Improving magnetic resonance imaging (MRI) examinations : Development and evaluation of an intervention to reduce movement in scanners and facilitate scan completion

© 2015 The British Psychological Society.

Supporting the Model-Driven Development of Real-time Embedded Systems with Run-Time Monitoring and Animation via Highly Customizable Code Generation

This paper presents a vision that allows the combined use of model-driven engineering, run-time monitoring, and animation for the development and analysis of components in real-time embedded systems. Key building block in the tool environment supporting this vision is a highly-customizable code generation process. Customization is performed via a configuration specification which describes the ways in which input is provided to the component, the ways in which run-time execution information can be observed, and how these observations drive animation tools. The environment is envisioned to be suitable for different activities ranging from quality assurance to supporting certification, teaching, and outreach and will be built exclusively with open source tools to increase impact. A preliminary prototype implementation is described.

Parametric CAD model based shape optimization using adjoint functions

Adjoint methods have proven to be an efficient way of calculating the gradient of an objective function with respect to a shape parameter for optimisation, with a computational cost nearly independent of the number of the design variables [1]. The approach in this paper links the adjoint surface sensitivities (gradient of objective function with respect to the surface movement) with the parametric design velocities (movement of the surface due to a CAD parameter perturbation) in order to compute the gradient of the objective function with respect to CAD variables.
For a successful implementation of shape optimization strategies in practical industrial cases, the choice of design variables or parameterisation scheme used for the model to be optimized plays a vital role. Where the goal is to base the optimization on a CAD model the choices are to use a NURBS geometry generated from CAD modelling software, where the position of the NURBS control points are the optimisation variables [2] or to use the feature based CAD model with all of the construction history to preserve the design intent [3]. The main advantage of using the feature based model is that the optimized model produced can be directly used for the downstream applications including manufacturing and process planning.
This paper presents an approach for optimization based on the feature based CAD model, which uses CAD parameters defining the features in the model geometry as the design variables. In order to capture the CAD surface movement with respect to the change in design variable, the “Parametric Design Velocity” is calculated, which is defined as the movement of the CAD model boundary in the normal direction due to a change in the parameter value.
The approach presented here for calculating the design velocities represents an advancement in terms of capability and robustness of that described by Robinson et al. [3]. The process can be easily integrated to most industrial optimisation workflows and is immune to the topology and labelling issues highlighted by other CAD based optimisation processes. It considers every continuous (“real value”) parameter type as an optimisation variable, and it can be adapted to work with any CAD modelling software, as long as it has an API which provides access to the values of the parameters which control the model shape and allows the model geometry to be exported. To calculate the movement of the boundary the methodology employs finite differences on the shape of the 3D CAD models before and after the parameter perturbation. The implementation procedure includes calculating the geometrical movement along a normal direction between two discrete representations of the original and perturbed geometry respectively. Parametric design velocities can then be directly linked with adjoint surface sensitivities to extract the gradients to use in a gradient-based optimization algorithm.
The optimisation of a flow optimisation problem is presented, in which the power dissipation of the flow in an automotive air duct is to be reduced by changing the parameters of the CAD geometry created in CATIA V5. The flow sensitivities are computed with the continuous adjoint method for a laminar and turbulent flow [4] and are combined with the parametric design velocities to compute the cost function gradients. A line-search algorithm is then used to update the design variables and proceed further with optimisation process.

Model based integration of management systems (MSs) – case study

Abstract Purpose – The purpose of this paper is to present a case study regarding the deployment of a previously developed model for the integration of management systems (MSs). The case study is developed at a manufacturing site of an international enterprise. The implementation of this model in a real business environment is aimed at assessing its feasibility. Design/methodology/approach – The presented case study takes into account different management systems standards (MSSs) progressively implemented, along the years, independently. The implementation of the model was supported by the results obtained from an investigation performed according to a structured diagnosis that was conducted to collect information related to the organizational situation of the enterprise. Findings – The main findings are as follows: a robust integrated management system (IMS), objectively more lean, structured and manageable was found to be feasible; this study provided an holistic view of the enterprise’s global management; clarifications of job descriptions and boundaries of action and responsibilities were achieved; greater efficiency in the use of resources was attained; more coordinated management of the three pillars of sustainability – environmental, economic and social, as well as risks, providing confidence and added value to the company and interested parties was achieved. Originality/value – This case study is pioneering in Portugal in respect to the implementation, at the level of an industrial organization, of the model previously developed for the integration of individualized MSs. The case study provides new insights regarding the implementation of IMSs including the rationalization of several resources and elimination of several types of organizational waste leveraging gains of efficiency. Due to its intrinsic characteristics, the model is able to support, progressively, new or revised MSSs according to the principles of annex SL (normative) – proposals for MSSs – of the International Organization for Standardization and the International Electrotechnical Commission, that the industrial organization can adopt beyond the current ones.

A Simple Model Describes Development of Early Peaks in Oomycete Zoospore Inoculum Detected in Southern UK Outdoors Horticultural Reservoirs

The numbers of water-borne oomycete propagules in outdoor reservoirs used in horticultural nurseries within the UK are investigated in this study. Water samples were recovered from 11 different horticultural nurseries in the southern UK during Jan-May in two ‘cool’ years (2010.and 2013; winter temperatures 2.0 and 0.4oC below UK Met Office 30 year winter average respectively) and two ‘warm’ years (2008 and 2012; winter temperatures 1.2 and 0.9oC above UK Met Office 30 year winter average respectively). Samples were analysed for total number of oomycete colony forming units (CFU), predominantly members of the families Saprolegniaceae and Pythiaceae, and these were combined to give monthly mean counts. The numbers of CFU were investigated with respect to prevailing climate in the region: mean monthly air temperatures calculated by using daily observations from the nearest climatological station. The investigations show that the number of CFU during spring can be explained by a linear first-order equation and a statistically significant r2 value of 0.66 with the simple relationship: [CFU] = a(T-Tb )-b, where a is the rate of inoculum development with temperature T, and b is the baseload population at temperatures below Tb. Despite the majority of oomycete CFU detected being non-phytopathogenic members of the Saprolegniaceae, total oomycete CFU counts are still of considerable value as indicators of irrigation water treatment efficacy and cleanliness of storage tanks. The presence/absence of Pythium spp. was also determined for all samples tested, and Pythium CFU were found to be present in the majority, the exceptions all being particularly cold months (January and February 2010 and January 2008). A simple scenario study (+2 deg C) suggests that abundance of water-borne oomycetes during spring could be affected by increased temperatures due to climate change.

The natural pilot model for flight proficiency evaluation

Cover title.

Meta-analysis and cross-validation of a hyperglycemic status predictor model based on salivary glucose

Poster presented at the First International Congress of CiiEM - From Basic Sciences To Clinical Research. Egas Moniz, Caparica, Portugal, 27-28 November 2015.

Development and evaluation of floating microspheres of curcumin in alloxan-induced diabetic rats

Purpose: To prepare and evaluate floating microspheres of curcumin for prolonged gastric residence and to study their effect on alloxan-induced diabetic rats. Methods: Floating microsphere were prepared by emulsion-solvent diffusion method, using hydroxylpropyl methylcellulose, chitosan and Eudragit S 100 polymer in varying proportions. Ethanol/dichloromethane blend was used as solvent in a ratio of 1:1. The floating microspheres were evaluated for flow properties, particle size, incorporation efficiency, as well as in-vitro floatability and drug release. The anti-diabetic activity of the floating microspheres of batch FM4 was performed on alloxaninduced diabetic rats. Result: The floating microspheres had particle size, buoyancy, drug entrapment efficiency and yield in the ranges of 255.32 - 365.65 μm, 75.58 - 89.59, 72.6 - 83.5, and 60.46 - 80.02 %, respectively. Maximum drug release after 24 h was 82.62 % for formulation FM4 and 73.879, 58.613 and 46.106 % for formulations FM1, FM2, and FM3 respectively. In-vivo data obtained over a 120-h period indicate that curcumin floating microspheres from batch FM4 showed the better glycemic control than control and a commercial brand of the drug. Conclusion: The developed floating curcumin delivery system seems economical and effective in diabetes management in rats, and enhances the bioavailability of the drug.

Model-Based Contrastive Explanations for XAIP: Towards a General Model and Prototype

Planning is an important sub-field of artificial intelligence (AI) focusing on letting intelligent agents deliberate on the most adequate course of action to attain their goals. Thanks to the recent boost in the number of critical domains and systems which exploit planning for their internal procedures, there is an increasing need for planning systems to become more transparent and trustworthy. Along this line, planning systems are now required to produce not only plans but also explanations about those plans, or the way they were attained. To address this issue, a new research area is emerging in the AI panorama: eXplainable AI (XAI), within which explainable planning (XAIP) is a pivotal sub-field. As a recent domain, XAIP is far from mature. No consensus has been reached in the literature about what explanations are, how they should be computed, and what they should explain in the first place. Furthermore, existing contributions are mostly theoretical, and software implementations are rarely more than preliminary. To overcome such issues, in this thesis we design an explainable planning framework bridging the gap between theoretical contributions from literature and software implementations. More precisely, taking inspiration from the state of the art, we develop a formal model for XAIP, and the software tool enabling its practical exploitation. Accordingly, the contribution of this thesis is four-folded. First, we review the state of the art of XAIP, supplying an outline of its most significant contributions from the literature. We then generalise the aforementioned contributions into a unified model for XAIP, aimed at supporting model-based contrastive explanations. Next, we design and implement an algorithm-agnostic library for XAIP based on our model. Finally, we validate our library from a technological perspective, via an extensive testing suite. Furthermore, we assess its performance and usability through a set of benchmarks and end-to-end examples.

Evaluation of 3D cell culture systems for host-pathogen interaction studies

Traditional cell culture models have limitations in extrapolating functional mechanisms that underlie strategies of microbial virulence. Indeed during the infection the pathogens adapt to different tissue-specific environmental factors. The development of in vitro models resembling human tissue physiology might allow the replacement of inaccurate or aberrant animal models. Three-dimensional (3D) cell culture systems are more reliable and more predictive models that can be used for the meaningful dissection of host–pathogen interactions. The lung and gut mucosae often represent the first site of exposure to pathogens and provide a physical barrier against their entry. Within this context, the tracheobronchial and small intestine tract were modelled by tissue engineering approach. The main work was focused on the development and the extensive characterization of a human organotypic airway model, based on a mechanically supported co-culture of normal primary cells. The regained morphological features, the retrieved environmental factors and the presence of specific epithelial subsets resembled the native tissue organization. In addition, the respiratory model enabled the modular insertion of interesting cell types, such as innate immune cells or multipotent stromal cells, showing a functional ability to release pertinent cytokines differentially. Furthermore this model responded imitating known events occurring during the infection by Non-typeable H. influenzae. Epithelial organoid models, mimicking the small intestine tract, were used for a different explorative analysis of tissue-toxicity. Further experiments led to detection of a cell population targeted by C. difficile Toxin A and suggested a role in the impairment of the epithelial homeostasis by the bacterial virulence machinery. The described cell-centered strategy can afford critical insights in the evaluation of the host defence and pathogenic mechanisms. The application of these two models may provide an informing step that more coherently defines relevant molecular interactions happening during the infection.

High-Level Modeling of Multimodal Interaction Techniques Using NiMMiT

The past few years, multimodal interaction has been gaining importance in virtual environments. Although multimodality renders interacting with an environment more natural and intuitive, the development cycle of such an application is often long and expensive. In our overall field of research, we investigate how modelbased design can facilitate the development process by designing environments through the use of highlevel diagrams. In this scope, we present ‘NiMMiT’, a graphical notation for expressing and evaluating multimodal user interaction; we elaborate on the NiMMiT primitives and demonstrate its use by means of a comprehensive example.

The Hydrophobic interaction: modeling hydrophobic interactions and aggregation of non-polar particles in aqueous solutions

Malgré son importance dans notre vie de tous les jours, certaines propriétés de l?eau restent inexpliquées. L'étude des interactions entre l'eau et les particules organiques occupe des groupes de recherche dans le monde entier et est loin d'être finie. Dans mon travail j'ai essayé de comprendre, au niveau moléculaire, ces interactions importantes pour la vie. J'ai utilisé pour cela un modèle simple de l'eau pour décrire des solutions aqueuses de différentes particules. Récemment, l?eau liquide a été décrite comme une structure formée d?un réseau aléatoire de liaisons hydrogènes. En introduisant une particule hydrophobe dans cette structure à basse température, certaines liaisons hydrogènes sont détruites ce qui est énergétiquement défavorable. Les molécules d?eau s?arrangent alors autour de cette particule en formant une cage qui permet de récupérer des liaisons hydrogènes (entre molécules d?eau) encore plus fortes : les particules sont alors solubles dans l?eau. A des températures plus élevées, l?agitation thermique des molécules devient importante et brise les liaisons hydrogènes. Maintenant, la dissolution des particules devient énergétiquement défavorable, et les particules se séparent de l?eau en formant des agrégats qui minimisent leur surface exposée à l?eau. Pourtant, à très haute température, les effets entropiques deviennent tellement forts que les particules se mélangent de nouveau avec les molécules d?eau. En utilisant un modèle basé sur ces changements de structure formée par des liaisons hydrogènes j?ai pu reproduire les phénomènes principaux liés à l?hydrophobicité. J?ai trouvé une région de coexistence de deux phases entre les températures critiques inférieure et supérieure de solubilité, dans laquelle les particules hydrophobes s?agrègent. En dehors de cette région, les particules sont dissoutes dans l?eau. J?ai démontré que l?interaction hydrophobe est décrite par un modèle qui prend uniquement en compte les changements de structure de l?eau liquide en présence d?une particule hydrophobe, plutôt que les interactions directes entre les particules. Encouragée par ces résultats prometteurs, j?ai étudié des solutions aqueuses de particules hydrophobes en présence de co-solvants cosmotropiques et chaotropiques. Ce sont des substances qui stabilisent ou déstabilisent les agrégats de particules hydrophobes. La présence de ces substances peut être incluse dans le modèle en décrivant leur effet sur la structure de l?eau. J?ai pu reproduire la concentration élevée de co-solvants chaotropiques dans le voisinage immédiat de la particule, et l?effet inverse dans le cas de co-solvants cosmotropiques. Ce changement de concentration du co-solvant à proximité de particules hydrophobes est la cause principale de son effet sur la solubilité des particules hydrophobes. J?ai démontré que le modèle adapté prédit correctement les effets implicites des co-solvants sur les interactions de plusieurs corps entre les particules hydrophobes. En outre, j?ai étendu le modèle à la description de particules amphiphiles comme des lipides. J?ai trouvé la formation de différents types de micelles en fonction de la distribution des regions hydrophobes à la surface des particules. L?hydrophobicité reste également un sujet controversé en science des protéines. J?ai défini une nouvelle échelle d?hydrophobicité pour les acides aminés qui forment des protéines, basée sur leurs surfaces exposées à l?eau dans des protéines natives. Cette échelle permet une comparaison meilleure entre les expériences et les résultats théoriques. Ainsi, le modèle développé dans mon travail contribue à mieux comprendre les solutions aqueuses de particules hydrophobes. Je pense que les résultats analytiques et numériques obtenus éclaircissent en partie les processus physiques qui sont à la base de l?interaction hydrophobe.<br/><br/>Despite the importance of water in our daily lives, some of its properties remain unexplained. Indeed, the interactions of water with organic particles are investigated in research groups all over the world, but controversy still surrounds many aspects of their description. In my work I have tried to understand these interactions on a molecular level using both analytical and numerical methods. Recent investigations describe liquid water as random network formed by hydrogen bonds. The insertion of a hydrophobic particle at low temperature breaks some of the hydrogen bonds, which is energetically unfavorable. The water molecules, however, rearrange in a cage-like structure around the solute particle. Even stronger hydrogen bonds are formed between water molecules, and thus the solute particles are soluble. At higher temperatures, this strict ordering is disrupted by thermal movements, and the solution of particles becomes unfavorable. They minimize their exposed surface to water by aggregating. At even higher temperatures, entropy effects become dominant and water and solute particles mix again. Using a model based on these changes in water structure I have reproduced the essential phenomena connected to hydrophobicity. These include an upper and a lower critical solution temperature, which define temperature and density ranges in which aggregation occurs. Outside of this region the solute particles are soluble in water. Because I was able to demonstrate that the simple mixture model contains implicitly many-body interactions between the solute molecules, I feel that the study contributes to an important advance in the qualitative understanding of the hydrophobic effect. I have also studied the aggregation of hydrophobic particles in aqueous solutions in the presence of cosolvents. Here I have demonstrated that the important features of the destabilizing effect of chaotropic cosolvents on hydrophobic aggregates may be described within the same two-state model, with adaptations to focus on the ability of such substances to alter the structure of water. The relevant phenomena include a significant enhancement of the solubility of non-polar solute particles and preferential binding of chaotropic substances to solute molecules. In a similar fashion, I have analyzed the stabilizing effect of kosmotropic cosolvents in these solutions. Including the ability of kosmotropic substances to enhance the structure of liquid water, leads to reduced solubility, larger aggregation regime and the preferential exclusion of the cosolvent from the hydration shell of hydrophobic solute particles. I have further adapted the MLG model to include the solvation of amphiphilic solute particles in water, by allowing different distributions of hydrophobic regions at the molecular surface, I have found aggregation of the amphiphiles, and formation of various types of micelle as a function of the hydrophobicity pattern. I have demonstrated that certain features of micelle formation may be reproduced by the adapted model to describe alterations of water structure near different surface regions of the dissolved amphiphiles. Hydrophobicity remains a controversial quantity also in protein science. Based on the surface exposure of the 20 amino-acids in native proteins I have defined the a new hydrophobicity scale, which may lead to an improvement in the comparison of experimental data with the results from theoretical HP models. Overall, I have shown that the primary features of the hydrophobic interaction in aqueous solutions may be captured within a model which focuses on alterations in water structure around non-polar solute particles. The results obtained within this model may illuminate the processes underlying the hydrophobic interaction.<br/><br/>La vie sur notre planète a commencé dans l'eau et ne pourrait pas exister en son absence : les cellules des animaux et des plantes contiennent jusqu'à 95% d'eau. Malgré son importance dans notre vie de tous les jours, certaines propriétés de l?eau restent inexpliquées. En particulier, l'étude des interactions entre l'eau et les particules organiques occupe des groupes de recherche dans le monde entier et est loin d'être finie. Dans mon travail j'ai essayé de comprendre, au niveau moléculaire, ces interactions importantes pour la vie. J'ai utilisé pour cela un modèle simple de l'eau pour décrire des solutions aqueuses de différentes particules. Bien que l?eau soit généralement un bon solvant, un grand groupe de molécules, appelées molécules hydrophobes (du grecque "hydro"="eau" et "phobia"="peur"), n'est pas facilement soluble dans l'eau. Ces particules hydrophobes essayent d'éviter le contact avec l'eau, et forment donc un agrégat pour minimiser leur surface exposée à l'eau. Cette force entre les particules est appelée interaction hydrophobe, et les mécanismes physiques qui conduisent à ces interactions ne sont pas bien compris à l'heure actuelle. Dans mon étude j'ai décrit l'effet des particules hydrophobes sur l'eau liquide. L'objectif était d'éclaircir le mécanisme de l'interaction hydrophobe qui est fondamentale pour la formation des membranes et le fonctionnement des processus biologiques dans notre corps. Récemment, l'eau liquide a été décrite comme un réseau aléatoire formé par des liaisons hydrogènes. En introduisant une particule hydrophobe dans cette structure, certaines liaisons hydrogènes sont détruites tandis que les molécules d'eau s'arrangent autour de cette particule en formant une cage qui permet de récupérer des liaisons hydrogènes (entre molécules d?eau) encore plus fortes : les particules sont alors solubles dans l'eau. A des températures plus élevées, l?agitation thermique des molécules devient importante et brise la structure de cage autour des particules hydrophobes. Maintenant, la dissolution des particules devient défavorable, et les particules se séparent de l'eau en formant deux phases. A très haute température, les mouvements thermiques dans le système deviennent tellement forts que les particules se mélangent de nouveau avec les molécules d'eau. A l'aide d'un modèle qui décrit le système en termes de restructuration dans l'eau liquide, j'ai réussi à reproduire les phénomènes physiques liés à l?hydrophobicité. J'ai démontré que les interactions hydrophobes entre plusieurs particules peuvent être exprimées dans un modèle qui prend uniquement en compte les liaisons hydrogènes entre les molécules d'eau. Encouragée par ces résultats prometteurs, j'ai inclus dans mon modèle des substances fréquemment utilisées pour stabiliser ou déstabiliser des solutions aqueuses de particules hydrophobes. J'ai réussi à reproduire les effets dûs à la présence de ces substances. De plus, j'ai pu décrire la formation de micelles par des particules amphiphiles comme des lipides dont la surface est partiellement hydrophobe et partiellement hydrophile ("hydro-phile"="aime l'eau"), ainsi que le repliement des protéines dû à l'hydrophobicité, qui garantit le fonctionnement correct des processus biologiques de notre corps. Dans mes études futures je poursuivrai l'étude des solutions aqueuses de différentes particules en utilisant les techniques acquises pendant mon travail de thèse, et en essayant de comprendre les propriétés physiques du liquide le plus important pour notre vie : l'eau.

Applying Information Foraging Theory to understand user interaction with content-based image retrieval

The paper proposes an ISE (Information goal, Search strategy, Evaluation threshold) user classification model based on Information Foraging Theory for understanding user interaction with content-based image retrieval (CBIR). The proposed model is verified by a multiple linear regression analysis based on 50 users' interaction features collected from a task-based user study of interactive CBIR systems. To our best knowledge, this is the first principled user classification model in CBIR verified by a formal and systematic qualitative analysis of extensive user interaction data. Copyright 2010 ACM.

Event-Code Interaction Directed Test Cases

The Graphical User Interface (GUI) is an integral component of contemporary computer software. A stable and reliable GUI is necessary for correct functioning of software applications. Comprehensive verification of the GUI is a routine part of most software development life-cycles. The input space of a GUI is typically large, making exhaustive verification difficult. GUI defects are often revealed by exercising parts of the GUI that interact with each other. It is challenging for a verification method to drive the GUI into states that might contain defects. In recent years, model-based methods, that target specific GUI interactions, have been developed. These methods create a formal model of the GUI’s input space from specification of the GUI, visible GUI behaviors and static analysis of the GUI’s program-code. GUIs are typically dynamic in nature, whose user-visible state is guided by underlying program-code and dynamic program-state. This research extends existing model-based GUI testing techniques by modelling interactions between the visible GUI of a GUI-based software and its underlying program-code. The new model is able to, efficiently and effectively, test the GUI in ways that were not possible using existing methods. The thesis is this: Long, useful GUI testcases can be created by examining the interactions between the GUI, of a GUI-based application, and its program-code. To explore this thesis, a model-based GUI testing approach is formulated and evaluated. In this approach, program-code level interactions between GUI event handlers will be examined, modelled and deployed for constructing long GUI testcases. These testcases are able to drive the GUI into states that were not possible using existing models. Implementation and evaluation has been conducted using GUITAR, a fully-automated, open-source GUI testing framework.

Evaluation of the conductor-like screening model for real solvents for the prediction of the water activity coefficient at infinite dilution in ionic liquids

Ionic liquids (ILs) have attracted great attention, from both industry and academia, as alternative fluids for very different types of applications. The large number of cations and anions allow a wide range of physical and chemical characteristics to be designed. However, the exhaustive measurement of all these systems is impractical, thus requiring the use of a predictive model for their study. In this work, the predictive capability of the conductor-like screening model for real solvents (COSMO-RS), a model based on unimolecular quantum chemistry calculations, was evaluated for the prediction water activity coefficient at infinite dilution, gamma(infinity)(w), in several classes of ILs. A critical evaluation of the experimental and predicted data using COSMO-RS was carried out. The global average relative deviation was found to be 27.2%, indicating that the model presents a satisfactory prediction ability to estimate gamma(infinity)(w) in a broad range of ILs. The results also showed that the basicity of the ILs anions plays an important role in their interaction with water, and it considerably determines the enthalpic behavior of the binary mixtures composed by Its and water. Concerning the cation effect, it is possible to state that generally gamma(infinity)(w) increases with the cation size, but it is shown that the cation-anion interaction strength is also important and is strongly correlated to the anion ability to interact with water. The results here reported are relevant in the understanding of ILs-water interactions and the impact of the various structural features of its on the gamma(infinity)(w) as these allow the development of guidelines for the choice of the most suitable lLs with enhanced interaction with water.