Modelling and Refinement in CODA

This paper provides an overview of the CODA framework for modelling and refinement of component-based embedded systems. CODA is an extension of Event-B and UML-B and is supported by a plug-in for the Rodin toolset. CODA augments Event-B with constructs for component-based modelling including components, communications ports, port connectors, timed communications and timing triggers. Component behaviour is specified through a combination of UML-B state machines and Event-B. CODA communications and timing are given an Event-B semantics through translation rules. Refinement is based on Event-B refinement and allows layered construction of CODA models in a consistent way.Comment: In Proceedings Refine 2013, arXiv:1305.563

A Bayesian spatial random effects model characterisation of tumour heterogeneity implemented using Markov chain Monte Carlo (MCMC) simulation

The focus of this study is the development of a statistical modelling procedure for characterising intra-tumour heterogeneity, motivated by recent clinical literature indicating that a variety of tumours exhibit a considerable degree of genetic spatial variability. A formal spatial statistical model has been developed and used to characterise the structural heterogeneity of a number of supratentorial primitive neuroecto-dermal tumours (PNETs), based on diffusionweighted magnetic resonance imaging. Particular attention is paid to the spatial dependence of diffusion close to the tumour boundary, in order to determine whether the data provide statistical evidence to support the proposition that water diffusivity in the boundary region of some tumours exhibits a deterministic dependence on distance from the boundary, in excess of an underlying random 2D spatial heterogeneity in diffusion. Tumour spatial heterogeneity measures were derived from the diffusion parameter estimates obtained using a Bayesian spatial random effects model. The analyses were implemented using Markov chain Monte Carlo (MCMC) simulation. Posterior predictive simulation was used to assess the adequacy of the statistical model. The main observations are that the previously reported relationship between diffusion and boundary proximity remains observable and achieves statistical significance after adjusting for an underlying random 2D spatial heterogeneity in the diffusion model parameters. A comparison of the magnitude of the boundary-distance effect with the underlying random 2D boundary heterogeneity suggests that both are important sources of variation in the vicinity of the boundary. No consistent pattern emerges from a comparison of the boundary and core spatial heterogeneity, with no indication of a consistently greater level of heterogeneity in one region compared with the other. The results raise the possibility that DWI might provide a surrogate marker of intra-tumour genetic regional heterogeneity, which would provide a powerful tool with applications in both patient management and in cancer research

Loanword adaptation as first-language phonological perception

We show that loanword adaptation can be understood entirely in terms of phonological and phonetic comprehension and production mechanisms in the first language. We provide explicit accounts of several loanword adaptation phenomena (in Korean) in terms of an Optimality-Theoretic grammar model with the same three levels of representation that are needed to describe L1 phonology: the underlying form, the phonological surface form, and the auditory-phonetic form. The model is bidirectional, i.e., the same constraints and rankings are used by the listener and by the speaker. These constraints and rankings are the same for L1 processing and loanword adaptation

Sounds of Waitakere: Using practitioner research to explore how Year 6 recorder players compose responses to visual representations of a natural environment

How might primary students utilise the stimulus of a painting in a collaborative composition drawing on a non-conventional sound palette of their own making? This practitioner research features 17 recorder players from a Year 6 class (10–11-year-olds) who attend a West Auckland primary school in New Zealand. These children were invited to experiment with the instrument to produce collectively an expanded ‘repertoire’ or ‘palette’ of sounds. In small groups, they then discussed a painting by an established New Zealand painter set in the Waitakere Ranges and attempted to formulate an interpretation in musical terms. On the basis of their interpretation, drawing on sounds from the collective palette (complemented with other sounds), they worked collaboratively to develop, refine and perform a structured composition named for their chosen painting. This case study is primarily descriptive (providing narrative accounts and rich vignettes of practice) and, secondarily, exploratory (description and analysis leading to the development of hypotheses). It has implications for a range of current educational issues, including curriculum integration and the place of composition and notation in the primary-school music programme

Measuring the photo-ionization rate, neutral fraction and mean free path of HI ionizing photons at 4.9≤z≤6.04.9 \leq z \leq 6.0 from a large sample of XShooter and ESI spectra

We measure the mean free path ($\lambda_{\rm mfp,HI}$), photo-ionization rate ($\langle \Gamma_{\rm HI} \rangle$) and neutral fraction ($\langle f_{\rm HI} \rangle$) of hydrogen in 12 redshift bins at $4.85<z<6.05$ from a large sample of moderate resolution XShooter and ESI QSO absorption spectra. The fluctuations in ionizing radiation field are modeled by post-processing simulations from the Sherwood suite using our new code ''EXtended reionization based on the Code for Ionization and Temperature Evolution'' (EX-CITE). EX-CITE uses efficient Octree summation for computing intergalactic medium attenuation and can generate large number of high resolution $\Gamma_{\rm HI}$ fluctuation models. Our simulation with EX-CITE shows remarkable agreement with simulations performed with the radiative transfer code Aton and can recover the simulated parameters within $1\sigma$ uncertainty. We measure the three parameters by forward-modeling the Ly$\alpha$ forest and comparing the effective optical depth ($\tau_{\rm eff, HI}$) distribution in simulations and observations. The final uncertainties in our measured parameters account for the uncertainties due to thermal parameters, modeling parameters, observational systematics and cosmic variance. Our best fit parameters show significant evolution with redshift such that $\lambda_{\rm mfp,HI}$ and $\langle f_{\rm HI} \rangle$ decreases and increases by a factor $\sim 6$ and $\sim 10^{4}$, respectively from $z \sim 5$ to $z \sim 6$. By comparing our $\lambda_{\rm mfp,HI}$, $\langle \Gamma_{\rm HI} \rangle$ and $\langle f_{\rm HI} \rangle$ evolution with that in state-of-the-art Aton radiative transfer simulations and the Thesan and CoDa-III simulations, we find that our best fit parameter evolution is consistent with a model in which reionization completes by $z \sim 5.2$.Comment: 30 pages (+14 pages appendices), 14 figures (+18 figures appendices); submitted to MNRAS; Main results are summarized in Fig. 10, Fig. 11 and Table

L2 speech learning of European Portuguese /l/ and /ɾ/ by L1-Mandarin learners: experimental evidence and theoretical modelling

It has been long recognized that the poor distinction between /l/ and /ɾ/ is one of the most perceptible characteristics in Chinese-accented Portuguese. Recent empirical research revealed that this notorious L2 speech learning difficulty goes beyond the confusion between two L2 categories, as L1-Mandarin learners’ acquisition of Portuguese /l/ and /ɾ/ seems to be subject to the interaction among different prosodic positions, speech modalities and representational levels. This thesis aims to deepen our current understanding of this L2 speech learning process, by exploring what constrains the development of L2 phonological categories across syllable positions and how different modalities interact during this process. To achieve this goal, both experimental tasks and theoretical modelling were employed. The first study of this thesis explores the role of cross-linguistic influence and orthography on L2 category formation. In order to elicit cross-linguistic influence directly, a delayed-imitation task was performed with L1-Mandarin naïve listeners. This task examined how the Mandarin phonology parses the Portuguese input ([l], [ɾ]) in intervocalic onset and in word-internal coda position. Moreover, whether orthography plays a role during the construction of L2 phonological representation was tested by manipulating the input types that were given in the experiment (auditory input alone vs. auditory + written input). Our study shows that naïve Mandarin listeners’ responses corroborated with that of L1-Mandarin learners, suggesting that cross-linguistic influence is responsible for the observed L2 prosodic effects. Moreover, the Mandarin [ɻ] (a repair strategy for /ɾ/) occurred almost exclusively when the written form was given, providing evidence for the cross-linguistic interaction between phonological categorization and orthography during the construction of L2 categories. In the second study, we first investigate the interaction between speech perception and production in L2 speech learning, by examining whether the L2 deviant productions stem from misperception and whether the order of acquisition in L2 speech perception mirrors that in production. Secondly, we test whether L2 phonological categories remain malleable at a mid-late stage of L2 speech learning. Two perceptual experiments were performed to test L1-Mandarin learners on their discrimination ability between the target Portuguese form and the deviant form employed in L2 production. Expanding on prior research, in this study, the perceptual motivation for L2 speech difficulties was assessed in different syllable constituents (onset and coda) and at both segmental and suprasegmental levels (structural modification). The results demonstrate that some deviant forms observed in L2 production indeed have a perceptual motivation ([w] for the velarised lateral; [l] and [ɾə] for the tap), while some others cannot be attributed to misperception (deletion of syllable-final tap). Furthermore, learners confused the intervocalic /l/ and /ɾ/ bidirectionally in perception, while in production they never misproduced the lateral (/ɾ/ → [l], */l/ → [ɾ]), revealing a mismatch between two speech modalities. By contrast, the order of acquisition (/ɾ/coda > /ɾ/onset) was shown to be consistent in L2 perception and production. The correspondence and discrepancy between the two speech modalities signal a complex relationship between L2 speech perception and production. To assess the plasticity of L2 categories /l/ and /ɾ/, two groups of L1-Mandarin learners who differ substantially in terms of L2 experience were recruited in the perceptual tasks. Our study shows that both groups behaved similarly in terms of the discrimination performance. No evidence for a role of L2 experience was found. The implication of this null result on L2 phonological development is discussed. The third study of the thesis aims to contribute to bridging the gap between the L2 experimental evidence and formal theories. Adopting the Bidirectional Phonology and Phonetics Model, we formalise some of the experimental findings that cannot be elucidated by current L2 speech theories, namely, the between and within-subject variation in L2 phonological categorization; the interaction between phonological categorization and orthography during L2 category construction; and the asymmetry between L2 perception and production. Overall, this thesis sheds light on the complex nature of L2 phonological acquisition and provides a formal account of how different modalities interact in shaping L2 speech learning. Moreover, it puts forward testable predictions for future research and suggestions for improving foreign language teaching/training methodologies.É bem conhecido o facto de as trocas associadas a /l/ e /ɾ/ constituírem uma das caraterísticas mais percetíveis no português articulado pelos aprendentes chineses. Recentemente, estudos empíricos revelam que a dificuldade por parte dos aprendentes chineses não se restringe à discriminação moderada entre as duas categorias da L2, dado que a aquisição de /l/ e /ɾ/ do português por aprendentes chineses parece estar sujeita à interação entre contextos prosódicos, entre modalidades de fala e entre níveis representacionais diferentes. Esta tese visa aprofundar a nossa compreensão deste processo da aquisição fonológica L2, explorando o que condiciona o desenvolvimento das categorias fonológicas L2 em diferentes constituintes silábicos e de que modo as modalidades interagem durante este processo, recorrendo para tal a tarefas experimentais bem como a formalização teórica. O primeiro estudo averigua o papel da influência interlinguística e o da ortografia na construção das categorias de L2. Para elicitar a influência interlinguística diretamente, uma tarefa de imitação retardada foi aplicada aos falantes nativos do mandarim sem conhecimento de português, investigando assim como a fonologia do mandarim categoriza o input do português ([l], [ɾ]) em ataque simples intervocálico e em coda medial. Para além disso, a influência ortográfica na construção de representações fonológicas em L2 foi examinada através da manipulação do tipo do input apresentado na experiência (input auditivo vs. input auditivo + ortográfico). Os resultados da situação experimental em que os participantes receberam input de ambos os tipos replicaram o efeito prosódico observado na literatura, evidenciando a interação entre categorização fonológica e ortografia na construção das categorias de L2. No segundo estudo, investigamos a interação entre a perceção e a produção de fala na aquisição das líquidas do PE por aprendentes chineses e a plasticidade destas categorias fonológicas, respondendo às questões seguintes: 1) as produções desviantes de L2 resultam da perceção incorreta? 2) a ordem da aquisição em L2 é consistente na perceção e na produção? 3) as categorias da L2 permanecem maleáveis numa fase intermédia da aquisição? Duas tarefas percetivas foram conduzidas para testar a capacidade percetiva dos aprendentes nativos do mandarim em relação à discriminação entre a forma alvo do português e as formas desviantes utilizadas na produção. No presente estudo, a motivação percetiva das dificuldades em L2 foi testada nos constituintes silábicos diferentes (ataque simples e coda) e nos níveis segmental e suprassegmental (modificação estrutural). Os resultados demonstram que algumas formas desviantes que os aprendentes chineses produzem têm uma motivação percetiva (i.e. [w] para a lateral velarizada; [l] e [ɾə] para a vibrante alveolar), enquanto outras não podem ser analisadas como casos de perceção incorreta (como é o caso do o apagamento da vibrante em coda). Para além disso, na posição intervocálica, os aprendentes manifestam dificuldade na discriminação entre /l/ e /ɾ/ de forma bidirecional, mas, na produção, a lateral nunca é produzida incorretamente (/ɾ/ → [l], */l/ → [ɾ]). Tal revela uma divergência entre as duas modalidades de fala. Por contraste, mostrou-se que a ordem da aquisição (/ɾ/coda > /ɾ/ataque) é consistente na perceção e na produção da L2. A correspondência e a discrepância entre as duas modalidades de fala, sinalizam uma relação complexa entre a perceção e a produção na aquisição fonológica de L2. Em relação à questão da plasticidade das categorias de L2, recrutaram-se para as tarefas percetivas dois grupos de aprendentes nativos do mandarim que se diferenciavam substancialmente em termos da experiência em L2. Não se encontrou um efeito significativo da experiência da L2. A implicação deste resultado nulo no desenvolvimento fonológico de L2 foi discutida. O terceiro estudo desta tese tem como objetivo contribuir para a colmatação das lacunas entre estudos empíricos de L2 e as teorias formais. Adotando o Modelo Bidirecional de Fonologia e Fonética, formalizamos os resultados experimentais que as teorias atuais da aquisição fonológica de L2 não conseguem explicar, nomeadamente, a variação inter e intra-sujeitos na categorização fonológica em L2; a interação entre categorização fonológica e ortografia na construção das categorias na L2; a assimetria entre a perceção e a produção na L2. Em suma, esta tese contribui com dados empíricos para a discussão da relação complexa entre a perceção, produção e ortografia na aquisição fonológica de L2 e formaliza a interação entre essas modalidades através de um modelo linguístico generativo. Além disso, apresentam-se predições testáveis para investigação futura e sugestões para o aperfeiçoamento das metodologias de ensino/treino da língua não materna

Influence of geometry, elasticity properties and boundary conditions on the Mode I purity in sandwich composites

The present work addresses the problem of skin/core debonding in sandwich materials. The main goal is to carry out parametric analyses for studying the influence of various materials, geometrical parameters and boundary conditions of sandwich fracture specimens such as a Single Cantilever Beam and a Double Cantilever Beam on the skin/core opening (KI ) and shearing (KII ) modes. The analyses have been performed by means of fracture mechanics tools implemented into the commercial finite element code ABAQUS™. A two-dimensional model of the fracture specimens has been developed with plane strain finite elements. The dependence of the stress intensity factors in the sandwich specimens on the skin thickness, ratio between the Young’s moduli of the skin and core materials and boundary conditions imposed on the specimens has been examined under quasi-static loading by using the interaction integral method

RPBS: a web resource for structural bioinformatics

RPBS (Ressource Parisienne en Bioinformatique Structurale) is a resource dedicated primarily to structural bioinformatics. It is the result of a joint effort by several teams to set up an interface that offers original and powerful methods in the field. As an illustration, we focus here on three such methods uniquely available at RPBS: AUTOMAT for sequence databank scanning, YAKUSA for structure databank scanning and WLOOP for homology loop modelling. The RPBS server can be accessed at and the specific services at

Retrospective sampling in MCMC with an application to COM-Poisson regression

The normalization constant in the distribution of a discrete random variable may not be available in closed form; in such cases, the calculation of the likelihood can be computationally expensive. Approximations of the likelihood or approximate Bayesian computation methods can be used; but the resulting Markov chain Monte Carlo (MCMC) algorithm may not sample from the target of interest. In certain situations, one can efficiently compute lower and upper bounds on the likelihood. As a result, the target density and the acceptance probability of the Metropolis–Hastings algorithm can be bounded. We propose an efficient and exact MCMC algorithm based on the idea of retrospective sampling. This procedure can be applied to a number of discrete distributions, one of which is the Conway–Maxwell–Poisson distribution. In practice, the bounds on the acceptance probability do not need to be particularly tight in order to accept or reject a move. We demonstrate this method using data on the emergency hospital admissions in Scotland in 2010, where the main interest lies in the estimation of the variability of admissions, as it is considered as a proxy for health inequalities