Elements pour adapter les systemes de recherche d'information aux dyslexiques [Elements to adapt information retrieval systems to dyslexic users]

RÉSUMÉ. La prise en compte des troubles de la communication dans l’utilisation des systèmes de recherche d’information tels qu’on peut en trouver sur le Web est généralement réalisée par des interfaces utilisant des modalités n’impliquant pas la lecture et l’écriture. Peu d’applications existent pour aider l’utilisateur en difficulté dans la modalité textuelle. Nous proposons la prise en compte de la conscience phonologique pour assister l’utilisateur en difficulté d’écriture de requêtes (dysorthographie) ou de lecture de documents (dyslexie). En premier lieu un système de réécriture et d’interprétation des requêtes entrées au clavier par l’utilisateur est proposé : en s’appuyant sur les causes de la dysorthographie et sur les exemples à notre disposition, il est apparu qu’un système combinant une approche éditoriale (type correcteur orthographique) et une approche orale (système de transcription automatique) était plus approprié. En second lieu une méthode d’apprentissage automatique utilise des critères spécifiques , tels que la cohésion grapho-phonémique, pour estimer la lisibilité d’une phrase, puis d’un texte. ABSTRACT. Most applications intend to help disabled users in the information retrieval process by proposing non-textual modalities. This paper introduces specific parameters linked to phonological awareness in the textual modality. This will enhance the ability of systems to deal with orthographic issues and with the adaptation of results to the reader when for example the reader is dyslexic. We propose a phonology based sentence level rewriting system that combines spelling correction, speech synthesis and automatic speech recognition. This has been evaluated on a corpus of questions we get from dyslexic children. We propose a specific sentence readability measure that involves phonetic parameters such as grapho-phonemic cohesion. This has been learned on a corpus of reading time of sentences read by dyslexic children.

Modeling intrinsic noise and delays in chemical kinetics of coupled autoregulated oscillating cells

Delays are an important feature in temporal models of genetic regulation due to slow biochemical processes, such as transcription and translation. In this paper, we show how to model intrinsic noise effects in a delayed setting by either using a delay stochastic simulation algorithm (DSSA) or, for larger and more complex systems, a generalized Binomial τ-leap method (Bτ-DSSA). As a particular application, we apply these ideas to modeling somite segmentation in zebra fish across a number of cells in which two linked oscillatory genes (her1 and her7) are synchronized via Notch signaling between the cells.

Stochastic chemical kinetics and the quasi-steady-state assumption : application to the stochastic simulation algorithm and chemical master equation

Recently the application of the quasi-steady-state approximation (QSSA) to the stochastic simulation algorithm (SSA) was suggested for the purpose of speeding up stochastic simulations of chemical systems that involve both relatively fast and slow chemical reactions [Rao and Arkin, J. Chem. Phys. 118, 4999 (2003)] and further work has led to the nested and slow-scale SSA. Improved numerical efficiency is obtained by respecting the vastly different time scales characterizing the system and then by advancing only the slow reactions exactly, based on a suitable approximation to the fast reactions. We considerably extend these works by applying the QSSA to numerical methods for the direct solution of the chemical master equation (CME) and, in particular, to the finite state projection algorithm [Munsky and Khammash, J. Chem. Phys. 124, 044104 (2006)], in conjunction with Krylov methods. In addition, we point out some important connections to the literature on the (deterministic) total QSSA (tQSSA) and place the stochastic analogue of the QSSA within the more general framework of aggregation of Markov processes. We demonstrate the new methods on four examples: Michaelis–Menten enzyme kinetics, double phosphorylation, the Goldbeter–Koshland switch, and the mitogen activated protein kinase cascade. Overall, we report dramatic improvements by applying the tQSSA to the CME solver.

A Krylov-based finite state projection algorithm for solving the chemical master equation arising in the discrete modelling of biological systems

Biochemical reactions underlying genetic regulation are often modelled as a continuous-time, discrete-state, Markov process, and the evolution of the associated probability density is described by the so-called chemical master equation (CME). However the CME is typically difficult to solve, since the state-space involved can be very large or even countably infinite. Recently a finite state projection method (FSP) that truncates the state-space was suggested and shown to be effective in an example of a model of the Pap-pili epigenetic switch. However in this example, both the model and the final time at which the solution was computed, were relatively small. Presented here is a Krylov FSP algorithm based on a combination of state-space truncation and inexact matrix-vector product routines. This allows larger-scale models to be studied and solutions for larger final times to be computed in a realistic execution time. Additionally the new method computes the solution at intermediate times at virtually no extra cost, since it is derived from Krylov-type methods for computing matrix exponentials. For the purpose of comparison the new algorithm is applied to the model of the Pap-pili epigenetic switch, where the original FSP was first demonstrated. Also the method is applied to a more sophisticated model of regulated transcription. Numerical results indicate that the new approach is significantly faster and extendable to larger biological models.

Accelerated leap methods for simulating discrete stochastic chemical kinetics

Biologists are increasingly conscious of the critical role that noise plays in cellular functions such as genetic regulation, often in connection with fluctuations in small numbers of key regulatory molecules. This has inspired the development of models that capture this fundamentally discrete and stochastic nature of cellular biology - most notably the Gillespie stochastic simulation algorithm (SSA). The SSA simulates a temporally homogeneous, discrete-state, continuous-time Markov process, and of course the corresponding probabilities and numbers of each molecular species must all remain positive. While accurately serving this purpose, the SSA can be computationally inefficient due to very small time stepping so faster approximations such as the Poisson and Binomial τ-leap methods have been suggested. This work places these leap methods in the context of numerical methods for the solution of stochastic differential equations (SDEs) driven by Poisson noise. This allows analogues of Euler-Maruyuma, Milstein and even higher order methods to be developed through the Itô-Taylor expansions as well as similar derivative-free Runge-Kutta approaches. Numerical results demonstrate that these novel methods compare favourably with existing techniques for simulating biochemical reactions by more accurately capturing crucial properties such as the mean and variance than existing methods.

Augmenting mobile computing with video game elements to support, motivate and engage young people in educational, real-world events

Video games have shown great potential as tools that both engage and motivate players to achieve tasks and build communities in fantasy worlds. We propose that the application of game elements to real world activities can aid in delivering contextual information in interesting ways and help young people to engage in everyday events. Our research will explore how we can unite utility and fun to enhance information delivery, encourage participation, build communities and engage users with utilitarian events situated in the real world. This research aims to identify key game elements that work effectively to engage young digital natives, and provide guidelines to influence the design of interactions and interfaces for event applications in the future. This research will primarily contribute to areas of user experience and pervasive gaming.

Influence of physical and chemical parameters on the treatment of heavy metals in polluted stormwater using zeolite : A review

Zeolite-based technology can provide a cost effective solution for stormwater treatment for the removal of toxic heavy metals under increasing demand of safe water from alternative sources. This paper reviews the currently available knowledge relating to the effect of properties of zeolites such as pore size, surface area and Si:Al ratio and the physico-chemical conditions of the system such as pH, temperature, initial metal concentration and zeolite concentration on heavy metal removal performance. The primary aims are, to consolidate available knowledge and identify knowledge gaps. It was established that an in-depth understanding of operational issues such as, diffusion of metal ions into the zeolite pore structure, pore clogging, zeolite surface coverage by particulates in stormwater as well as the effect of pH on stormwater quality in the presence of zeolites is essential for developing a zeolite-based technology for the treatment of polluted stormwater. The optimum zeolite concentration to treat typical volumes of stormwater and initial heavy metal concentrations in stormwater should also be considered as operational issues in this regard. Additionally, leaching of aluminium and sodium ions from the zeolite structure to solution were identified as key issues requiring further research in the effort to develop cost effective solutions for the removal of heavy metals from stormwater.

Relationship to the bereaved and perceptions of severity of trauma differentiate elements of posttraumatic growth

The field of bereavement and grief has been expanding to recognise the potential for growth following the loss of a loved one. This study sought to examine the effect of the relationship to the deceased and perceptions of the severity of the trauma on dimensions of posttraumatic growth. Participants were 146 people who had lost either: a) a first degree relative, b) a second degree relative, or c) a non-related friend. Results demonstrated that both severity and the relationship to the bereaved differentiate posttraumatic growth outcomes. For example, participants who had lost a first degree relative reported higher levels of growth than those who had lost a second degree relative. Consistent with previous research in general trauma populations, the more severe the loss was rated, the higher the levels of growth. Implications for practice are discussed.

Characterisation of the TaNF-Y family of transcription factors in wheat

Light plays a unique role for plants as it is both a source of energy for growth and a signal for development. Light captured by the pigments in the light harvesting complexes is used to drive the synthesis of the chemical energy required for carbon assimilation. The light perceived by photoreceptors activates effectors, such as transcription factors (TFs), which modulate the expression of light-responsive genes. Recently, it has been speculated that increasing the photosynthetic rate could further improve the yield potential of three carbon (C3) crops such as wheat. However, little is currently known about the transcriptional regulation of photosynthesis genes, particularly in crop species. Nuclear factor Y (NF-Y) TF is a functionally diverse regulator of growth and development in the model plant species, with demonstrated roles in embryo development, stress response, flowering time and chloroplast biogenesis. Furthermore, a light-responsive NF-Y binding site (CCAAT-box) is present in the promoter of a spinach photosynthesis gene. As photosynthesis genes are co-regulated by light and co-regulated genes typically have similar regulatory elements in their promoters, it seems likely that other photosynthesis genes would also have light-responsive CCAAT-boxes. This provided the impetus to investigate the NF-Y TF in bread wheat. This thesis is focussed on wheat NF-Y members that have roles in light-mediated gene regulation with an emphasis on their involvement in the regulation of photosynthesis genes. NF-Y is a heterotrimeric complex, comprised of the three subunits NF-YA, NF-YB and NF-YC. Unlike the mammalian and yeast counterparts, each of the three subunits is encoded by multiple genes in Arabidopsis. The initial step taken in this study was the identification of the wheat NF-Y family (Chapter 3). A search of the current wheat nucleotide sequence databases identified 37 NF-Y genes (10 NF-YA, 11 NF-YB, 14 NF-YC & 2 Dr1). Phylogenetic analysis revealed that each of the three wheat NF-Y (TaNF-Y) subunit families could be divided into 4-5 clades based on their conserved core regions. Outside of the core regions, eleven motifs were identified to be conserved between Arabidopsis, rice and wheat NF-Y subunit members. The expression profiles of TaNF-Y genes were constructed using quantitative real-time polymerase chain reaction (RT-PCR). Some TaNF-Y subunit members had little variation in their transcript levels among the organs, while others displayed organ-predominant expression profiles, including those expressed mainly in the photosynthetic organs. To investigate their potential role in light-mediated gene regulation, the light responsiveness of the TaNF-Y genes were examined (Chapters 4 and 5). Two TaNF-YB and five TaNF-YC members were markedly upregulated by light in both the wheat leaves and seedling shoots. To identify the potential target genes of the light-upregulated NF-Y subunit members, a gene expression correlation analysis was conducted using publically available Affymetrix Wheat Genome Array datasets. This analysis revealed that the transcript expression levels of TaNF-YB3 and TaNF-YC11 were significantly correlated with those of photosynthesis genes. These correlated express profiles were also observed in the quantitative RT-PCR dataset from wheat plants grown under light and dark conditions. Sequence analysis of the promoters of these wheat photosynthesis genes revealed that they were enriched with potential NF-Y binding sites (CCAAT-box). The potential role of TaNF-YB3 in the regulation of photosynthetic genes was further investigated using a transgenic approach (Chapter 5). Transgenic wheat lines constitutively expressing TaNF-YB3 were found to have significantly increased expression levels of photosynthesis genes, including those encoding light harvesting chlorophyll a/b-binding proteins, photosystem I reaction centre subunits, a chloroplast ATP synthase subunit and glutamyl-tRNA reductase (GluTR). GluTR is a rate-limiting enzyme in the chlorophyll biosynthesis pathway. In association with the increased expression of the photosynthesis genes, the transgenic lines had a higher leaf chlorophyll content, increased photosynthetic rate and had a more rapid early growth rate compared to the wild-type wheat. In addition to its role in the regulation of photosynthesis genes, TaNF-YB3 overexpression lines flower on average 2-days earlier than the wild-type (Chapter 6). Quantitative RT-PCR analysis showed that there was a 13-fold increase in the expression level of the floral integrator, TaFT. The transcript levels of other downstream genes (TaFT2 and TaVRN1) were also increased in the transgenic lines. Furthermore, the transcript levels of TaNF-YB3 were significantly correlated with those of constans (CO), constans-like (COL) and timing of chlorophyll a/b-binding (CAB) expression 1 [TOC1; (CCT)] domain-containing proteins known to be involved in the regulation of flowering time. To summarise the key findings of this study, 37 NF-Y genes were identified in the crop species wheat. An in depth analysis of TaNF-Y gene expression profiles revealed that the potential role of some light-upregulated members was in the regulation of photosynthetic genes. The involvement of TaNF-YB3 in the regulation of photosynthesis genes was supported by data obtained from transgenic wheat lines with increased constitutive expression of TaNF-YB3. The overexpression of TaNF-YB3 in the transgenic lines revealed this NF-YB member is also involved in the fine-tuning of flowering time. These data suggest that the NF-Y TF plays an important role in light-mediated gene regulation in wheat.

A physico-chemical characterisation of particulate emissions from a compression ignition engine : the influence of biodiesel feedstock

This study undertook a physico-chemical characterisation of particle emissions from a single compression ignition engine operated at one test mode with 3 biodiesel fuels made from 3 different feedstocks (i.e. soy, tallow and canola) at 4 different blend percentages (20%, 40%, 60% and 80%) to gain insights into their particle-related health effects. Particle physical properties were inferred by measuring particle number size distributions both with and without heating within a thermodenuder (TD) and also by measuring particulate matter (PM) emission factors with an aerodynamic diameter less than 10 μm (PM10). The chemical properties of particulates were investigated by measuring particle and vapour phase Polycyclic Aromatic Hydrocarbons (PAHs) and also Reactive Oxygen Species (ROS) concentrations. The particle number size distributions showed strong dependency on feedstock and blend percentage with some fuel types showing increased particle number emissions, whilst others showed particle number reductions. In addition, the median particle diameter decreased as the blend percentage was increased. Particle and vapour phase PAHs were generally reduced with biodiesel, with the results being relatively independent of the blend percentage. The ROS concentrations increased monotonically with biodiesel blend percentage, but did not exhibit strong feedstock variability. Furthermore, the ROS concentrations correlated quite well with the organic volume percentage of particles – a quantity which increased with increasing blend percentage. At higher blend percentages, the particle surface area was significantly reduced, but the particles were internally mixed with a greater organic volume percentage (containing ROS) which has implications for using surface area as a regulatory metric for diesel particulate matter (DPM) emissions.

Thermal profile of a near-adiabatic compression process in a cylindrical tube and establishment of critical control elements for repeatable process control

The compressed gas industry and government agencies worldwide utilize "adiabatic compression" testing for qualifying high-pressure valves, regulators, and other related flow control equipment for gaseous oxygen service. This test methodology is known by various terms including adiabatic compression testing, gaseous fluid impact testing, pneumatic impact testing, and BAM testing as the most common terms. The test methodology will be described in greater detail throughout this document but in summary it consists of pressurizing a test article (valve, regulator, etc.) with gaseous oxygen within 15 to 20 milliseconds (ms). Because the driven gas1 and the driving gas2 are rapidly compressed to the final test pressure at the inlet of the test article, they are rapidly heated by the sudden increase in pressure to sufficient temperatures (thermal energies) to sometimes result in ignition of the nonmetallic materials (seals and seats) used within the test article. In general, the more rapid the compression process the more "adiabatic" the pressure surge is presumed to be and the more like an isentropic process the pressure surge has been argued to simulate. Generally speaking, adiabatic compression is widely considered the most efficient ignition mechanism for directly kindling a nonmetallic material in gaseous oxygen and has been implicated in many fire investigations. Because of the ease of ignition of many nonmetallic materials by this heating mechanism, many industry standards prescribe this testing. However, the results between various laboratories conducting the testing have not always been consistent. Research into the test method indicated that the thermal profile achieved (i.e., temperature/time history of the gas) during adiabatic compression testing as required by the prevailing industry standards has not been fully modeled or empirically verified, although attempts have been made. This research evaluated the following questions: 1) Can the rapid compression process required by the industry standards be thermodynamically and fluid dynamically modeled so that predictions of the thermal profiles be made, 2) Can the thermal profiles produced by the rapid compression process be measured in order to validate the thermodynamic and fluid dynamic models; and, estimate the severity of the test, and, 3) Can controlling parameters be recommended so that new guidelines may be established for the industry standards to resolve inconsistencies between various test laboratories conducting tests according to the present standards?

A phenomenological model for the structure-composition relationship of the high Tc cuprates based on simple chemical principles

A simple phenomenological model for the relationship between structure and composition of the high Tc cuprates is presented. The model is based on two simple crystal chemistry principles: unit cell doping and charge balance within unit cells. These principles are inspired by key experimental observations of how the materials accommodate large deviations from stoichiometry. Consistent explanations for significant HTSC properties can be explained without any additional assumptions while retaining valuable insight for geometric interpretation. Combining these two chemical principles with a review of Crystal Field Theory (CFT) or Ligand Field Theory (LFT), it becomes clear that the two oxidation states in the conduction planes (typically d8 and d9) belong to the most strongly divergent d-levels as a function of deformation from regular octahedral coordination. This observation offers a link to a range of coupling effects relating vibrations and spin waves through application of Hund’s rules. An indication of this model’s capacity to predict physical properties for HTSC is provided and will be elaborated in subsequent publications. Simple criteria for the relationship between structure and composition in HTSC systems may guide chemical syntheses within new material systems.

Combined time- and space-resolved Raman spectrometer for the non-invasive depth profiling of chemical hazards

A time-resolved inverse spatially offset Raman spectrometer was constructed for depth profiling of Raman-active substances under both the lab and the field environments. The system operating principles and performance are discussed along with its advantages relative to traditional continuous wave spatially offset Raman spectrometer. The developed spectrometer uses a combination of space- and time-resolved detection in order to obtain high-quality Raman spectra from substances hidden behind coloured opaque surface layers, such as plastic and garments, with a single measurement. The time-gated spatially offset Raman spectrometer was successfully used to detect concealed explosives and drug precursors under incandescent and fluorescent background light as well as under daylight. The average screening time was 50 s per measurement. The excitation energy requirements were relatively low (20 mW) which makes the probe safe for screening hazardous substances. The unit has been designed with nanosecond laser excitation and gated detection, making it of lower cost and complexity than previous picosecond-based systems, to provide a functional platform for in-line or in-field sensing of chemical substances.

Source characterisation of road dust based on chemical and mineralogical composition

Road dust contain potentially toxic pollutants originating from a range of anthropogenic sources common to urban land uses and soil inputs from surrounding areas. The research study analysed the mineralogy and morphology of dust samples from road surfaces from different land uses and background soil samples to characterise the relative source contributions to road dust. The road dust consist primarily of soil derived minerals (60%) with quartz averaging 40-50% and remainder being clay forming minerals of albite, microcline, chlorite and muscovite originating from surrounding soils. About 2% was organic matter primarily originating from plant matter. Potentially toxic pollutants represented about 30% of the build-up. These pollutants consist of brake and tire wear, combustion emissions and fly ash from asphalt. Heavy metals such as Zn, Cu, Pb, Ni, Cr and Cd primarily originate from vehicular traffic while Fe, Al and Mn primarily originate from surrounding soils. The research study confirmed the significant contribution of vehicular traffic to dust deposited on urban road surfaces.

Deep Raman spectroscopy for the non-invasive standoff detection of concealed chemical threat agents

Deep Raman spectroscopy has been utilized for the standoff detection of concealed chemical threat agents from a distance of 15 meters under real life background illumination conditions. By using combined time and space resolved measurements, various explosive precursors hidden in opaque plastic containers were identified non-invasively. Our results confirm that combined time and space resolved Raman spectroscopy leads to higher selectivity towards the sub-layer over the surface layer as well as enhanced rejection of fluorescence from the container surface when compared to standoff spatially offset Raman spectroscopy. Raman spectra that have minimal interference from the packaging material and good signal-to-noise ratio were acquired within 5 seconds of measurement time. A new combined time and space resolved Raman spectrometer has been designed with nanosecond laser excitation and gated detection, making it of lower cost and complexity than picosecond-based laboratory systems.