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Recent documents in Articlesen-usSun, 12 Feb 2017 01:37:22 PST3600Hamiltonian Model for Coupled Surface and Internal Waves in the Presence of Currents
http://arrow.dit.ie/scschmatart/229
http://arrow.dit.ie/scschmatart/229Fri, 10 Feb 2017 01:57:09 PST
We examine a two dimensional fluid system consisting of a lower medium bounded underneath by a flatbed and an upper medium with a free surface. The two media are separated by a free common interface. The gravity driven surface and internal water waves (at the common interface between the media) in the presence of a depth-dependent current are studied under certain physical assumptions. Both media are considered incompressible and with prescribed vorticities. Using the Hamiltonian approach the Hamiltonian of the system is constructed in terms of ’wave’ variables and the equations of motion are calculated. The resultant equations of motion are then analysed to show that wave-current interaction is influenced only by the current profile in the ’strips’ adjacent to the surface and the interface. Small amplitude and long-wave approximations are also presented.
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Rossen IvanovMode-Sum Prescription for the Vacuum Polarization in odd Dimensions
http://arrow.dit.ie/scschmatart/228
http://arrow.dit.ie/scschmatart/228Tue, 03 Jan 2017 06:38:20 PST
We present a new mode-sum regularization prescription for computing the vacuum polarization of a scalar field in static spherically-symmetric black hole spacetimes in odd dimensions. This is the first general and systematic approach to regularized vacuum polarization in higher dimensions. Remarkably, the regularization parameters can be computed in closed form in arbitrary dimensions and for arbitrary metric function $f(r)$. In fact, we show that in spite of the increasing severity and number of the divergences to be regularized, the method presented is mostly agnostic to the number of dimensions. Finally, as an explicit example of our method, we show plots for vacuum polarization in the Schwarzschild-Tangherlini spacetime for odd $d=5,...,11$.
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Peter Taylor et al.Modelling Random Antibody Adsorption and Immunoassay Activity
http://arrow.dit.ie/scschmatart/227
http://arrow.dit.ie/scschmatart/227Mon, 19 Dec 2016 05:03:19 PST
One of the primary considerations in immunoassay design is optimizing the concentration of capture antibody in order to achieve maximal antigen binding and, subsequently, improved sensitivity and limit of detection. Many immunoassay technologies involve immobilization of the antibody to solid surfaces. Antibodies are large molecules in which the position and accessibility of the antigen-binding site depend on their orientation and packing density. In this paper we propose a simple mathematical model, based on the theory known as random sequential adsorption (RSA), in order to calculate how the concentration of correctly oriented antibodies (active site exposed for subsequent reactions) evolves during the deposition process. It has been suggested by experimental studies that high concentrations will decrease assay performance, due to molecule denaturation and obstruction of active binding sites. However, crowding of antibodies can also have the opposite effect by favouring upright orientations. A specific aim of our model is to predict which of these competing effects prevails under different experimental conditions and study the existence of an optimal coverage, which yields the maximum expected concentration of active particles (and hence the highest signal).
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Dana Mackey et al.The Dynamics of Flat Surface Internal Geophysical Waves with Currents
http://arrow.dit.ie/scschmatart/226
http://arrow.dit.ie/scschmatart/226Mon, 12 Dec 2016 09:57:57 PST
A two-dimensional water wave system is examined consisting of two discrete incompressible fluid domains separated by a free common interface. In a geophysical context this is a model of an internal wave, formed at a pycnocline or thermocline in the ocean. The system is considered as being bounded at the bottom and top by a flatbed and wave-free surface respectively. A current profile with depth-dependent currents in each domain is considered. The Hamiltonian of the system is determined and expressed in terms of canonical wave-related variables. Limiting behavior is examined and compared to that of other known models. The linearised equations as well as long-wave approximations are presented.
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Alan Compelli et al.Theoretical Modeling of the Effect of Polymer Chain Immobilization Rates on Holographic Recording in Photopolymers
http://arrow.dit.ie/scschmatart/225
http://arrow.dit.ie/scschmatart/225Mon, 12 Dec 2016 08:43:00 PST
This paper introduces an improved mathematical model for holographic grating formation in an acrylamide-based photopolymer, which consists of partial differential equations derived from physical laws. The model is based on the two-way diffusion theory of \cite{izabela}, which assumes short polymer chains are free to diffuse, and generalizes a similar model presented in \cite{josab} by introducing an immobilization rate governed by chain growth and cross-linking. Numerical simulations were carried out in order to investigate the behaviour of the photopolymer system for short and long exposures, with particular emphasis on the effect of recording parameters (such as illumination frequency and intensity), as well as material permeability, on refractive index modulation, refractive index profile and grating distortion. The model reproduces many well-known experimental observations, such as decrease of refractive index modulation at high spatial frequencies and appearance of higher harmonics in the refractive index profile when the diffusion rate is much slower than polymerization rate. These properties are supported by a theoretical investigation which uses perturbation techniques to approximate the solution over various time scales.
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Dana Mackey et al.Bayesian exponential random graph modeling of whole-brain structural networks across lifespan
http://arrow.dit.ie/scschmatart/224
http://arrow.dit.ie/scschmatart/224Fri, 09 Dec 2016 08:23:12 PSTMichel Sinke et al.An Examination of the Neural Unreliability Thesis of Autism
http://arrow.dit.ie/scschmatart/223
http://arrow.dit.ie/scschmatart/223Fri, 09 Dec 2016 02:28:09 PST
An emerging neuropathological theory of Autism, referred to here as “the neural unreliability thesis,” proposes greater variability in moment-to-moment cortical representation of environmental events, such that the system shows general instability in its impulse response function. Leading evidence for this thesis derives from functional neuroimaging, a methodology ill-suited for detailed assessment of sensory transmission dynamics occurring at the millisecond scale. Electrophysiological assessments of this thesis, however, are sparse and unconvincing. We conducted detailed examination of visual and somatosensory evoked activity using high-density electrical mapping in individuals with autism (N = 20) and precisely matched neurotypical controls (N = 20), recording large numbers of trials that allowed for exhaustive timefrequency analyses at the single-trial level. Measures of intertrial coherence and event-related spectral perturbation revealed no convincing evidence for an unreliability account of sensory responsivity in autism. Indeed, results point to robust, highly reproducible response functions marked for their exceedingly close correspondence to those in neurotypical controls.
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John Butler et al.Mathematics Learning Support Across a Multi-Campus Institution: A Prototype of Virtual Support
http://arrow.dit.ie/scschmatart/222
http://arrow.dit.ie/scschmatart/222Thu, 03 Nov 2016 09:48:10 PDT
In this paper, a study on Mathematics Learning Support (MLS) that was undertaken across three institutes intending to form the Technological University for Dublin is outlined. This study consisted of a survey that was circulated to both staff and students in each of the three institutes. The survey had two objectives. Firstly it sought to identify the students’ needs for MLS in each of the three institutes. Secondly, it sought to ascertain the preferred method of provision of MLS, on a scale ranging from exclusively online, to exclusively in person. Following on the results of this survey it was decided to prototype a virtual MLS drop-in service. The operational details of the prototyping of this virtual drop-in service and the feedback obtained from the students involved are also presented in this paper.
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Cormac Breen et al.Atypical Visual and Somatosensory Adaptation in Schizophrenia-spectrum Disorders
http://arrow.dit.ie/scschmatart/221
http://arrow.dit.ie/scschmatart/221Wed, 26 Oct 2016 05:44:31 PDT
Neurophysiological investigations in patients with schizophrenia consistently show early sensory processing deficits in the visual system. Importantly, comparable sensory deficits have also been established in healthy first-degree biological relatives of patients with schizophrenia and in first-episode drug-naive patients. The clear implication is that these measures are endophenotypic, related to the underlying genetic liability for schizophrenia. However, there is significant overlap between patient response distributions and those of healthy individuals without affected first-degree relatives. Here we sought to develop more sensitive measures of sensory dysfunction in this population, with an eye to establishing endophenotypic markers with better predictive capabilities. We used a sensory adaptation paradigm in which electrophysiological responses to basic visual and somatosensory stimuli presented at different rates (ranging from 250 to 2550 ms interstimulus intervals, in blocked presentations) were compared. Our main hypothesis was that adaptation would be substantially diminished in schizophrenia, and that this would be especially prevalent in the visual system. High-density event-related potential recordings showed amplitude reductions in sensory adaptation in patients with schizophrenia (N = 15 Experiment 1, N = 12 Experiment 2) compared with age-matched healthy controls (N=15 Experiment 1, N = 12 Experiment 2), and this was seen for both sensory modalities. At the individual participant level, reduced adaptation was more robust for visual compared with somatosensory stimulation. These results point to significant impairments in short-term sensory plasticity across sensory modalities in schizophrenia. These simple-to-execute measures may prove valuable as candidate endophenotypes and will bear follow-up in future work.
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Gizely Andrade et al.Exploring the Unknown: Electrophysiological and Behavioural Measures of Visuospatial Learning
http://arrow.dit.ie/scschmatart/220
http://arrow.dit.ie/scschmatart/220Wed, 26 Oct 2016 05:44:26 PDT
Visuospatial memory describes our ability to temporarily store and manipulate visual and spatial information, and is employed for a wide variety of complex cognitive tasks. Here, a visuospatial learning task requiring fine motor control is employed to investigate visuospatial learning in a group of typically developing adults. Electrophysiological and behavioural data are collected during a target location task under two experimental conditions: Target Learning and Target Cued. Movement times (MTs) are employed as a behavioural metric of performance, while dynamic P3b amplitudes and power in the alpha band (approximately 10 Hz) are explored as electrophysiological metrics during visuospatial learning. Results demonstrate that task performance, as measured by MT, is highly correlated with P3b amplitude and alpha power at a consecutive trial level (trials 1–30). The current set of results, in conjunction with the existing literature, suggests that changes in P3b amplitude and alpha power could correspond to different aspects of the learning process. Here it is hypothesized that changes in P3b correspond to a diminishing inter-stimulus interval and reduced stimulus relevance, while the corresponding changes in alpha power represent an automation of response as habituation occurs in participants. The novel analysis presented in the current study demonstrates how gradual electrophysiological changes can be tracked during the visuospatial learning process under the current paradigm.
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Brendan Quinlivan et al.On the N-wave Equations with PT-symmetry
http://arrow.dit.ie/scschmatart/219
http://arrow.dit.ie/scschmatart/219Wed, 26 Oct 2016 04:31:54 PDT
We study extensions of N-wave systems with PT-symmetry. The types of (nonlocal) reductions leading to integrable equations invariant with respect to P- (spatial reflection) and T- (time reversal) symmetries is described. The corresponding constraints on the fundamental analytic solutions and the scattering data are derived. Based on examples of 3-wave (related to the algebra sl(3,C)) and 4-wave (related to the algebra so(5,C)) systems, the properties of different types of 1- and 2-soliton solutions are discussed. It is shown that the PT symmetric 3-wave equations may have regular multi-soliton solutions for some specific choices of their parameters.
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Vladimir Gerdjikov et al.Application of Virtual Reality Head Mounted Display for Investigation of Movement: a Novel Effect of Orientation of Attention
http://arrow.dit.ie/scschmatart/218
http://arrow.dit.ie/scschmatart/218Tue, 06 Sep 2016 01:28:17 PDT
Objective. To date human kinematics research has relied on video processing, motion capture and magnetic search coil data acquisition techniques. However, the use of head mounted display virtual reality systems, as a novel research tool, could facilitate novel studies into human movement and movement disorders. These systems have the unique ability of presenting immersive 3D stimulus while also allowing participants to make ecologically valid movement-based responses. Approach. We employed one such system (Oculus Rift DK2) in this study to present visual stimulus and acquire head-turn data from a cohort of 40 healthy adults. Participants were asked to complete head movements towards eccentrically located visual targets following valid and invalid cues. Such tasks are commonly employed for investigating the effects orientation of attention and are known as Posner cueing paradigms. Electrooculography was also recorded for a subset of 18 participants. Main results. A delay was observed in onset of head movement and saccade onset during invalid trials, both at the group and single participant level. We found that participants initiated head turns 57.4 ms earlier during valid trials. A strong relationship between saccade onset and head movement onset was also observed during valid trials. Significance. This work represents the first time that the Posner cueing effect has been observed in onset of head movement in humans. The results presented here highlight the role of head-mounted display systems as a novel and practical research tool for investigations of normal and abnormal movement patterns.
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Brendan Quinlivan et al.Free Energies For Singleton Minimal States
http://arrow.dit.ie/scschmatart/217
http://arrow.dit.ie/scschmatart/217Wed, 31 Aug 2016 02:38:49 PDT
It is assumed that any free energy funcuon exhibits strict periodic benav10r tor histories that havebeen periodic for all past times. This is not the case for the work function, which, however, has the usual defining properties of a free energy. Fonns given m fairly recent years for the minimum and related free energies of linear materials with memory have this property. Materials for which the minimal states are all singletons are those for which at least some of the singularities of the Fourier transfonn of the relaxation function are not isolated. For such materials, the maximum free energy is the work function, and free energies intermediate between the minimum free energy and the work function should be given by a linear relation involving these two quantities. All such functionals, except the minimum free energy, therefore do not have strict periodic behavior for periodic histories, which contradicts our assumption. A way out of the difficulty is explored which involves approximating the relaxation function by a form for which the minimal states arc no longer singletons. A representation can then be given of an arbitrary free energy as a linear combination of the minimum, maximum and intennediate free energies derived in earlier work. This representation obeys our periodicity assumption. Numerical data are presented, supporting the consistency of this approach.
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Murrough GoldenSimultaneous Modelling of Initial Conditions and Time Heterogeneity in Dynamic Networks: An Application to Foreign Direct Investments
http://arrow.dit.ie/scschmatart/216
http://arrow.dit.ie/scschmatart/216Wed, 27 Apr 2016 02:54:37 PDT
In dynamic networks, the presence of ties are subject both to endogenous network dependencies and spatial dependencies. Current statistical models for change over time are typically defined relative to some initial condition, thus skirting the issue of where the first network came from. Additionally, while these longitudinal network models may explain the dynamics of change in the network over time, they do not explain the change in those dynamics. We propose an extension to the longitudinal exponential random graph model that allows for simultaneous inference of the changes over time and the initial conditions, as well as relaxing assumptions of time-homogeneity. Estimation draws on recent Bayesian approaches for cross-sectional exponential random graph models and Bayesian hierarchical models. This is developed in the context of foreign direct investment relations in the global electricity industry in 1995–2003. International investment relations are known to be affected by factors related to: (i) the initial conditions determined by the geographical locations; (ii) time-dependent fluctuations in the global intensity of investment flows; and (iii) endogenous network dependencies. We rely on the well-known gravity model used in research on international trade to represent how spatial embedding and endogenous network dependencies jointly shape the dynamics of investment relations.
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Johan Koskinen et al.Knowledge Sharing in Organisations: a Bayesian Analysis of the Role of Reciprocity and Formal Structure
http://arrow.dit.ie/scschmatart/215
http://arrow.dit.ie/scschmatart/215Wed, 27 Apr 2016 02:54:28 PDT
We examine the conditions under which knowledge embedded in advice relations is likely to reach across intraorganizational boundaries and be shared between distant organizational members. We emphasize boundary-crossing relations because activities of knowledge transfer and sharing across subunit boundaries are systematically related to desirable organizational outcomes. Our main objective is to understand how organizational and social processes interact to sustain the transfer of knowledge carried by advice relations. Using original fieldwork and data that we have collected on members of the top management team in a multiunit industrial group, we show that knowledge embedded in task advice relations is unlikely to crosscut intra- organizational boundaries, unless advice relations are reciprocated, and supported by the pres- ence of hierarchical relations linking managers in different subunits. The results we report are based on a novel Bayesian Exponential Random Graph Models (BERGMs) framework that allows us to test and assess the empirical value of our hypotheses while at the same time accounting for structural characteristics of the intraorganizational network of advice relations. We rely on computational and simulation methods to establish the consistency of the network implied by the model we propose with the structure of the intraorganizational network that we actually observed.
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Alberto Caimo et al.Bayesian Exponential Random Graph Models with Nodal Random Effects
http://arrow.dit.ie/scschmatart/214
http://arrow.dit.ie/scschmatart/214Mon, 25 Apr 2016 05:17:55 PDT
We extend the well-known and widely used Exponential Random Graph Model (ERGM) by including nodal random effects to compensate for heterogeneity in the nodes of a network. The Bayesian framework for ERGMs proposed by Caimo and Friel (2011) yields the basis of our modelling algorithm. A central question in network models is the question of model selection and following the Bayesian paradigm we focus on estimating Bayes factors. To do so we develop an approximate but feasible calculation of the Bayes factor which allows one to pursue model selection. Two data examples and a small simulation study illustrate our mixed model approach and the corresponding model selection.
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Stephanie Thiemichen et al.Efficient Computational Strategies for Doubly Intractable Problems with Applications to Bayesian Social Networks
http://arrow.dit.ie/scschmatart/213
http://arrow.dit.ie/scschmatart/213Mon, 25 Apr 2016 04:58:25 PDT
Powerful ideas recently appeared in the literature are adjusted and combined to design improved samplers for doubly intractable target distributions with a focus on Bayesian exponential random graph models. Different forms of adaptive Metropolis–Hastings proposals (vertical, horizontal and rectangular) are tested and merged with the delayed rejection (DR) strategy with the aim of reducing the variance of the resulting Markov chain Monte Carlo estimators for a given computational time. The DR is modified in order to integrate it within the approximate exchange algorithm (AEA) to avoid the computation of intractable normalising constant that appears in exponential random graph models. This gives rise to the AEA + DR: a new methodology to sample doubly intractable distributions that dominates the AEA in the Peskun ordering (Peskun Biometrika 60:607– 612, 1973) leading to MCMC estimators with a smaller asymptotic variance. The Bergm package for R (Caimo and Friel J. Stat. Softw. 22:518–532, 2014) has been updated to incorporate the AEA + DR thus including the possibility of adding a higher stage proposals and different forms of adaptation.
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Alberto Caimo et al.Bergm: Bayesian Exponential Random Graphs in R
http://arrow.dit.ie/scschmatart/212
http://arrow.dit.ie/scschmatart/212Mon, 25 Apr 2016 04:32:59 PDT
In this paper we describe the main featuress of the Bergm package for the open-source R software which provides a comprehensive framework for Bayesian analysis for exponential random graph models: tools for parameter estimation, model selection and goodness-of-fit diagnostics. We illustrate the capabilities of this package describing the algorithms through a tutorial analysis of three network datasets.
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Alberto Caimo et al.Delayed Rejection Algorithm to Estimate Bayesian Social Networks
http://arrow.dit.ie/scschmatart/211
http://arrow.dit.ie/scschmatart/211Mon, 25 Apr 2016 04:28:30 PDT
Statistical social network analysis has become a very active and fertile area of research in the recent past. Recent developments in Bayesian computational methods have been successfully applied to estimate social network models. The Delayed rejection (DR) strategy is a modification of the Metropolis-Hastings (MH) algorithms that reduces the variance of the resulting Markov chain Monte Carlo estimators and allows partial adaptation of the proposal distribution. In this paper we show how the DR strategy can be exploited to estimate dyadic independence social network models leading to an average 40% variance reduction relative to the competing MH algorithm, confirming that DR dominates, in terms of Peskun ordering, the MH algorithm.
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Alberto Caimo et al.Bayesian Model Selection for Exponential Random Graph Models
http://arrow.dit.ie/scschmatart/210
http://arrow.dit.ie/scschmatart/210Mon, 25 Apr 2016 04:18:23 PDT
Exponential random graph models are a class of widely used exponential family models for social networks. The topological structure of an observed network is modelled by the relative prevalence of a set of local sub-graph configurations termed network statistics. One of the key tasks in the application of these models is which network statistics to include in the model. This can be thought of as statistical model selection problem. This is a very challenging problem---the posterior distribution for each model is often termed ``doubly intractable'' since computation of the likelihood is rarely available, but also, the evidence of the posterior is, as usual, intractable. The contribution of this paper is the development of a fully Bayesian model selection method based on a reversible jump Markov chain Monte Carlo algorithm extension of Caimo & Friel (2011) which estimates the posterior probability for each competing model.
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Alberto Caimo et al.