cancer has been postulated by other authors.
Aim: we focused on analyzing polymorphisms in DNA-repair genes in CRC. We
considered the following genes involved in DNA-repair pathways: base excision repair
(OGG1 Ser326Cys, XRCC1 Trp194Arg and Arg399Gln); nucleotide excision repair [XPA (- 4)G/A, XPC C/A (i11) and A33512C (Lys939Gln), XPD Asp312Asn and A18911C
(Lys751Gln), XPF Arg415Gln, XPG Asp1104His, ERCC1 C118T]; homologous
recombination repair [ NBS1 Glu185Gln, Rad51 135G/C, XRCC3 C18067 (Thr241Met)].
Material and methods: The study group consisted of 133 patients diagnosed with
sporadic CRC, while the control group was composed of 100 age-matched non-cancer
volunteers. Genotyping was performed by PCR and PCR-RFLP. Fisher’s exact test with a
Bonferroni correction for multiple testing was used.
Results: We found that: i) XPC C/A (i11) heterozygous variant is associated with
increased risk of CRC [OR is 2.07 (95% CI 1.1391,3.7782) p=0.038], ii) XPD A18911C
(Lys751Gln) is associated with decreased risk of CRC [OR=0.4497, (95% CI 0.2215,0,9131) p=0.031] for an individual with at least one A allele at this locus.
Conclusions: 1. the XPC C/A (i11) genotype is associated with an increased risk of sporadic colorectal cancer.
2. the NER pathway has been highlighted in our study, as a most important in modulation of individual susceptibility to sCRC.
2013-05-20T10:44:13Z
2013-05-20T10:44:13Z
2012
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3101
eng
Molecular Biology Reports;39(1), pp. 527-534
http://dx.doi.org/10.1007/s11033-011-0767-5
1423/P01/2007/32
07/MI/012
The original publication is available at www.springerlink.com
info:eu-repo/semantics/openAccess
Springer-Verlag
oai:ulir.ul.ie:10344/3102
2019-09-13T09:22:35Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_20
hdl_10344_2626
Detection of viral DNA sequences in sporadic colorectal cancers in relation to CpG island methylation and methylator phenotype
Karpinski, Pawel
Myszka, Aleksander
Ramsey, David
Kielan, Wojciech
Sasiadek, Maria Malgorzata
SFI
CIMP
virus
JCV
EBV
CRC
colorectal
peer-reviewed
There is evidence that insertion of viral DNA into a mammalian genome can lead to
alterations of methylation patterns. The aim of the present study was to examine the presence of DNA sequences of five human DNA viruses (assessed by PCR): JC polyoma virus (JCV), human adenovirus (AdV), Epstein-Barr virus (EBV), Kaposi sarcoma-associated herpesvirus (KSHV/HHV8) and human papillomavirus (HPV) in a cohort of 186 sporadic colorectal cancers (CRCs) and related these data with the methylation status of six CIMP-specific genes (MLH1, CACNA1G, NEUROG1, IGF2, SOCS1, RUNX3) and seven cancer-related genes markers (p16, MINT1, MINT2, MINT31, EN1, SCTR and INHBB) assessed by methylationspecific PCR in 186 and 134 CRC cases, respectively. The AdV, KSHV and HPV were detected in 4 (2%), 2 (1%) and 0 CRC cases, respectively and thus were excluded from further analyses. Althought, 19% and 9% of the CRCs were positive for EBV and JCV respectively, no associations between virus presence and CpG island methylation were found after correction for multiple testing. Our results demonstrate that the presence of DNA sequences of JCV and EBV in CRC is unrelated to the methylation of the 13 cancer-related CpG islands and CIMP.
2013-05-20T11:22:48Z
2013-05-20T11:22:48Z
2011
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3102
eng
2011;32(4), pp. 653-659
http://dx.doi.org/10.1007/s13277-011-0165-6
07/MI/012
The original publication is available at www.springerlink.com
info:eu-repo/semantics/openAccess
Springer-Verlag
oai:ulir.ul.ie:10344/3103
2019-09-13T09:21:53Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
The CpG island methylator phenotype correlates with long-range epigenetic silencing in colorectal cancer
Karpinski, Pawel
Ramsey, David
Grzebieniak, Zygmunt
Sasiadek, Maria Malgorzata
Blin, Nikolaus
State Committee for Scientific Research, Polish Ministry for Scientific Research and Information Technology
SFI
cytosine methylation
methylator phenotype
CIMP
gene silencing
long-range epigenetic silencing
LRES
peer-reviewed
2013-05-20T13:30:08Z
2013-05-20T13:30:08Z
2008
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3103
eng
Moelcular Cancer Research;6(4), pp. 585-591
1423/P01/2007/32, 2007-
07/MI/012
info:eu-repo/semantics/openAccess
American Association for Cancer Research
oai:ulir.ul.ie:10344/3112
2021-12-03T15:17:48Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
On the interval estimation of the parameters of a generalized time-dependent logistic model
Louzada-Neto, Francisco
MacKenzie, Gilbert
Cremasco, Caroline Pires
Ferreira-Silva, Paulo Henrique
Brazilian Organizations FAPESP
CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico – www.cnpq.br)
SFI
bootstrap method
coverage probability
Monte Carlo simulation
non-PH model
generalized time-dependent logistic
peer-reviewed
In order to accommodating crossing hazard curves, which are non-
proportional hazards, we consider in this paper a generalized time-dependent logistic
hazard survival model, which has a time-dependent term. The model is a wholly
parametric competitor for the Cox proportional hazard model. We compare different
procedures to compute confiddence intervals for the model parameters in presence of
random censoring. Our simulation study focus on the study of the coverage probabilities
of these different confidence intervals and on the significance levels of some hypothesis
tests. We discovered that parametric and non-parametric resampling methods can be
successfully used for hypothesis testing and generating precise confidence intervals for
the parameters even on small and moderate sized samples.
2013-05-22T11:21:36Z
2013-05-22T11:21:36Z
2011
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
gilbert.mackenzie@ul.ie
http://hdl.handle.net/10344/3112
eng
Revista Brasileira de Biometria;Biometric Brazilian Journal;29(3), pp. 512-519
http://jaguar.fcav.unesp.br/RME/biometria/instrucao_i.php
07/MI/012
info:eu-repo/semantics/openAccess
UNESP
oai:ulir.ul.ie:10344/3113
2019-05-01T12:10:11Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Modelling covariance structure in bivariate marginal models for longitudinal data
Xu, Jing
MacKenzie, Gilbert
SFI
longitudinal data
bivariate marginal models
covariance modelling
block triangular factorization
matrix logarithm
modelling log-innovation matrices
peer-reviewed
It can be more challenging and demanding to efficiently model the covariance matrices for
multivariate longitudinal data than for univariate case because of the correlations between
responses arising from multiple variables and repeated measurements over time. In addition to the more complicated covariance structures, the positive-definiteness constraint
is still the major obstacle in modelling covariance matrices as in univariate case. In this
paper, we develop a data-based method to model the covariance structures. Using this
method, the constrained and hard-to-model parameters of ∑i are traded in for uncon-
strained and interpretable parameters. Estimates of these parameters, together with the
parameters in the mean, are obtained by maximum likelihood approach, and the large-
sample asymptotic properties are derived when the observations are normally distributed.
A simulation is carried out to illustrate the asymptotics. Application to a set of bivariate
visual data shows that our method performs very well even when modelling bivariate
nonstationary dependence structures.
2013-05-22T13:42:17Z
2013-05-22T13:42:17Z
2012
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3113
eng
Biometrika;99(3), pp. 649-662
http:/dx.doi.org/10.1093/biomet/ass031
07/MI/012
This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Biometrika following peer review. The definitive publisher-authenticated version Modelling covariance structure in bivariate marginal models for longitudinal data, 2012,99(3), pp. 649-662 is available online at:http://dx.doi.org/10.1093/biomet/ass031
info:eu-repo/semantics/openAccess
Oxford University Press
oai:ulir.ul.ie:10344/3129
2021-07-09T08:51:06Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
How real is intention-to-treat (ITT) analysis in non-interventional post authorization safety studies? we can do better
Kiri, Victor A.
MacKenzie, Gilbert
SFI
cohort study
selection bias
case-control design
counter-matching
peer-reviewed
Although cohort studies which are based on intention-to-treat (ITT) approach offer a
simple design with data which are simpler to analyse and results easier to interpret,
such studies also intrinsically assume that any time-varying treatment effect that exits
can be adequately estimated by a fixed-effect component. However, such an
assumption may not reflect real-life drug use. Reflection of real-life clinical practice is a
major strength of epidemiologic safety studies. The failure to properly reflect reality may
result in effect under-estimation leading to false and irreproducible conclusions due to
exposure misclassification. In effect, the use of nested case-control design is a
concession that ITT in cohort design may not be adequate. But the nested design also
has its own sources of bias, including confounding by indication. We present an
overview of the counter-matched version of the nested case-control, case-crossover,
case-in-time, case series and case-cohort designs as alternatives in prospective postauthorization safety studies.
2013-06-05T15:01:37Z
2013-06-05T15:01:37Z
2009
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3129
eng
Current Drug Safety;4(2), pp. 137-142
http://www.benthamscience.com/cds/
07/MI/012
info:eu-repo/semantics/openAccess
Bentham Science Publishers
oai:ulir.ul.ie:10344/3130
2021-07-09T08:51:24Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_20
hdl_10344_2626
Programming challenges of sampling controls to cases from the dynamic risk sets in nested case control studies
Kiri, Victor A.
SFI
pharmacoepidemiological studies
real-life drug use
peer-reviewed
Pharmacoepidemiological studies based on the cohort design are simpler to analyse and their results easier to interpret. However, these may not reflect real-life drug use which is a major strength of such studies. The nested case-control design is often used instead to avoid the computational burden associated with time-dependent explanatory variables. Unlike the classical case-control design which is generally easy to programme, that of the nested case-control can pose a number of challenges. Subjects can be chosen as controls more than once and a subject who is chosen as a control can later become a
case. Indeed controls are chosen from among those in the cohort who are at risk of the event at that time (i.e. we sample from the risk set defined by the case). We highlight the main programming challenges of the design as well as describe and demonstrate approaches for resolution and appropriate implementation.
2013-06-06T08:23:26Z
2013-06-06T08:23:26Z
2012
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3130
eng
Pharmaceutical Programming;5(1/2), pp. 29-33
http://dx.doi.org/10.1179/1757092112Z.0000000004
07/MI/012
info:eu-repo/semantics/openAccess
Maney Publishing
oai:ulir.ul.ie:10344/3254
2013-08-21T13:55:11Z
hdl_10344_10
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hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_504
hdl_10344_20
Improving mathematics teaching at second level through the design of a model of teacher knowledge and an intervention aimed at developing teachers’ knowledge
O'Meara, Niamh
O'Donoghue, John
Gill, Olivia
mathematics
teaching
second level
Ireland
peer-reviewed
The importance of mathematics is recognised and acknowledged worldwide and its
importance as a school subject has been confirmed universally. A primary concern in
Ireland among educators, policy makers and the Department of Education and Skills
is the finding that many students complete their second level studies with a poor
grasp of mathematics and are not prepared for the mathematics they will face at third
level or in the workplace. Researchers now accept that the supply of well qualified
second level students in mathematics for higher education or the workplace is
crucially dependent upon the quality of teaching they receive especially in the
formative years. Teachers’ levels of knowledge helps determine the quality of
mathematics teaching and underpin much of what is done in the mathematics
classroom.
Research has shown that numerous attributes of effective teaching are affected by,
inter alia, a mathematics teacher’s knowledge base. Furthermore an extensive
knowledge base on the part of teachers will allow them to teach for understanding
and foster an appreciation of mathematics among their students while research also
suggests that this knowledge can result in increased uptake and attainment levels in
mathematics. However, despite such findings, research indicates that at the moment
teachers simply do not have a sufficient knowledge base to carry out their duties
effectively and as a result the teaching and learning of mathematics is being
detrimentally affected in Ireland and elsewhere worldwide.
Such considerations and findings led the author to investigate the issue of the
knowledge required for mathematics teaching. The research analysed the special
relationship between the teaching and learning of mathematics and teachers subject
knowledge. The author then focussed on defining a model of the knowledge base
required for teaching and examined the types of knowledge required in order to teach
mathematics effectively. The author then developed and supported, and validated
this model through a proof of concept approach involving an action research
Continuous Professional Development (CPD) initiative. This enabled the author to
see if her model is a ‘fit for purpose’ vehicle for improving of knowledge among
teachers and in turn improving the teaching and learning of mathematics in Ireland.
2013-07-30T14:45:49Z
2013-07-30T14:45:49Z
2011
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/3254
eng
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/3255
2013-07-31T13:32:00Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_504
hdl_10344_20
An investigation into the teaching and learning of applications of mathematics in senior-cycle schools in Ireland
Carroll, Brian
O'Donoghue, John
National Centre for Excellence in Mathematics and Science, Teaching and
Learning (NCE-MSTL)
mathermatics
Ireland
teaching
senior-cycle schools
peer-reviewed
Current practises in Irish mathematics classrooms generally fail to make the necessary
connections between mathematics and its place in real-life, as documents
from the NCCA and the Chief Examiners Report have shown (NCCA, 2005; State
Examinations Commission, 2005). This study focuses on the problem of improving
the teaching and learning of mathematics, particularly upper secondary level
in Ireland, by making a provision for the e ective teaching of applications. The
author anticipated the national focus on the use of applications in mathematics
education with the inception of ‘Project Maths’.
APOS theory was adapted for use in this study and the resultant approach has
been field tested in a small scale intervention in Irish Senior-Cycle schools. APOS
Theory is a purpose built theory for mathematics teaching which was developed by
Dubinsky (1996) and his colleagues in the Research for Undergraduate Mathematics
Education Community (RUMEC) for the purpose of mathematics education
at third level.
The author harnessed the three-stage approach employed by APOS Theory (Exploratory,
Implementation and Reflective Phase) to develop, pilot, implement and
evaluate the subsequent teaching intervention. Bajpai’s Integrated Approach (1975)
and the Harvard Calculus Approach (1991) influence the research design in that
they offer a perspective on introducing mathematical concepts through multiple
approaches (numerical, analytical, graphical, verbal) as opposed to the over-emphasis
on analytical techniques widely practised in schools. Their emphasis on applications,
modelling and case studies allows the author to achieve the overall aims
of the research project. Results of the intervention showed that students find mathematics
more interesting when taught through applications. In addition, the
intervention highlighted the issue of assessment in the teaching of applications
and modelling, where the participating students and teachers called for a review
of assessment procedures in senior-cycle mathematics here in Ireland
2013-07-30T15:29:07Z
2013-07-30T15:29:07Z
2011
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/3255
eng
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/3281
2019-05-02T07:48:09Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_20
hdl_10344_243
hdl_10344_504
Hydrophobicity, hydrophilicity and two-phase flow in the gas diffusion layer of a polymer electrolyte fuel cell
Gordon, Andrew
Vynnycky, Michael
O'Brien, Stephen B.G.
electrochemical devices
fuel
chemical energy
PEFCs
peer-reviewed
Polymer electrolyte fuel cells (PEFCs) are versatile electrochemical devices
that convert the chemical energy of a fuel, such as hydrogen, and an oxidant,
such as air-derived oxygen, directly into electricity, both cleanly and efficiently.
In spite of their promise as alternative energy sources, design issues remain
when the cell operates at high current density: condensing water vapour at
the reacting catalyst layer, on the cathode side of the cell, blocks the pores
in the gas diffusion layer (GDL), which is detrimental to cell performance.
Substantial experimental evidence indicates that using a hydrophobic, rather
than hydrophilic, GDL on the cathode alleviates the problem. However, whilst
existing theory confirms the advantages of using a hydrophobic GDL, it does
not simultaneously confirm the disadvantage of using a hydrophilic GDL. This
thesis uses a combination of asymptotic and numerical methods to investigate
this apparent anomaly by considering an isothermal, steady state, generalized
Darcy model for two-phase flow in a porous medium; mathematically, this
leads to a free-boundary problem to determine the location of the interface
between one-phase and two-phase flow. After extensive analysis, it is found
that the model predicts significant differences between the flow regimes found
in hydrophobic and hydrophilic GDLs. Furthermore, the model results show
that hydrophobic GDLs are found to lead to higher current density, and hence
better cell performance, than hydrophilic GDLs, as is the case in experiment.
The importance of temperature differences across the GDL is also analysed by
means of a non-isothermal model. It is found that temperature gradients in the
GDL significantly affect the cathode overpotential and outlet temperature at
which the onset of two-phase flow occurs; high enough overpotential can lead
to the return of gas-phase only flow, which is not the case in the isothermal
model
2013-08-06T13:22:09Z
2013-08-06T13:22:09Z
2013
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/3281
eng
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/3309
2015-05-05T19:12:04Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Microlocal analysis of SAR imaging of a dynamic reflectivity function
Felea, Raluca
Gaburro, Romina
Nolan, Clifford J.
SFI
moving SAR
peer-reviewed
In this article we consider four particular cases of Synthetic Aperture
Radar imaging with moving objects. In each case, we analyze
the forward operator F and the normal operator F∗F, which appear
in the mathematical expression for the recovered reflectivity function
(i.e. the image). In general, by applying the backprojection operator
F∗ to the scattered waveform (i.e. the data), artifacts appear in the
reconstructed image. In the first case, the full data case, we show
that F∗F is a pseudodifferential operator which implies that there is
no artifact. In the other three cases, which have less data, we show
that F∗F belongs to a class of distributions associated to two cleanly
intersecting Lagrangians Ip,l(Δ; Λ), where Λ is associated to a strong
artifact. At the and of the article, we show how to microlocally reduce
the strength of the artifact.
2013-08-12T15:10:49Z
2013-08-12T15:10:49Z
2013
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3309
eng
SIAM Journal on Mathematical Analysis;July
06/MI/005
info:eu-repo/semantics/openAccess
Society for Industrial and Applied Mathematics
oai:ulir.ul.ie:10344/3324
2015-05-05T19:07:15Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Determining the absorption in anisotropic media
Gaburro, Romina
Lionheart, William R. B.
EPSRC
optical tomography
non-peer-reviewed
The problem in Optical Tomography of determining the spacially dependent
absorption coefficient in an anisotropic medium with a-priori known strong
scattering is considered. The problem is modelled by the diffusion approximation
of the Radiative Transfer Equation and the time-harmonic case is studied. In this
particular situation the diffusion approximation leads to an elliptic second order partial
differential equation with complex variable coefficients which allows to treat the
problem equivalently to the inverse conductivity problem in Electrical Impedance Tomography
(EIT). Results of uniqueness and stability for the absorption coefficient are
proven by using the approach of the work in SIAM J. Math. Anal. 33 (2001), no. 1,
153–171 for the inverse conductivity problem in EIT
2013-08-14T14:16:58Z
2013-08-14T14:16:58Z
2010
info:eu-repo/semantics/preprint
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3324
eng
Inverse Problems & Imaging: Under revision
EP/FO33974/1
This publication is under revision to American Institute of Mathematical Sciences
info:eu-repo/semantics/openAccess
oai:ulir.ul.ie:10344/3312
2015-05-05T19:06:19Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Determining conductivity with special aniostropy by boundary measurements
Alessandrini, Giovanni
Gaburro, Romina
inverse conductivity problem
anisotropy
peer-reviewed
We prove results of uniqueness and stability at the boundary for the inverse problem
of electrical impedance tomography in the presence of possibly anisotropic conduct.ivities. We assume that the unknown conductivity has the forrn A = A(x, a(x)), where a(x) is an unknown scalar function and A(x, t) is a given matrix-valued function. We also deduce results of uniqueness in the interior among conductivities A obtained by piecewise analytic perturbations of the scalar term a.
2013-08-13T09:12:03Z
2013-08-13T09:12:03Z
2001
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3312
eng
SIAM Journal on Mathematical Analysis;33,(1), pp. 153-171
http://dx.doi.org/10.1137/S0036141000369563
© Society for Industrial and Applied Mathematics
info:eu-repo/semantics/openAccess
Society for Industrial and Applied Mathematics
oai:ulir.ul.ie:10344/3313
2015-05-05T19:08:46Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Enhanced imaging from multiply scattered waves
Gaburro, Romina
Nolan, Clifford J.
SFI
static object
microlocal analysis
peer-reviewed
Many imaging methods involve probing a material with a wave and
observing the back-scattered wave. The back-scattered wave measurements are
used to compute an image of the internal structure of the material. Many of
the conventional methods make the assumption that the wave has scattered
just once from the region to be imaged before returning to the sensor to be
recorded. The purpose of this paper is to show how this restriction can be
partially removed and also how its removal leads to an enhanced image, free
of the artifacts often associated with the conventionally reconstructed image.
2013-08-13T09:22:42Z
2013-08-13T09:22:42Z
2008
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3313
eng
Inverse Problems and Imaging;2(2), pp. 225-250
http://dx.doi.org/10.3934/ipi.2008.2.225
03/IN3/I401
info:eu-repo/semantics/openAccess
American Institute of Mathematical Sciences
oai:ulir.ul.ie:10344/3315
2015-05-05T19:13:34Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Recovering Riemannian metrics in monotone families from boundary data
Gaburro, Romina
Lionheart, William R. B.
SFI
inverse conductivity problem
anisotropy
Riemannian metrics
peer-reviewed
We discuss the inverse problem of determining the anisotropic
conductivity of a body described by a compact, orientable, Riemannian manifold M
with boundary @M, when measurements of electric voltages and currents are taken
on all of @M. Specifically we consider a one parameter family of conductivity tensors,
extending results obtained in [3] where the simpler Euclidean case is considered. Our
problem is equivalent to the geometric one of determining a Riemannian metric in
monotone one parameter family of metrics from its Dirichlet to Neumann map on @M.
2013-08-13T13:47:55Z
2013-08-13T13:47:55Z
2009
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3315
eng
Inverse Problems;25(4) 14pgs
http://dx.doi.org/10.1088/0266-5611/25/4/045004
03/IN3/I401
© Institute of Physics Publishing
info:eu-repo/semantics/openAccess
Institute of Physics Publishing
oai:ulir.ul.ie:10344/3317
2015-05-05T19:12:44Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Microlocal analysis of synthetic aperture radar imaging in the presence of a vertical wall
Gaburro, Romina
Nolan, Clifford J.
SFI
enhanced image of SAR
vertical wall
peer-reviewed
We consider the problem of imaging a target located nearby a perfectly reflective
vertical wall by making use of a SAR system in the case where a single pass is made over
the scene of which we expect to be able to reconstruct a two-dimensional image. Many of the
conventional methods make the assumption that the wave has scattered just once from the
region to be imaged before returning to the sensor to be recorded. The purpose of this paper
is to give a brief idea about how this restriction can be partially removed from a microlocal
analysis point of view, in the case where the radar is operating with a poor directivity. The
simple case where the antenna is flying perpendicularly to the wall is presented here, while a
more in-depth study of this method will be analyzed elsewhere.
2013-08-13T14:38:22Z
2013-08-13T14:38:22Z
2008
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3317
eng
Journal of Physics: conference series;124(1) 12 pgs
http:dx.doi.org/10.1088/1742-6596/124/1/012025
03/IN3/I401
06/MI/005
info:eu-repo/semantics/openAccess
Institute of Physics
oai:ulir.ul.ie:10344/3316
2015-05-05T19:11:24Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
The local Caldero'n problem and the determination at the boundary of the conductivity
Alessandrini, Giovanni
Gaburro, Romina
inverse conductivity problem
anisotropy
local data
peer-reviewed
2013-08-13T14:19:16Z
2013-08-13T14:19:16Z
2009
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3316
eng
Communications in Partial Differential Equations;34(8), pp. 918-936
http://dx.doi.org/10.1080/03605300903017397
This is an electronic version of an article published in Communications in Partial Differential Equations;34 (8), pp. 918-936. Available online at http://dx.doi.org/10.1080/03605300903017397
info:eu-repo/semantics/openAccess
Taylor & Francis
oai:ulir.ul.ie:10344/3314
2015-05-05T19:10:25Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Imaging from multiply scattered waves
Gaburro, Romina
Nolan, Clifford J.
Dowling, Thomas
Cheney, Margaret
ultrasonic
imaging
backprojection
peer-reviewed
We consider the problem of imaging in a region where ultrasonic waves are multiply scattered. A transducer
emits ultrasonic pulses in tissue where they scatter from a heterogeneity (e.g. a tumor) in the region of interest
(ROI). The reflected signals are recorded and used to produce an image of tissue. Many of the conventional
imaging methods assume the wave has scattered just once (Born-approximation) from the heterogeneity before
returning to the sensor to be recorded. In reality, waves can scatter several times before returning to the detector.
The purpose of this paper is to show how this restriction (the Born approximation or weak, single-scattering
approximation) can be partially removed by incorporating a-priori known environmental scatterers, such as a
cavity wall or bones into the background velocity model in the context of acoustic medical imaging. We also
show how the partial removal of the Born approximation assumption leads to an enhanced angular resolution of
heterogeneities that are present. We will illustrate our method using a locally planar scatterer, which is one of
the simplest possible environments for the scatterer.
2013-08-13T13:26:16Z
2013-08-13T13:26:16Z
2007
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3314
eng
SPIE Conference on Medical Imaging;6513, article id 651304
http://dx.doi.org/10.1117/12.712569
Copyright © 2007 Society of Photo-Optical Instrumentation Engineers. One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper are prohibited.
info:eu-repo/semantics/openAccess
Society of Photo-Optical Instrumentation Engineers
oai:ulir.ul.ie:10344/3325
2021-12-01T09:55:24Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Solar Reflector Design
Bandeira, Afonso
Bell, Christopher G.
Charpin, Jean P.F.
Gaburro, Romina
Soussi, Sofiane
Wilson, Eddie R.
SFI
solar reflector
inverse problem
peer-reviewed
The design of solar panels is investigated. Different aspects of this problem are presented. A
formula averaging the solar energy received on a given location is derived first. The energy received by the collecting solar panel is then calculated using a specially designed algorithm. The
geometry of the device collecting the energy may then be optimised using different algorithms.
The results show that for a given depth, devices of smaller width are more energy efficient than
those of wider dimensions. This leads to a more economically efficient design.
2013-08-14T14:18:44Z
2013-08-14T14:18:44Z
2009
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3325
eng
Proceeding of the Seventy European Study Group with Industry (EGSI70);pp. 183-210
06/MI/005
info:eu-repo/semantics/openAccess
oai:ulir.ul.ie:10344/3323
2018-08-07T07:56:53Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Haptic Touchscreens
Cooker, Mark
Cribbin, Laura B.
Dellar, Paul
Fitt, Alistair
Gaburro, Romina
Gibb, Tony
Kennedy, James
King, John
Kubat, Irnis
Lapin, Vladimir Nikolaevich
Lee, William T.
Murphy, Ellen
Nolan, Clifford J.
Parker, Joseph
Power, Oliver
Timoney, Catherine M.
SFI
study group
touchscreen
non-peer-reviewed
Background. The development of haptic touchscreens, that is touchscreens with the ability to mimic the feel of
a real keyboard, would be a significant advance in the mobile phone and tablet market. This report investigates
one possible route to developing such touchscreens using piezoelectric actuators placed at the edge of the screen
and driven at a range of frequencies.
Scope. The report addresses the following questions: Can an array of piezoelectric transducers placed round
the edge of the screen create localised vibrations in the right physiological range to produce the sensation of a
keyboard? If so how many transducers are needed? Where should they be placed? How should they be driven?
We consider both the excitation of longitudinal and transverse waves but do not discuss surface waves.
Methods. We first consider the full inverse problem in which a key shaped vibration is to be constructed by
driving a touchscreen embedded in a phone. We argue that a useful subproblem is to construct a localised
vibration in a one dimensional beam driven at one end. If such solutions do exist, that would (1) provide
strong evidence that solutions to the full inverse problem do exist, (2) act as good initial starting points towards
solutions of the full inverse problem.
Results. We show that in the case of longitudinal waves the mathematical formalism set up for sonar can be
exploited. In the case of transverse waves the system is highly dispersive and so a ready-made formalism does
not exist. However we show that localised solutions can likewise be constructed.
Conclusions and Recommendations. Our results suggest that it is indeed possible to construct virtual keyboards
by driving the edges of a touchscreen. The minimum number of transducers needed is two although
we expect that using more would increase resolution. However, before a practical implementation can be made
there is still a great deal of work to be done both on the simplified models and on the full problem.
2013-08-14T13:50:37Z
2013-08-14T13:50:37Z
2011
info:eu-repo/semantics/conferenceObject
all_ul_research
http://hdl.handle.net/10344/3323
eng
Proceedings of the Eighty-Second European Study Group with Industry;pp. 51-73
06/MI/005
info:eu-repo/semantics/openAccess
oai:ulir.ul.ie:10344/3329
2015-05-05T19:07:57Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Enhanced angular resolution from multiply scattered waves
Nolan, Clifford J.
Cheney, Margaret
Dowling, Thomas
Gaburro, Romina
SFI
IPAM
AFOSR
SAR
multiple scattering
peer-reviewed
Multiply scattered waves are often neglected in imaging methods;
largely because of the inability of popular algorithms to deal with the associated nonlinear
models. This paper shows that by incorporating a known environment into the
background model, we can retain both the benefits of imaging techniques based on
linear models, as well as obtaining different views of the target scatterer. The net
result is an enhanced angular resolution of the target to be imaged.
We carry out our analysis in the context of Synthetic Aperture Radar (SAR)
imaging, which is used to produce an image of a region on the earth’s surface (the
target scatterers being buildings, etc). A plane or satellite carrying an antenna moves
along a flight track, emitting pulses of electromagnetic radiation, which scatter off
the ground, and the scattered radio waves are detected with the same antenna. The
received signals are then used to produce an image of the terrain. We consider the
case where the target we want to image is situated in the vicinity of an a-priori known
reflecting wall. This is one of the simplest possible environments for the scatterer,
and we will illustrate the enhanced angular resolution in this situation.
Although we carry out our analysis here in the context of SAR, our technique is a
general enough that it can be adapted to many imaging modalities, such as acoustics,
ultrasound, elasticity, etc. The extension of the method to other more complicated
environments is also possible.
2013-08-15T13:04:30Z
2013-08-15T13:04:30Z
2006
info:eu-repo/semantics/preprint
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3329
eng
Inverse Problems;22(5), pp. 1817-1834
http://dx.doi.org/10.1088/0266-5611/22/5/017
03/IN3/I401
FA9550-06-1-0017
This is a preprint of article submitted to Institute of Physics Publishing
info:eu-repo/semantics/openAccess
Institute of Physics Publishing
oai:ulir.ul.ie:10344/3646
2014-07-01T15:45:53Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_20
hdl_10344_504
hdl_10344_243
Survival modelling with frailty
Lynch, Joseph
MacKenzie, Gilbert
IRCSET
data analysis
breast cancer
GTDL
PH Weibull model
peer-reviewed
In the survival analysis literature, the standard model for data analysis is the
semi-parametric Proportional Hazard (PH) model of Cox (1972). MacKenzie
(1996) introduced the Generalised Time Dependent Logistic (GTDL) family
of non-PH parametric survival models, which compete with Cox’s PH model.
This thesis develops the GTDL model side-by-side with the PH Weibull
model.
In many datasets, some attributes that might be deemed relevant may not
be available. The effect of the unmeasured covariates can be quantified in
a variety of ways. The technique employed here is to incorporate a random
effect, called frailty, into both the Weibull and GTDL models. Further model
generalisation is effected by including covariates in the frailty dispersion
parameters, thus leading to structured dispersion models (Lee and Nelder,
2001). The PH Piecewise Exponential model is also developed and it is seen
to not accommodate frailty.
These models are used to analyse a large breast cancer registry dataset. The
goodness of fit of each model is evaluated by use of a modified χ2 statistic. A
comparison is also drawn between the survival predictions of the Cox model
and the Nottingham Prognostic Index, which is the model used by physicians
to predict survival from breast cancer.
Multivariate Weibull and GTDL models, which are capable of handling more
than one survival component simultaneously, are also developed.
2014-01-30T15:00:34Z
2014-01-30T15:00:34Z
2011
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/3646
eng
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/3761
2021-01-13T16:07:51Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
Temporal trends in misclassification patterns of measured and self-report based body mass index categories - findings from three population surveys in Ireland
Shiely, Frances
Perry, Ivan J.
Lutomski, Jennifer E.
Harrington, Janas M.
Kelleher, Cecily C.
McGee, Hannah
Hayes, Kevin
Health Promotion and Policy Unit of the Department of Health and Children
nutrition examination survey
national-health
weight
height
obesity
prevalence
accuracy
validity
bias
peer-reviewed
Background: As the use of self-reported data to classify obesity continues, the temporal change in the accuracy of self-report measurement when compared to clinical measurement remains unclear. The objective of this study was to examine temporal trends in misclassification patterns, as well as sensitivity and specificity, of clinically measured versus self-report based body mass index (BMI) from three national lifestyle surveys over a 10-year period. Methods: The Surveys of Lifestyle Attitudes and Nutrition (SLAN) were interview based cross-sectional survey/measurements involving nationally representative samples in 1998, 2002 and 2007. Data from a subsample of both self-reported and measured height and weight were available from 66 men and 142 women in 1998, 147 men and 184 women in 2002 and 909 men and 1128 women in 2007. Respondents were classified into the BMI categories normal (= 30 kg m(-2)). Results: Underreporting of BMI increased across the three surveys (14%-> 21%-> 24%; p = 0.002). Sensitivity scores for the normal category exceeded 94% in all three surveys but decreased for the overweight (75%-> 68%-> 66%) and obese categories (80%-> 64%-> 53%). Simultaneously, specificity levels remained high. Conclusions: BMI values based on self-reported determinations of height and weight in population samples are underestimating the true prevalence of the obesity epidemic and this underestimation is increasing with time. The decreased sensitivity and consistently high specificity scores in the obese category across time, highlights the limitation of self-report based BMI classifications and the need for simple, readily comprehensible indicators of obesity.
PUBLISHED
peer-reviewed
2014-04-04T10:12:36Z
2014-04-04T10:12:36Z
2010
2014-04-04T09:09:16Z
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
Shiely, F; Perry, IJ; Lutomski, J; Harrington, J; Kelleher, CC; Mcgee, H; Hayes, K (2010) 'Temporal trends in misclassification patterns of measured and self-report based body mass index categories - findings from three population surveys in Ireland'. BMC PUBLIC HEALTH, 10 .
1471-2458
http://hdl.handle.net/10344/3761
10.1186/1471-2458-10-560
BMC Public Health
eng
BMC Public Health;10: 560
http://www.biomedcentral.com/1471-2458/10/560
info:eu-repo/semantics/openAccess
BioMed Central
oai:ulir.ul.ie:10344/3822
2019-04-03T11:54:51Z
hdl_10344_10
hdl_10344_9
hdl_10344_20
The impact of adjustment for socioeconomic status on comparisons of cancer incidence between two European countries
Donnelly, David W.
Hegarty, Avril C.
Sharp, Linda
Carsin, Anne-Elie
Deady, Sandra
McCluskey, Neil
Comber, Harry
Gavin, Anna
Public Health (Agency) Northern Ireland
HRB
cancer
socioeconomic status
SES
Northern Ireland
Republic of Ireland
peer-reviewed
Background. Cancer incidence rates vary considerably between countries and by socioeconomic status (SES). We investigate the
impact of SES upon the relative cancer risk in two neighbouring countries. Methods. Data on 229,824 cases for 16 cancers diagnosed
in 1995–2007 were extracted from the cancer registries in Northern Ireland (NI) and Republic of Ireland (RoI). Cancers in the two
countries were compared using incidence rate ratios (IRRs) adjusted for age and age plus area-based SES. Results. Adjusting for SES
in addition to age had a considerable impact on NI/RoI comparisons for cancers strongly related to SES. Before SES adjustment,
lung cancer incidence rates were 11% higher for males and 7% higher for females in NI, while after adjustment, the IRR was not
statistically significant. Cervical cancer rates were lower in NI than in RoI after adjustment for age (IRR: 0.90 (0.84–0.97)), with
this difference increasing after adjustment for SES (IRR: 0.85 (0.79–0.92)). For cancers with a weak or nonexistent relationship to
SES, adjustment for SES made little difference to the IRR. Conclusion. Socioeconomic factors explain some international variations
but also obscure other crucial differences; thus, adjustment for these factors should not become part of international comparisons
2014-05-16T13:11:52Z
2014-05-16T13:11:52Z
2013
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3822
eng
Journal of Cancer Epidemiology;Article ID 612514
http://dx.doi.org/10.1155/2013/612514
info:eu-repo/semantics/openAccess
Hindawi Publishing Corporation
oai:ulir.ul.ie:10344/3855
2014-06-07T00:10:08Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_20
hdl_10344_2626
Multi-parameter regression survival models
Burke, Kevin
MacKenzie, Gilbert
SFI
IRCSET
multi-parameter regression survival models
non-PH models
shape and scale regression
time-dependent hazards
peer-reviewed
The proportional hazards (PH) assumption in survival analysis may
not always be appropriate. If data do not obey the assumption then we will
reach incorrect conclusions by making it. For example we may find a covariate
to be statistically insignificant when in fact it is important, but on a non-PH
scale. Even if a PH model does pick up the statistical significance of such a
covariate, the nature of the effect of the covariate on survival, as determined by
this simplistic model, will clearly be incorrect. We introduce a regression-based
extension of parametric PH modelling which we call multi-parameter regression,
MPR, modelling.
2014-06-06T15:06:23Z
2014-06-06T15:06:23Z
2013
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3855
eng
28th International Workshop on Statistical Modelling,Vito M.R. Muggeo, Vincenza Capursi, Giovanni Boscaino, Gianfranco Lovison (Eds.);
http://www.statmod.org/workshops.htm
07/MI012
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/3869
2019-09-13T09:24:06Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
A likelihood ratio test for detection of single nucleotide polymorphisms (SNPs)
Sheikhi, Ali
Ramsey, David
SFI
single nucleotide polymorphisms
allele
genome sequencing
peer-reviewed
A single nucleotide polymorphism or SNP is a site of the genome
where variation occurs within a population. Almost all SNPs have only two alleles
(variants). In this work, we consider a statistical method based on a likelihood
ratio test to detect these SNPs. We will also present some initial results of the
analysis of real genome sequence data.
2014-06-30T15:54:47Z
2014-06-30T15:54:47Z
2012
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3869
eng
Proceedings of the 27th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
07MI012
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/3870
2014-07-02T00:09:06Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Relation between obesity and depression using structural equation modelling
Sheikhi, Ali
Janghorbani, Mohsen
Soleimani, Bahram
SFI
SEM
LISREL
obesity
depression
peer-reviewed
no abstract available
2014-07-01T08:30:30Z
2014-07-01T08:30:30Z
2010
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3870
eng
CASI Conference;
http://www.istat.ie/casi.php?subLookup=26
info:eu-repo/semantics/openAccess
Irish Statistical Association
oai:ulir.ul.ie:10344/3871
2019-09-13T09:27:28Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Statistical methods for the detection of single nucleotide polymorphisms (SNPs) using new generation genome sequencers
Sheikhi, Ali
Ramsey, David
SFI
statistical methods
genome sequencing
peer-reviewed
Genome sequencing includes methods and technologies that are used
for determining the order of nucleotides (A, T, C or G) along a DNA
sequence. A single nucleotide polymorphism or SNP is a DNA sequence
variation occurring when a single nucleotide in the genome differs within
population members. Initially, we consider a particular site under a model
where there are just two possible alleles. The following results can be then
adapted to the case in which all four possible alleles (variants) may occur.
The most common (rare) allele is termed the major (minor) allele respectively.
2014-07-01T08:46:57Z
2014-07-01T08:46:57Z
2012
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3871
eng
2012 CASI Proceedings;
info:eu-repo/semantics/openAccess
Irish Statistical Association
oai:ulir.ul.ie:10344/3907
2019-09-13T09:22:59Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Global DNA methylation status in laryngeal cancer
Stembalska, Agnieszka
Leszczynski, Przemyslaw
Gil, Justyna
Ramsey, David
Pitala, Grzegorz
Maciejczyk, Adam
Frączek, Marcin
SFI
epigenetic
DNA hypomethylation
laryngeal cancer
head and neck cancer
peer-reviewed
Laryngeal squamous cell carcinoma (LSCC) belongs to the heterogeneous group of head and neck cancers. In the etiology of LSCC, beside important environmental factors, genetic and epigenetic factors play a role in defining an individual's susceptibility to LSCC. One such epigenetic factor is DNA hypomethylation, which due to the large heterogeneity of the tissue, and invasiveness of the methods used, is often evaluated in easily available tissue, such as peripheral blood, for cancer screening.
In this study we evaluated global DNA methylation status in laryngeal cancer tissues compared to normal laryngeal tissues and peripheral blood leukocytes in a homogeneous group of 72 patients with LSCC using a UPLC-based method (ultra performance liquid chromatography) to assess the total content of 5‘-methylcytosine.
Among the 72 patients, aged from 43 to 86 (mean 59.19, standard deviation 7.99), were 64 men and 8 women. A survey of the patients was carried out regarding their age at onset, exposure to environmental carcinogens (alcohol, cigarettes, etc.), the type of treatment, duration of treatment from the time of diagnosis and family history. Each tumor was characterized in terms of clinical and pathological features.
We found DNA hypomethylation both in tumor tissue and normal tissue (about 56% and 49% of tumor and normal tissues, respectively, were substantially hypomethylated. There was a highly significant correlation between the levels of 5‘-methylcytosine in these two types of tissue (p = 0.001, Spearman‘s test for correlation). The level of 5-methylcytosine in blood leukocytes was higher than in cancerous and normal tissues. A negative correlation was found between tumor grade and blood levels of 5-methylcytosine.
The level of leukocyte DNA methylation measured using total 5-methylcytosine content cannot be used as a surrogate marker for genome methylation status in cancer tissues. Further studies are necessary to determine the correlation between the tumor grade and blood levels of 5-methylcytosine.
2014-07-23T11:30:19Z
2014-07-23T11:30:19Z
2014
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3907
10.1002/hed.23315
eng
Head and Neck;36 (3), pp. 419-424
http://dx.doi.org/10.1002/hed.23315
This is the author's version of the following article:The definitive version is available at www.blackwell-synergy.com
info:eu-repo/semantics/openAccess
Wiley
oai:ulir.ul.ie:10344/3873
2019-09-13T09:24:27Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_20
hdl_10344_2626
Optimal DNA pooling for the detection of single nucleotide polymorphisms
Ramsey, David
Futschik, Andreas
SFI
genome sequencing
optimal pooling
single nucleotide polymorphisms
peer-reviewed
We consider the optimal pooling of DNA to detect single nucleotide
polymorphisms (SNPs), sites along the genome at which a population shows variation.
The focus is on the detection of low frequency variants. Pooling individuals
increases the probability that a rare variant appears in the sample. However, as
the pool size increases, the mean number of reads from an individual decreases,
making it harder to distinguish reads of a rare variant from errors. A hypothesis
test for the detection of SNPs is defined. On the basis of this test, we determine
the asymptotically optimal pool size given the parameters of the genome
sequencer used, the number of lanes available and a specified significance level.
2014-07-01T13:41:50Z
2014-07-01T13:41:50Z
2011
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3873
eng
Proceedings of the 26th International Workshop on Statistical Modelling;
http://www.statmod.org/workshops.htm
07MI012
info:eu-repo/semantics/openAccess
IWSM
oai:ulir.ul.ie:10344/3874
2019-09-13T09:26:52Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Protein tyrosine phosphatase receptor-like genes are frequently hypermethylated in sporadic colorectal cancer
Laczmanska, Izabela
Karpinski, Pawel
Bebenek, Marek
Sedziak, Tomasz
Ramsey, David
Szmida, Elżbieta
Sasiadek, Maria Malgorzata
State Committee for Scientific Research, Polish Ministry for Scientific Research and Information Technology
European Social Fund, Human Capital, National Cohesion Strategy
SFI
colorectal cancer
methylation
protein tyrosine phosphatase receptor-like
PTPRM
PTPRT
PTPRR
PTPRZ1
peer-reviewed
Introduction: The activity of phosphatases could be influenced by genetic, as well as epigenetic alterations. In our study we have investigated the methylation status of four PTPRs: PTPRM, PTPRT, PTPRR and PTPRZ1, which were pre-selected using microarray techniques as being alternatively methylated in sporadic colorectal cancer.
Materials and methods: The analyses were carried out on 131 surgical specimens obtained from sporadic colorectal cancer patients. The methylation status of the four genes was examined using MSP.
Results: The analysis of promoter methylation using an Illumina 27K microarray revealed four protein tyrosine phosphatases PTPRM, PTPRT, PTPRR and PTPRZ1 as being hypermethylated with beta-value ≥ 0.2 and p≤0.05. Subsequent analysis using MSP confirmed these observations - the frequency of promoter methylation was significantly higher in tumor cells compared to matched normal tissue for each of the analyzed genes. There was no association observed between the methylation status of PTPRs and either CIMP, K-ras (codon 12) and BRAF (exon 15, V600E) mutations or tumor localization (proximal/distal).
The results of our study show a statistically significant difference between promoter methylation in cancerous and healthy tissue. This result supports the hypothesis that the PTPR family plays an important role in the etiology of colorectal cancer.
2014-07-01T14:43:59Z
2014-07-01T14:43:59Z
2013
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3874
eng
Journal of Human Genetics;58 (1), pp. 11-5
http://dx.doi.org/ 10.1038/jhg.2012.119
(grant no. N N401 601438), 2010-2013
Contract No:UDA-POKL 04.01.01-00-010/08-00
07/MI012
info:eu-repo/semantics/openAccess
Nature Publishing Group
oai:ulir.ul.ie:10344/3899
2019-11-07T15:18:53Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_20
hdl_10344_2626
Assessment of three epigenotypes in colorectal cancer by combined bisulphite restriction analysis.
Karpinski, Pawel
Szmida, Elżbieta
Misiak, Blazej
Ramsey, David
Leszczynski, Przemyslaw
Bebenek, Marek
Sedziak, Tomasz
Grzebieniak, Zygmunt
Jonkisz, Anna
Lebioda, Arleta
Sasiadek, Maria Malgorzata
SFI
colorectal cancer
epigenotypes
methylation
methylator
peer-reviewed
Background: Recent investigations have demonstrated the clear heterogeneity of sporadic colorectal cancer (CRC) with regard to CpG island methylation. Two unsupervised cluster analyses revealed that CRCs form three distinct DNA methylation subsets, which are referred to as the high-, intermediate- and low-methylation epigenotypes (HME, IME, and LME, respectively). A recent study by Yagi et al. found a fairly sensitive and specific identification of HME, IME and LME using two marker panels analysed by MALDI-TOF mass spectrometry (MassARRAY). However, the expensive equipment required for this method substantially increases the cost and complexity of the assay.
Findings: In this article, we demonstrate the assessment of HME, IME and LME in a group of 233 sporadic CRCs using seven markers proposed by Yagi et al. The DNA methylation of each marker was quantified using combined bisulphite restriction analysis (COBRA) together with an analysis of various genetic factors associated with CRC (the BRAF and KRAS mutations and microsatellite instability (MSI)). The baseline methylation of each marker was generated from pooled DNA isolated from 50 normal colon tissues. Conclusions: We demonstrate that the correlation of HME, IME and LME epigenotyped by COBRA using different molecular classifiers is similar to that achieved by MassARRAY. Therefore, epigenotyping CRCs using COBRA is a simple, specific and cost-effective method that has the potential to be widely used in CRC research.
2014-07-22T10:19:11Z
2014-07-22T10:19:11Z
2012
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3899
eng
Molecular Carcinogenesis;51, (12), pp. 1003-1008
http://dx.doi.org/10.1002/mc.20871
07/MI/012
This is the author's version of the following article:The definitive version is available at www.blackwell-synergy.com"
info:eu-repo/semantics/openAccess
Wiley
oai:ulir.ul.ie:10344/3900
2019-09-13T09:26:25Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Polymorphisms in methyl-group metabolism genes and risk of sporadic colorectal cancer with relation to the CpG island methylator phenotype .
Karpinski, Pawel
Myszka, Aleksander
Ramsey, David
Misiak, Blazej
Gil, Justyna
Laczmanska, Izabela
Grzebieniak, Zygmunt
Sebzda, Tadeusz
Smigiel, Robert
Stembalska, Agnieszka
Sasiadek, Maria Malgorzata
SFI
cytosine methylation
colorectal cancer
methylator phenotype
CIMP
gene silencing
peer-reviewed
The CpG island methylator phenotype (CIMP), together with extensive promoter methylation, is regarded as one of the mechanisms involved in colorectal carcinogenesis (CRC). The mechanisms underlying the presence of CIMP in sporadic colorectal cancer are poorly understood. Genes involved in methyl-group metabolism are likely to affect DNA methylation and thereby influence an individual's susceptibility to CIMP. To test this hypothesis, we examined the potential association between the polymorphisms of MTHFR 677C>T, TS 5’UTR 2R/3RG>C, TS 3’UTR 1494del6, MTHFD1 401G>A, DNMT3B -149C>T and DNMT3B -283T>C and the presence of CIMP in a group of 186 sporadic CRC cases and 100 controls. The CIMP status of the tumors was determined by a panel of five markers (CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1), which was also followed by analysing hMLH1 methylation and BRAF V600E mutation. Individuals with TS 3R/3R had an increased risk of CIMP- colorectal cancer (OR = 2.38, 95% CI = 1.0-5.7; P = 0.042, Fisher's exact test) when compared with 2R/2R homozygotes. Individuals with DNMT3B -283 CC reduced risk of CIMP+ colorectal cancer (OR = 0.220, 95% CI = 0.0226-1.07; P = 0.046, Fisher's exact test) when compared to -283 TT carriers. This study provides some support to the hypothesis that methyl-group metabolism plays a role in the etiology of both CIMP+ and CIMP - colorectal cancers.
2014-07-22T11:17:42Z
2014-07-22T11:17:42Z
2010
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3900
eng
Cancer Epidemiology;34 (3), pp. 338-344
http://dx.doi.org/10.1016/j.canep.2010.03.002
This is the author’s version of a work that was accepted for publication in Cancer Epidemiology. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Cancer Epidemiology, 2010, 34 (3), pp. 338-344, http://dx.doi.org/10.1016/j.canep.2010.03.002
info:eu-repo/semantics/openAccess
Elsevier
oai:ulir.ul.ie:10344/3901
2019-09-13T09:26:03Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Partnership formation with age-dependent preferences
Alpern, S.
Katrantzi, I.
Ramsey, David
SFI
game theory
partnership formation
policy iteration
equilibrium profile 91A13, 91A25
peer-reviewed
We analyze a model of partnership formation in which players’ preferences are based on the
age of a prospective partner. There are two classes of individuals, called for convenience
here male and female. Males and females are fertile for the same length of time, normalized
to one unit. A male enters the mating pool at age 0 and meets prospective partners
according to a Poisson process. At equilibrium, he accepts a female if the utility from
mating exceeds the expected utility from future search, which depends on the acceptance
strategies of all males and females and the corresponding steady-state distribution of age
in the pool of unmated individuals. Females face an analogous problem. Mating pairs are
only formed by mutual consent and individuals leave the pool of unmated individuals on
finding a mating partner or reaching the age of 1. A policy iteration algorithm is used
to determine the equilibrium acceptance strategies and the corresponding steady-state
distribution of the age of individuals in the mating pool. Two examples are presented.
2014-07-22T13:03:31Z
2014-07-22T13:03:31Z
2013
info:eu-repo/semantics/preprint
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3901
eng
European Journal of Operational Research;225 (1), pp. 91-99
http://dx.doi.org/10.1016/j.ejor.2012.09.012
07/MI012
This is the author’s version of a work that was accepted for publication in European Journal of Operational Research. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in European Journal of Operational Research, 225 (1), pp. 91-99, http://dx.doi.org/10.1016/j.ejor.2012.09.012,
info:eu-repo/semantics/openAccess
Elsevier
oai:ulir.ul.ie:10344/3902
2019-09-13T09:27:53Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_2626
hdl_10344_20
Statistical tests for the detection of single nucleotide polymorphisms using DNA pooling
Ramsey, David
Futschik, Andreas
SFI
genetics
single nucleotide polymorphisms
SNPs
DNA pooling
peer-reviewed
An important problem in genetics is detecting single nucleotide polymorphisms (SNPs),
sites along the genome at which a population shows variation. The focus is on the detection
of rare variants. Pooling individuals allows us to increase the probability that a rare variant
appears in the sample. However, as the pool size increases, the mean number of reads from an
individual decreases, making it harder to distinguish reads of a rare variant from errors. This
paper compares three statistical tests for detecting SNPs using data from pooled DNA samples.
2014-07-22T13:57:53Z
2014-07-22T13:57:53Z
2011
info:eu-repo/semantics/conferenceObject
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3902
eng
Proceedings of the 58th Wrold Statistics Congress of the International Statistical Institute;
http://2011.isiproceedings.org/
07/MI012
info:eu-repo/semantics/openAccess
Internaitonal Statistical Institute
oai:ulir.ul.ie:10344/3903
2019-09-13T09:25:45Z
hdl_10344_10
hdl_10344_9
hdl_10344_21
hdl_10344_20
hdl_10344_2626
Partnership formation based on multiple traits
Ramsey, David
SFI
game theory
partnership formation
multiple traits
subgame perfect equilibrium
peer-reviewed
A model of partnership formation based on two traits, called beauty and character,
is presented. There are two classes of individual and partners must be of di erent classes.
Individuals prefer prospective partners with a high beauty measure and of a similar character.
This problem may be interpreted as e.g. a job search problem in which the classes are employer
and employee, or a mate choice problem in which the classes are male and female. Beauty can be
observed instantly. However, a costly date (or interview) is required to observe the character of
a prospective partner. On observing the beauty of a prospective partner, an individual decides
whether he/she wishes to date. During a date, the participants observe each other's character
and then decide whether to form a pair. Mutual acceptance is required both for a date to
occur and pair formation. On nding a partner, an individual stops searching. Beauty has a
continuous distribution on a nite interval, while character 'forms a circle' and has a uniform
distribution. Criteria based on the concept of a subgame perfect Nash equilibrium are used to
de ne a symmetric equilibrium of this game. It is argued that this equilibrium is unique. When
dating costs are high, this equilibrium is a block separating equilibrium as in more classical
formulations of two-sided job search problems. However, for su ciently small dating costs the
form of this equilibrium is essentially different.
2014-07-22T14:16:43Z
2014-07-22T14:16:43Z
2012
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/3903
eng
European Journal of Operational Research;216 (3), pp. 624-637
http://dx.doi.org/10.1016/j.ejor.2011.08.013
07/MI102
This is the author’s version of a work that was accepted for publication in European Journal of Operational Research. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in European Journal of Operational Research, 2012, 216 (3), pp. 624-637, http://dx.doi.org/10.1016/j.ejor.2011.08.013
info:eu-repo/semantics/openAccess
Elsevier
oai:ulir.ul.ie:10344/4021
2019-09-16T13:00:00Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_20
hdl_10344_504
Free surface flows in industry
Murphy, Ellen
Lee, William T.
IRC
SFI
applied mathematics
industry
manufacturing
peer-reviewed
Applied mathematicians have long sourced problems from industrial processes.
The relationship between mathematics and industry is mutually beneficial. Mathematical
models provide industry with invaluable insights into the fundamental physical
processes at play in a system and give mathematicians the opportunity to apply
known techniques to new problems. In this thesis, two independent problems originating
in industrial processes are studied, with a common feature of a
fluid free surface.
The first problem concerns the manufacture of contact lenses. Contact lenses are
produced by placing a
fluid between two moulds and squeezing the
fluid outwards to
form the shape of the lens. The manufacturers reported an issue with the process,
finding that at times the
fluid moves outwards asymmetrically, resulting in partially
formed lenses. The system is modelled using the thin flim equations and the results
are analysed to find the optimal operating setup to reduce asymmetrical
flow.
The second problem comes from the production of stout beer. Stout beer is made
with a mixture of nitrogen and carbon dioxide gases to create a creamy long-lasting
head. Nitrogen gas is much less soluble in water than carbon dioxide, causing the
bubbles it forms to be small and stable. Stout beers require initiation by mechanical
methods. Previous work has suggested that cellulose bres may be used to initiate
stout beer but a better understanding of the fundamental science behind bubble
nucleation by cellulose fibres is needed. In this work, a gas pocket in a cellulose
fibre is modelled to estimate the parameters governing disjoining pressure and to
determine the mechanism for bubble detachment.
2014-09-22T09:55:30Z
2014-09-22T09:55:30Z
2014
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/4021
eng
06/MI/005
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/4034
2019-05-01T09:05:52Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_20
hdl_10344_504
Soil bacterial processes and dynamics
Cribbin, Laura B.
Fowler, Andrew C.
Mitchell, Sarah L.
SFI
pollution
soil bacteria
environment
peer-reviewed
Under the influence of regional groundwater
ow, pollution in an aquifer can
migrate to streams or wells. This can have catastrophic consequences for human
health and local ecosystems. Fortunately, there is a suite of microorganisms that
exist in the subsurface that can convert contaminants into less toxic chemicals. In
this thesis, we seek to model the interaction between these microbial populations
and the contaminant.
A reaction-transport model is created to describe the migration of chemical
species in a subsurface environment. With this model, we derive an expression for
the location of a reaction front in the plume and the speed at which it moves.
Oscillatory chemical concentration pro les are frequently observed in borehole
readings but they are often dismissed as noisy data without closer examination. We
propose that such oscillations are a result of microbial populations competing for
nutrient sources. A description of this interaction is provided which is found to
exhibit temporal and spatial oscillatory behaviour.
A recent thesis by Razak (2009) is reviewed in which the phenol degradation rate
by a particular strain of bacteria was experimentally measured. Building a modi ed
version of the Van Impe et al. (2005) model, a description is derived of the biomass
growth, oxygen depletion and phenol consumption in a continuous
ow environment.
2014-09-24T16:03:18Z
2014-09-24T16:03:18Z
2013
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/4034
eng
09/IN.1/I2645
06/MI/005
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/4173
2019-05-01T08:38:19Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_20
hdl_10344_504
An investigation into the nature of mathematics textbooks at junior cycle and their role in mathematics education
O'Keeffe, Lisa
O'Donoghue, John
mathematics
junior cycle
textbooks
peer-reviewed
This research study is aimed at improving the quality of the mathematics textbooks
available for junior cycle students. It is widely agreed that there is room for
improvement with regard to the quality of mathematics at both junior and senior
cycle level in Ireland. One such area which can be improved is the e ectiveness of
the resources available in both junior and senior cycle mathematics classrooms.
While the TIMSS report (Valverde et al., 2002) has explored textbooks on an
international scale, minimal research (minor role in TIMSS Report) has been
carried out on Irish mathematics textbooks. Considering the level of responsibility
shouldered by mathematics textbooks, there is an obvious gap in mathematics
education research.
The aim of this study is to investigate the quality of the mathematics textbooks
currently in use at junior secondary school level in Ireland. This is achieved by
investigating, extending and applying suitable methodological tools for textbook
analysis. Ultimately the aim of this research is to improve the quality of teaching
and learning of mathematics at junior cycle level which should feed directly into
improving the quality of mathematics at senior cycle. This will be achieved by
rst measuring the quality of the current junior cycle mathematics textbooks and
then highlighting the role of improved textbooks in students' conceptual under-
standing. At present in Ireland, there is a move away from the more traditional
didactical approaches to teaching and learning towards teaching and learning for
understanding. This move towards teaching and learning for understanding is as
a result of the new curriculum initiative - project m, which requires students
to understand and apply mathematics. This change in focus within mathematics
classrooms across Ireland highlights the need for teachers to be more aware of
students' conceptual development and hence in
uenced the author as this research
study evolved.
The study presented here provides a theoretical framework for a complete analysis
of mathematics textbooks which will allow for an in-depth analysis of any mathe-
matics textbook. This research builds on the work of international studies such as
the TIMSS report and established frameworks for mathematics textbook analysis
such as Morgan (2004), Mikk (2000) and Rivers (1990) to create a single frame-
work for a complete mathematics textbook analysis. This study also highlights
key design features of mathematics textbooks which are signi cant in students'
conceptual development. The author's investigation into the quality of the current
junior cycle mathematics textbooks is the rst large scale study of its kind in
Ireland. This research not only identi es the quality of the current mathematics
textbooks but it also highlights key design features which impact on students'
understanding of mathematics.
2014-11-17T17:51:48Z
2014-11-17T17:51:48Z
2011
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/4173
eng
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/4243
2019-05-02T10:05:06Z
hdl_10344_10
hdl_10344_9
hdl_10344_242
hdl_10344_240
hdl_10344_480
hdl_10344_243
hdl_10344_20
hdl_10344_504
The effect of contact lines on the dynamics of drops and liquid bridges
Cummins, Cathal Pádraig
Benilov, Eugene
capillarity
liquid drops
mathematics
peer-reviewed
In the first part of the thesis, the evolution of a three-dimensional liquid drop on an
inclined substrate oscillating vertically is examined. The oscillations are assumed
to be weak and slow, which effectively makes the inertia and viscosity of the liquid
negligible. The effects of the vibration-induced inertial force and gravity are balanced
by surface tension forces. Asymptotic expressions are derived for the mean
velocity of the drop up to the second order, where the small parameter, , is the
ratio of the vibration-induced inertia to surface tension.
There is no assumption made regarding the thickness of the drop. This distinguishes
this study from other theoretical studies of the problem, all of which relied
on the thin-film approximation. From an experimental point of view, this approximation
is highly restrictive, whereas, crucially, the conclusions of this study may be
tested through a specially-designed experiment.
It is shown that, if the amplitude of the substrate’s oscillations exceeds a certain
threshold value, , drops climb uphill. itself depends strongly on the thickness
of the drop that, in turn, depends on the drop’s equilibrium contact angle, 0. It is
found that, as 0 grows, there is a dramatic decrease in ?, which means that thick
drops can climb for much weaker substrate vibrations.
In the second part of the thesis, the stability of a static liquid bridge rising from
an infinite pool, with its top attached to a horizontal plate suspended at a certain
height above the pool’s surface is studied. Two different models are examined for
the bridge’s contact line. Model 1 assumes that the contact angle always equals
Young’s equilibrium value. Model 2 assumes a functional dependence between the
contact angle and the velocity of the contact line, and it is further argued that, if
this dependence involves a hysteresis interval, the contact line is effectively pinned
to the plate.
It is shown that, within the framework of Model 1, all liquid bridges are unstable.
In Model 2, in turn, both stable and unstable bridges exist (the former have larger
contact angles and/or larger heights H than the latter). For Model 2, the marginalstability
curve in the ( ,H)-parameter space is computed.
2015-01-23T18:53:36Z
2015-01-23T18:53:36Z
2014
info:eu-repo/semantics/doctoralThesis
all_ul_research
ul_published_reviewed
ul_theses_dissertations
http://hdl.handle.net/10344/4243
eng
info:eu-repo/semantics/openAccess
University of Limerick
oai:ulir.ul.ie:10344/4401
2017-11-15T15:43:54Z
hdl_10344_10
hdl_10344_9
hdl_10344_26
hdl_10344_25
hdl_10344_36
hdl_10344_35
hdl_10344_33
hdl_10344_42
hdl_10344_20
Dance for people with Parkinson disease: what is the evidence telling us?
Shanahan, Joanne
Morris, Meg E.
Ni Bhriain, Orfhlaith
Saunders, Jean
Clifford, Amanda M.
dance therapy
exercise
Parkinson disease
rehabilitation
peer-reviewed
Objectives: (1) To appraise and synthesize the literature on dance interventions for individuals with Parkinson disease (PD); (2) to provide information regarding the frequency, intensity, duration, and type of dance used in these programs; and (3) to inform the development of future studies evaluating dance interventions in this population.
Data Sources: Eight databases (MEDLINE, Cumulative Index to Nursing and Allied Health Literature [CINAHL], the Allied and Complementary Medicine Database [AMED], SPORTDiscus, PubMed, PubMed Central, Sage, and ScienceDirect) were electronically searched in April 2014. The references lists from the included articles were also searched.
Study Selection: Studies retrieved during the literature search were reviewed by 2 reviewers independently. Suitable articles were identified by applying inclusion criteria.
Data Extraction: Data regarding participants and the frequency, intensity, duration, and type of dance form used were extracted. The effect that each dance program had on defined outcomes and the feasibility of each program were also reviewed.
Data Synthesis: Thirteen articles were identified. The quality of studies varied, and methodological limitations were evident in some. The evidence evaluated suggests that two 1-hour dance classes per week over 10 to 13 weeks may have beneficial effects on endurance, motor impairment, and balance.
Conclusions: Dance may be helpful for some people with PD. This article provides preliminary information to aid clinicians when implementing dance programs for people with PD. Higher-quality multicenter studies are needed to determine the effect of other dance genres and the optimal therapy volume and intensity.
2015-04-07T21:38:01Z
2015-04-07T21:38:01Z
2015
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/4401
10.1016/j.apmr.2014.08.017
eng
Archives of Physical Medicine and Rehabilitation;96 (1), pp. 141-153
http://dx.doi.org/ 10.1016/j.apmr.2014.08.017
This is the author’s version of a work that was accepted for publication in Archives of Physical Medicine and Rehabilitation . Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Archives of Physical Medicine and Rehabilitation, 96 (1), pp. 141-153, http://dx.doi.org/ 10.1016/j.apmr.2014.08.017
info:eu-repo/semantics/openAccess
Elsevier
oai:ulir.ul.ie:10344/4409
2021-12-08T16:02:06Z
hdl_10344_10
hdl_10344_9
hdl_10344_26
hdl_10344_25
hdl_10344_20
hdl_10344_31
Structured care of diabetes in general practice: a qualitative study of the barriers and facilitators
O'Connor, Ray
Mannix, M
Mullen, J
Powys, L.
Mannion, M
Nolan, H.A
Kearney, E
Cullen, Walter
Griffin, M.
Saunders, Jean
diabetes
general practitioner
practice nurse
peer-reviewed
This qualitative study explored general practitionerâ s and practice nurseâ s perceptions of barriers and
facilitators to the proposed transfer of diabetes care to general practice. Qualitative data were collected through
five focus groups. Participants included GPs (n=55) and practice nurses (n=11) representing urban (44%), rural (29%)
and mixed (27%) practices, in the Irish Mid-West region. Barriers and facilitators were mentioned 631 times (100%).
Barriers were mentioned 461 times (73%), facilitators 170 times (27%). The most frequently identified barriers were
lack of financial incentive (119/631; 19%), lack of access to secondary resources (93/631; 15%), lack of staff and
increased workload (59/631; 9%) and time constraints (52/631; 8%). Identified facilitators were access to secondary
care (49/631;7.8%), the holistic nature of general practice and continuity of care (48/631;7.6%). Although many are
enthusiastic, there remains significant reluctance among GPs and practice nurses to take responsibility for diabetes
care without addressing these barriers.
2015-04-09T17:35:34Z
2015-04-09T17:35:34Z
2013
info:eu-repo/semantics/article
all_ul_research
ul_published_reviewed
http://hdl.handle.net/10344/4409
eng
Irish Medical Journal;106 (3)
http://www.imj.ie/
info:eu-repo/semantics/openAccess
Irish Medical Organization
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