Memory and attention problems in children with brain tumors at diagnosis

Purpose: Results from previous studies indicate that children with brain tumors (BT) might present with cognitive problems at diagnosis and thus before the start of any medical treatment. The question remains whether these problems are due to the underlying tumor itself or due to the high level of emotional and physical stress which is involved at diagnosis of a malignant disorder. All children with a de novo oncological diagnosis not involving the central nervous systems (CNS) are usually exposed to a comparable level of distress. However, patients with cancer not involving the CNS are not expected to show disease-related cognitive problems. Thus they serve as a well-balanced control group (CG) to help distinguish between the probable causes of the effect. Method: In a pilot study we analyzed an array of cognitive functions in 16 children with BT and 17 control patients. In both groups, tests were administered in-patient at diagnosis before any therapeutic intervention such as surgery, chemotherapy od irradiation. Results: Performance of children with BT was comparable to that of CG patients in the areas of intelligence, perceptual reasoning, verbal comprehension, working memory, and processing speed. In contrast, however, BT patients performded significantly worse in verbal memory and attention. Conclusion: Memory and attention seem to be the most vulnerable funstions affected by BT, with other functions being preserved at the time of diagnosis. It ist to be expected that this vulnerability might exacerbate the cognitive decline after chemotherapy and radiation treatment - known to impair intellectual performance. The findings highlight the need of early cognitive assessments in children with BT in order to introduce cognitive training as early as possible to minimize or even prevent cognitive long-term sequelae. This might improve long-term academic and professional outcome of these children, but especially helps their return to school after hospitalization.

Characterization of OSIRIS NAC filters for the interpretation of multispectral data of comet 67P/Churyumov-Gerasimenko

Context. We interpret multicolor data from OSIRIS NAC for the remote-sensing exploration of comet 67P/Churyumov-Gerasimenko. Aims. We determine the most meaningful definition of color maps for the characterization of surface variegation with filters available on OSIRIS NAC. Methods. We analyzed laboratory spectra of selected minerals and olivine-pyroxene mixtures seen through OSIRIS NAC filters, with spectral methods existing in the literature: reflectance ratios, minimum band wavelength, spectral slopes, band tilt, band curvature, and visible tilt. Results. We emphasize the importance of reflectance ratios and particularly the relation of visible tilt vs. band tilt. This technique provides a reliable diagnostic of the presence of silicates. Color maps constructed by red-green-blue colors defined with the green, orange, red, IR, and Fe2O3 filters let us define regions that may significantly differ in composition.

Laser pulse shaping with liquid crystals

A method of unpolarized laser pulses shaping is reported. The basis of the method is the use of an hybrid optical bistable device with nematic liquid-crystals, similar to the one previously reported by us. A sample of the input light constrols, by an asymmetrical electronic comparator, a 1 x 2 electro-optical total switch. The output pulses are reshaped and maintain the same polarization properties as the input light. From triangular input light signals, symmetriacl and asymmetrical output pulses have been obtained. The minimum pulse width achieved was 0.1 msec. A representation of the output versus input light signals gives an hysteresys cycle in the asymmetrical case.

Transcriptional changes and oxidative stress associated with the synergistic interaction between potato virus X and potato virus Y and their relationship with symptom expression.

Many virus diseases of economic importance to agriculture result from mixtures of different pathogens invading the host at a given time. This contrasts with the relatively scarce studies available on the molecular events associated with virus---host interactions in mixed infections. Compared with single infections, co-infection of Nicotiana benthamiana with Potato virus X (PVX) and Potato virus Y (PVY) resulted in increased systemic symptoms (synergism) that led to necrosis of the newly emerging leaves and death of the plant. A comparative transcriptional analysis was undertaken to identify quantitative and qualitative differences in gene expression during this synergistic infection and correlate these changes with the severe symptoms it caused. Global transcription profiles of doubly infected leaves were compared with those from singly infected leaves using gene ontology enrichment analysis and metabolic pathway annotator software. Functional gene categories altered by the double infection comprise suites of genes regulated coordinately, which are associated with chloroplast functions (downregulated), protein synthesis and degradation (upregulated), carbohydrate metabolism (upregulated), and response to biotic stimulus and stress (upregulated). The expressions of reactive oxygen species?generating enzymes as well as several mitogen-activated protein kinases were also significantly induced. Accordingly, synergistic infection induced a severe oxidative stress in N. benthamiana leaves, as judged by increases in lipid peroxidation and by the generation of superoxide radicals in chloroplasts, which correlated with the misregulation of antioxidative genes in microarray data. Interestingly, expression of genes encoding oxylipin biosynthesis was uniquely upregulated by the synergistic infection. Virus-induced gene silencing of ?-dioxygenase1 delayed cell death during PVX?PVY infection.

Digital light beam deflector with liquid cristal (1980)

In this letter , we report a new method for óptical switching based on the electro-optical properties of liquid crystal materials and, in particular, of the nematic type. The basis of this new method is the use of twisted wedge structure that has not been reported before elsewhere. In the past several years , great efforts in integrated optics have been made to develop optical switching devices with fast speed by using electro-optic, acousto-optic or magneto -optic materials. A mechanically operated óptical switch made of grade-index rod 1enses and e1ectromagnets has been proposed too . Switches of this kind include one input and two output waveguides and, depending on the app1ied voltage, one incident light on the switch exits either in one or another of the two output waveguides.

Color uniformity in spotligths - visual perception and system design

La iluminación con diodos emisores de luz (LED) está reemplazando cada vez en mayor medida a las fuentes de luz tradicionales. La iluminación LED ofrece ventajas en eficiencia, consumo de energía, diseño, tamaño y calidad de la luz. Durante más de 50 años, los investigadores han estado trabajando en mejoras LED. Su principal relevancia para la iluminación está aumentando rápidamente. Esta tesis se centra en un campo de aplicación importante, como son los focos. Se utilizan para enfocar la luz en áreas definidas, en objetos sobresalientes en condiciones profesionales. Esta iluminación de alto rendimiento requiere una calidad de luz definida, que incluya temperaturas ajustables de color correlacionadas (CCT), de alto índice de reproducción cromática (CRI), altas eficiencias, y colores vivos y brillantes. En el paquete LED varios chips de diferentes colores (rojo, azul, fósforo convertido) se combinan para cumplir con la distribución de energía espectral con alto CRI. Para colimar la luz en los puntos concretos deseados con un ángulo de emisión determinado, se utilizan blancos sintonizables y diversos colores de luz y ópticas secundarias. La combinación de una fuente LED de varios colores con elementos ópticos puede causar falta de homogeneidad cromática en la distribución espacial y angular de la luz, que debe resolverse en el diseño óptico. Sin embargo, no hay necesidad de uniformidad perfecta en el punto de luz debido al umbral en la percepción visual del ojo humano. Por lo tanto, se requiere una descripción matemática del nivel de uniformidad del color con respecto a la percepción visual. Esta tesis está organizada en siete capítulos. Después de un capítulo inicial que presenta la motivación que ha guiado la investigación de esta tesis, en el capítulo 2 se presentan los fundamentos científicos de la uniformidad del color en luces concentradas, como son: el espacio de color aplicado CIELAB, la percepción visual del color, los fundamentos de diseño de focos respecto a los motores de luz y ópticas no formadoras de imágenes, y los últimos avances en la evaluación de la uniformidad del color en el campo de los focos. El capítulo 3 desarrolla diferentes métodos para la descripción matemática de la distribución espacial del color en un área definida, como son la diferencia de color máxima, la desviación media del color, el gradiente de la distribución espacial de color, así como la suavidad radial y axial. Cada función se refiere a los diferentes factores que influyen en la visión, los cuales necesitan un tratamiento distinto que el de los datos que se tendrán en cuenta, además de funciones de ponderación que pre- y post-procesan los datos simulados o medidos para la reducción del ruido, la luminancia de corte, la aplicación de la ponderación de luminancia, la función de sensibilidad de contraste, y la función de distribución acumulativa. En el capítulo 4, se obtiene la función de mérito Usl para la estimación de la uniformidad del color percibida en focos. Se basó en los resultados de dos conjuntos de experimentos con factor humano realizados para evaluar la percepción visual de los sujetos de los patrones de focos típicos. El primer experimento con factor humano dio lugar al orden de importancia percibida de los focos. El orden de rango percibido se utilizó para correlacionar las descripciones matemáticas de las funciones básicas y la función ponderada sobre la distribución espacial del color, que condujo a la función Usl. El segundo experimento con factor humano probó la percepción de los focos bajo condiciones ambientales diversas, con el objetivo de proporcionar una escala absoluta para Usl, para poder así sustituir la opinión subjetiva personal de los individuos por una función de mérito estandarizada. La validación de la función Usl se presenta en relación con el alcance de la aplicación y condiciones, así como las limitaciones y restricciones que se realizan en el capítulo 5. Se compararon los datos medidos y simulados de varios sistemas ópticos. Se discuten los campos de aplicación , así como validaciones y restricciones de la función. El capítulo 6 presenta el diseño del sistema de focos y su optimización. Una evaluación muestra el análisis de sistemas basados en el reflector y la lente TIR. Los sistemas ópticos simulados se comparan en la uniformidad del color Usl, sensibilidad a las sombras coloreadas, eficiencia e intensidad luminosa máxima. Se ha comprobado que no hay un sistema único que obtenga los mejores resultados en todas las categorías, y que una excelente uniformidad de color se pudo alcanzar por la conjunción de dos sistemas diferentes. Finalmente, el capítulo 7 presenta el resumen de esta tesis y la perspectiva para investigar otros aspectos. ABSTRACT Illumination with light-emitting diodes (LED) is more and more replacing traditional light sources. They provide advantages in efficiency, energy consumption, design, size and light quality. For more than 50 years, researchers have been working on LED improvements. Their main relevance for illumination is rapidly increasing. This thesis is focused on one important field of application which are spotlights. They are used to focus light on defined areas, outstanding objects in professional conditions. This high performance illumination required a defined light quality including tunable correlated color temperatures (CCT), high color rendering index (CRI), high efficiencies and bright, vivid colors. Several differently colored chips (red, blue, phosphor converted) in the LED package are combined to meet spectral power distribution with high CRI, tunable white and several light colors and secondary optics are used to collimate the light into the desired narrow spots with defined angle of emission. The combination of multi-color LED source and optical elements may cause chromatic inhomogeneities in spatial and angular light distribution which needs to solved at the optical design. However, there is no need for perfect uniformity in the spot light due to threshold in visual perception of human eye. Therefore, a mathematical description of color uniformity level with regard to visual perception is required. This thesis is organized seven seven chapters. After an initial one presenting the motivation that has guided the research of this thesis, Chapter 2 introduces the scientific basics of color uniformity in spot lights including: the applied color space CIELAB, the visual color perception, the spotlight design fundamentals with regards to light engines and nonimaging optics, and the state of the art for the evaluation of color uniformity in the far field of spotlights. Chapter 3 develops different methods for mathematical description of spatial color distribution in a defined area, which are the maximum color difference, the average color deviation, the gradient of spatial color distribution as well as the radial and axial smoothness. Each function refers to different visual influencing factors, and they need different handling of data be taken into account, along with weighting functions which pre- and post-process the simulated or measured data for noise reduction, luminance cutoff, the implementation of luminance weighting, contrast sensitivity function, and cumulative distribution function. In chapter 4, the merit function Usl for the estimation of the perceived color uniformity in spotlights is derived. It was based on the results of two sets of human factor experiments performed to evaluate the visual perception of typical spotlight patterns by subjects. The first human factor experiment resulted in the perceived rank order of the spotlights. The perceived rank order was used to correlate the mathematical descriptions of basic functions and weighted function concerning the spatial color distribution, which lead to the Usl function. The second human factor experiment tested the perception of spotlights under varied environmental conditions, with to objective to provide an absolute scale for Usl, so the subjective personal opinion of individuals could be replaced by a standardized merit function. The validation of the Usl function is presented concerning the application range and conditions as well as limitations and restrictions in carried out in chapter 5. Measured and simulated data of various optical several systems were compared. Fields of applications are discussed as well as validations and restrictions of the function. Chapter 6 presents spotlight system design and their optimization. An evaluation shows the analysis of reflector-based and TIR lens systems. The simulated optical systems are compared in color uniformity Usl , sensitivity to colored shadows, efficiency, and peak luminous intensity. It has been found that no single system which performed best in all categories, and that excellent color uniformity could be reached by two different system assemblies. Finally, chapter 7 summarizes the conclusions of the present thesis and an outlook for further investigation topics.

Design, Technology and Characterization of Micromechanised Sensors and Actuators for Harsh Environments

Los sistemas micro electro mecánicos (MEMS) han demostrado ser una exitosa familia de dispositivos que pueden usarse como plataforma para el desarrollo de dispositivos con aplicaciones en óptica, comunicaciones, procesado de señal y sensorización. Los dispositivos MEMS estándar suelen estar fabricados usando tecnología de silicio. Sin embargo, el rendimiento de estos MEMS se puede mejorar si se usan otros materiales. Por ejemplo, el diamante nanocristalino (NCD) ofrece unas excelentes propiedades mecánicas, transparencia y una superficie fácil de funcionalizar. Por otro lado, el sistema de materiales (In; Ga; Al)N, los materiales IIIN, se pueden usar para producir estructuras monocristalinas con alta sensibilidad mecánica y química. Además, el AlN se puede depositar por pulverización catódica reactiva sobre varios substratos, incluyendo NCD, para formar capas policristalinas orientadas con alta respuesta piezoeléctrica. Adicionalmente, tanto el NCD como los materiales III-N muestran una gran estabilidad térmica y química, lo que los hace una elección idónea para desarrollar dispositivos para aplicaciones para alta temperatura, ambientes agresivos e incluso para aplicaciones biocompatibles. En esta tesis se han usado estos materiales para el diseño y medición de demostradores tecnológicos. Se han perseguido tres objetivos principales: _ Desarrollo de unos procesos de fabricación apropiados. _ Medición de las propiedades mecánicas de los materiales y de los factores que limitan el rendimiento de los dispositivos. _ Usar los datos medidos para desarrollar dispositivos demostradores complejos. En la primera parte de esta tesis se han estudiado varias técnicas de fabricación. La estabilidad de estos materiales impide el ataque y dificulta la producción de estructuras suspendidas. Los primeros capítulos de esta disertación se dedican al desarrollo de unos procesos de transferencia de patrones por ataque seco y a la optimización del ataque húmedo sacrificial de varios substratos propuestos. Los resultados de los procedimientos de ataque se presentan y se describe la optimización de las técnicas para la fabricación de estructuras suspendidas de NCD y materiales III-N. En un capítulo posterior se estudia el crecimiento de AlN por pulverización catódica. Como se ha calculado en esta disertación para obtener una actuación eficiente de MEMS, las capas de AlN han de ser finas, típicamente d < 200 nm, lo que supone serias dificultades para la obtención de capas orientadas con respuesta piezoeléctrica. Las condiciones de depósito se han mapeado para identificar las fronteras que proporcionan el crecimiento de material orientado desde los primeros pasos del proceso. Además, durante la optimización de los procesos de ataque se estudió un procedimiento para fabricar películas de GaN nanoporoso. Estas capas porosas pueden servir como capas sacrificiales para la fabricación de estructuras suspendidas de GaN con baja tensión residual o como capas para mejorar la funcionalización superficial de sensores químicos o biológicos. El proceso de inducción de poros se discutirá y también se presentarán experimentos de ataque y funcionalización. En segundo lugar, se han determinado las propiedades mecánicas del NCD y de los materiales III-N. Se han fabricado varias estructuras suspendidas para la medición del módulo de Young y de la tensión residual. Además, las estructuras de NCD se midieron en resonancia para calcular el rendimiento de los dispositivos en términos de frecuencia y factor de calidad. Se identificaron los factores intrínsecos y extrínsecos que limitan ambas figuras de mérito y se han desarrollado modelos para considerar estas imperfecciones en las etapas de diseño de los dispositivos. Por otra parte, los materiales III-N normalmente presentan grandes gradientes de deformación residual que causan la deformación de las estructuras al ser liberadas. Se han medido y modelado estos efectos para los tres materiales binarios del sistema para proporcionar puntos de interpolación que permitan predecir las características de las aleaciones del sistema III-N. Por último, los datos recabados se han usado para desarrollar modelos analíticos y numéricos para el diseño de varios dispositivos. Se han estudiado las propiedades de transducción y se proporcionan topologías optimizadas. En el último capítulo de esta disertación se presentan diseños optimizados de los siguientes dispositivos: _ Traviesas y voladizos de AlN=NCD con actuación piezoeléctrica aplicados a nanoconmutadores de RF para señales de alta potencia. _ Membranas circulares de AlN=NCD con actuación piezoeléctrica aplicadas a lentes sintonizables. _ Filtros ópticos Fabry-Pérot basados en cavidades aéreas y membranas de GaN actuadas electrostáticamente. En resumen, se han desarrollado unos nuevos procedimientos optimizados para la fabricación de estructuras de NCD y materiales III-N. Estas técnicas se han usado para producir estructuras que llevaron a la determinación de las principales propiedades mecánicas y de los parámetros de los dispositivos necesarios para el diseño de MEMS. Finalmente, los datos obtenidos se han usado para el diseño optimizado de varios dispositivos demostradores. ABSTRACT Micro Electro Mechanical Systems (MEMS) have proven to be a successful family of devices that can be used as a platform for the development of devices with applications in optics, communications, signal processing and sensorics. Standard MEMS devices are usually fabricated using silicon based materials. However, the performance of these MEMS can be improved if other material systems are used. For instance, nanocrystalline diamond (NCD) offers excellent mechanical properties, optical transparency and ease of surface functionalization. On the other hand, the (In; Ga; Al)N material system, the III-N materials, can be used to produce single crystal structures with high mechanical and chemical sensitivity. Also, AlN can be deposited by reactive sputtering on various substrates, including NCD, to form oriented polycrystalline layers with high piezoelectric response. In addition, both NCD and III-N materials exhibit high thermal and chemical stability, which makes these material the perfect choice for the development of devices for high temperatures, harsh environments and even biocompatible applications. In this thesis these materials have been used for the design and measurement of technological demonstrators. Three main objectives have been pursued: _ Development of suitable fabrication processes. _ Measurement of the material mechanical properties and device performance limiting factors. _ Use the gathered data to design complex demonstrator devices. In a first part of the thesis several fabrication processes have been addressed. The stability of these materials hinders the etching of the layers and hampers the production of free standing structures. The first chapters of this dissertation are devoted to the development of a dry patterning etching process and to sacrificial etching optimization of several proposed substrates. The results of the etching processes are presented and the optimization of the technique for the manufacturing of NCD and III-N free standing structures is described. In a later chapter, sputtering growth of thin AlN layers is studied. As calculated in this dissertation, for efficient MEMS piezoelectric actuation the AlN layers have to be very thin, typically d < 200 nm, which poses serious difficulties to the production of c-axis oriented material with piezoelectric response. The deposition conditions have been mapped in order to identify the boundaries that give rise to the growth of c-axis oriented material from the first deposition stages. Additionally, during the etching optimization a procedure for fabricating nanoporous GaN layers was also studied. Such porous layers can serve as a sacrificial layer for the release of low stressed GaN devices or as a functionalization enhancement layer for chemical and biological sensors. The pore induction process will be discussed and etching and functionalization trials are presented. Secondly, the mechanical properties of NCD and III-N materials have been determined. Several free standing structures were fabricated for the measurement of the material Young’s modulus and residual stress. In addition, NCD structures were measured under resonance in order to calculate the device performance in terms of frequency and quality factor. Intrinsic and extrinsic limiting factors for both figures were identified and models have been developed in order to take into account these imperfections in the device design stages. On the other hand, III-N materials usually present large strain gradients that lead to device deformation after release. These effects have been measured and modeled for the three binary materials of the system in order to provide the interpolation points for predicting the behavior of the III-N alloys. Finally, the gathered data has been used for developing analytic and numeric models for the design of various devices. The transduction properties are studied and optimized topologies are provided. Optimized design of the following devices is presented at the last chapter of this dissertation: _ AlN=NCD piezoelectrically actuated beams applied to RF nanoswitches for large power signals. _ AlN=NCD piezoelectrically actuated circular membranes applied to tunable lenses. _ GaN based air gap tunable optical Fabry-Pérot filters with electrostatic actuation. On the whole, new optimized fabrication processes has been developed for the fabrication of NCD and III-N MEMS structures. These processing techniques was used to produce structures that led to the determination of the main mechanical properties and device parameters needed for MEMS design. Lastly, the gathered data was used for the design of various optimized demonstrator devices.

Improving Optical Performance of Concentrator Cells by Means of a Deposited Nanopattern Layer

Multijunction solar cells (MJSC) use anti-reflective coatings (ARC) to minimize Fresnel reflection losses for a family of light incidence angles. These coatings adapt the refractive index of the cell to that of the surrounding medium. Patterns with sizes in the range of the light wavelength can be used to further reduce reflections through diffraction. Transparent nanopatterns with a gradual profile, called moth-eye nanostructures, can adapt the refractive index of the optical interfaces (often with n∼1.5) used to encapsulate concentrator solar cells to that of the air (n air∼1). Here we show the effect of a nanometric moth-eye ARC with a round motif deposited on commercial MJSC that achieves short-circuit current (I SC) gains greater than 2% at normal incidence and even higher in the case of tilted illumination. In this work, MJSC with different moth-eye ARC are characterized under quantum efficiency (QE) as well as under concentrated illumination I-V in order to assess their potential. Simulations based on coupled wave analysis (RCWA) are used to fit the experimental results with successful results.

A secreted Salmonella protein with homology to an avirulence determinant of plant pathogenic bacteria

Bacterial pathogens have evolved sophisticated mechanisms to interact with their hosts. A specialized type III protein secretion system capable of translocating bacterial proteins into host cells has emerged as a central factor in the interaction between a variety of mammalian and plant pathogenic bacteria with their hosts. Here we describe AvrA, a novel target of the centisome 63 type III protein secretion system of Salmonella enterica. AvrA shares sequence similarity with YopJ of the animal pathogen Yersinia pseudotuberculosis and AvrRxv of the plant pathogen Xanthomonas campestris pv. vesicatoria. These proteins are the first examples of putative targets of type III secretion systems in animal and plant pathogenic bacteria that share sequence similarity. They may therefore constitute a novel family of effector proteins with related functions in the cross-talk of these pathogens with their hosts.

Systemic gene expression in arabidopsis during an incompatible interaction with Alternaria brassicicola

Pathogen challenge can trigger an integrated set of signal transduction pathways, which ultimately leads to a state of high alert, otherwise known as systemic or induced resistance in tissue remote to the initial infection. Although large-scale gene expression during systemic acquired resistance, which is induced by salicylic acid or necrotizing pathogens has been previously reported using a bacterial pathogen, the nature of systemic defense responses triggered by an incompatible necrotrophic fungal pathogen is not known. We examined transcriptional changes that occur during systemic defense responses in Arabidopsis plants inoculated with the incompatible fungal pathogen Alternaria brassicicola. Substantial changes (2.00-fold and statistically significant) were demonstrated in distal tissue of inoculated plants for 35 genes (25 up-regulated and 10 down-regulated), and expression of a selected subset of systemically expressed genes was confirmed using real-time quantitative polymerase chain reaction. Genes with altered expression in distal tissue included those with putative functions in cellular housekeeping, indicating that plants modify these vital processes to facilitate a coordinated response to pathogen attack. Transcriptional up-regulation of genes encoding enzymes functioning in the beta-oxidation pathway of fatty acids was particularly interesting. Transcriptional up-regulation was also observed for genes involved in cell wall synthesis and modification and genes putatively involved in signal transduction. The results of this study, therefore, confirm the notion that distal tissue of a pathogen-challenged plant has a heightened preparedness for subsequent pathogen attacks.

Recursive filtering of images with symmetric extension

Recursive filters are widely used in image analysis due to their efficiency and simple implementation. However these filters have an initialisation problem which either produces unusable results near the image boundaries or requires costly approximate solutions such as extending the boundary manually. In this paper, we describe a method for the recursive filtering of symmetrically extended images for filters with symmetric denominator. We begin with an analysis of symmetric extensions and their effect on non-recursive filtering operators. Based on the non-recursive case, we derive a formulation of recursive filtering on symmetric domains as a linear but spatially varying implicit operator. We then give an efficient method for decomposing and solving the linear implicit system, along with a proof that this decomposition always exists. This decomposition needs to be performed only once for each dimension of the image. This yields a filtering which is both stable and consistent with the ideal infinite extension. The filter is efficient, requiring less computation than the standard recursive filtering. We give experimental evidence to verify these claims. (c) 2005 Elsevier B.V. All rights reserved.

Protein kinases associated with the yeast phosphoproteome

Background: Protein phosphorylation is an extremely important mechanism of cellular regulation. A large-scale study of phosphoproteins in a whole-cell lysate of Saccharomyces cerevisiae has previously identified 383 phosphorylation sites in 216 peptide sequences. However, the protein kinases responsible for the phosphorylation of the identified proteins have not previously been assigned. Results: We used Predikin in combination with other bioinformatic tools, to predict which of 116 unique protein kinases in yeast phosphorylates each experimentally determined site in the phosphoproteome. The prediction was based on the match between the phosphorylated 7-residue sequence and the predicted substrate specificity of each kinase, with the highest weight applied to the residues or positions that contribute most to the substrate specificity. We estimated the reliability of the predictions by performing a parallel prediction on phosphopeptides for which the kinase has been experimentally determined. Conclusion: The results reveal that the functions of the protein kinases and their predicted phosphoprotein substrates are often correlated, for example in endocytosis, cytokinesis, transcription, replication, carbohydrate metabolism and stress response. The predictions link phosphoproteins of unknown function with protein kinases with known functions and vice versa, suggesting functions for the uncharacterized proteins. The study indicates that the phosphoproteins and the associated protein kinases represented in our dataset have housekeeping cellular roles; certain kinases are not represented because they may only be activated during specific cellular responses. Our results demonstrate the utility of our previously reported protein kinase substrate prediction approach (Predikin) as a tool for establishing links between kinases and phosphoproteins that can subsequently be tested experimentally.

Ultra-long haul optical fibre transmission systems

This thesis examines experimentally options for optical fibre transmission over oceanic distances. Its format follows the chronological evolution of ultra-long haul optical systems, commencing with opto-electronic regenerators as repeaters, progressing to optically amplified NRZ systems and finally solitonic propagation. In each case recirculating loop techniques are deployed to simplify the transmission experiments. Advances in high speed electronics have allowed regenerators operating at 10 Gbit/s to become a practical reality. By augmenting such devices with optical amplifiers it is possible to greatly enhance the repeater spacing. Work detailed in this thesis has culminated in the propagation of 10 Gbit/s data over 400,000 km with a repeater spacing of 160 km. System reliability and robustness are enhanced by the use of a directly modulated DFB laser transmitter and total insensitivity of the system to the signal state of polarisation. Optically amplified ultra-long haul NRZ systems have taken on particular importance with the impending deployment of TAT 12/13 and TPC 5. The performance of these systems is demonstrated to be primarily limited by analogue impairments such as the accumulation of amplifier noise, polarisation effects and optical non-linearities. These degradations may be reduced by the use of appropriate dispersion maps and by scrambling the transmitted state of signal polarisation. A novel high speed optically passive polarisation scrambler is detailed for the first time. At bit rates in excess of 10 Gbit/s it is shown that these systems are severely limited and do not offer the advantages that might be expected over regenerated links. Propagation using solitons as the data bits appears particularly attractive since the dispersive and non-linear effects of the fibre allow distortion free transmission. However, the generation of pure solitons is difficult but must be achieved if the uncontrolled transmission distance is to be maximised. This thesis presents a new technique for the stabilisation of an erbium fibre ring laser that has aUowed propagation of 2.5 Gbit/s solitons to the theoretical limit of ~ 18,000 km. At higher bit rates temporal jitter becomes a significant impairment and to aUow an increase in the aggregate line rate multiplexing in both time and polarisation domains has been proposed. These techniques are shown to be of only limited benefit in practical systems and ultimately some form of soliton transmission control is required. The thesis demonstrates synchronous retiming by amplitude modulation that has allowed 20 Gbit/s data to propagate 125,000 km error free with an amplifier spacing approaching the soliton period. Ultimately the speed of operation of such systems is limited by the electronics used and, thus, a new form of soliton control is demonstrated using all optical techniques to achieve synchronous phase modulation.

Mechanism of action of the tetraflex accommodative intraocular lens

PURPOSE:To investigate the mechanism of action of the Tetraflex (Lenstec Kellen KH-3500) accommodative intraocular lens (IOL). METHODS:Thirteen eyes of eight patients implanted with the Tetraflex accommodating IOL for at least 2 years underwent assessment of their objective amplitude-of-accommodation by autorefraction, anterior chamber depth and pupil size with optical coherence tomography, and IOL flexure with aberrometry, each viewing a target at 0.0 to 4.00 diopters of accommodative demand. RESULTS:Pupil size decreased by 0.62+/-0.41 mm on increasing accommodative demand, but the Tetraflex IOL was relatively fixed in position within the eye. The ocular aberrations of the eye changed with increased accommodative demand, but not in a consistent manner among individuals. Those aberrations that appeared to be most affected were defocus, vertical primary and secondary astigmatism, vertical coma, horizontal and vertical primary and secondary trefoil, and spherical aberration. CONCLUSIONS:Some of the reported near vision benefits of the Tetraflex accommodating IOL appear to be due to changes in the optical aberrations because of the flexure of the IOL on accommodative effort rather than forward movement within the capsular bag.

Optical phase conjugation for dispersion and nonlinearity compensation in a 1600km, 42 Gb/s quasi-lossless system

We experimentally investigate a long-distance, high-bit-rate transmission system which combines optical-phase-conjugation with quasi-lossless amplification. Comparison with a conventional system configuration demonstrates the possibility of obtaining both dispersion compensation and improved nonlinear tolerance using proposed scheme.