Tokamak TCABR: Acquisition system, data analysis, and remote participation using MDSplus

Each plasma physics laboratory has a proprietary scheme to control and data acquisition system. Usually, it is different from one laboratory to another. It means that each laboratory has its own way to control the experiment and retrieving data from the database. Fusion research relies to a great extent on international collaboration and this private system makes it difficult to follow the work remotely. The TCABR data analysis and acquisition system has been upgraded to support a joint research programme using remote participation technologies. The choice of MDSplus (Model Driven System plus) is proved by the fact that it is widely utilized, and the scientists from different institutions may use the same system in different experiments in different tokamaks without the need to know how each system treats its acquisition system and data analysis. Another important point is the fact that the MDSplus has a library system that allows communication between different types of language (JAVA, Fortran, C, C++, Python) and programs such as MATLAB, IDL, OCTAVE. In the case of tokamak TCABR interfaces (object of this paper) between the system already in use and MDSplus were developed, instead of using the MDSplus at all stages, from the control, and data acquisition to the data analysis. This was done in the way to preserve a complex system already in operation and otherwise it would take a long time to migrate. This implementation also allows add new components using the MDSplus fully at all stages. (c) 2012 Elsevier B.V. All rights reserved.

SOAP processing performance and enhancement

The web services (WS) technology provides a comprehensive solution for representing, discovering, and invoking services in a wide variety of environments, including Service Oriented Architectures (SOA) and grid computing systems. At the core of WS technology lie a number of XML-based standards, such as the Simple Object Access Protocol (SOAP), that have successfully ensured WS extensibility, transparency, and interoperability. Nonetheless, there is an increasing demand to enhance WS performance, which is severely impaired by XML's verbosity. SOAP communications produce considerable network traffic, making them unfit for distributed, loosely coupled, and heterogeneous computing environments such as the open Internet. Also, they introduce higher latency and processing delays than other technologies, like Java RMI and CORBA. WS research has recently focused on SOAP performance enhancement. Many approaches build on the observation that SOAP message exchange usually involves highly similar messages (those created by the same implementation usually have the same structure, and those sent from a server to multiple clients tend to show similarities in structure and content). Similarity evaluation and differential encoding have thus emerged as SOAP performance enhancement techniques. The main idea is to identify the common parts of SOAP messages, to be processed only once, avoiding a large amount of overhead. Other approaches investigate nontraditional processor architectures, including micro-and macrolevel parallel processing solutions, so as to further increase the processing rates of SOAP/XML software toolkits. This survey paper provides a concise, yet comprehensive review of the research efforts aimed at SOAP performance enhancement. A unified view of the problem is provided, covering almost every phase of SOAP processing, ranging over message parsing, serialization, deserialization, compression, multicasting, security evaluation, and data/instruction-level processing.

Java Cryptographic Library for Smartphones

A JME-compliant cryptographic library for mobile application development is introduced in this paper. The library allows cryptographic protocols implementation over elliptic curves with different security levels and offers symmetric and asymmetric bilinear pairings operations, as Tate, Weil, and Ate pairings.

RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies

Abstract Background The development of protocols for RNA extraction from paraffin-embedded samples facilitates gene expression studies on archival samples with known clinical outcome. Older samples are particularly valuable because they are associated with longer clinical follow up. RNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue is problematic due to chemical modifications and continued degradation over time. We compared quantity and quality of RNA extracted by four different protocols from 14 ten year old and 14 recently archived (three to ten months old) FFPE breast cancer tissues. Using three spin column purification-based protocols and one magnetic bead-based protocol, total RNA was extracted in triplicate, generating 336 RNA extraction experiments. RNA fragment size was assayed by reverse transcription-polymerase chain reaction (RT-PCR) for the housekeeping gene glucose-6-phosphate dehydrogenase (G6PD), testing primer sets designed to target RNA fragment sizes of 67 bp, 151 bp, and 242 bp. Results Biologically useful RNA (minimum RNA integrity number, RIN, 1.4) was extracted in at least one of three attempts of each protocol in 86–100% of older and 100% of recently archived ("months old") samples. Short RNA fragments up to 151 bp were assayable by RT-PCR for G6PD in all ten year old and months old tissues tested, but none of the ten year old and only 43% of months old samples showed amplification if the targeted fragment was 242 bp. Conclusion All protocols extracted RNA from ten year old FFPE samples with a minimum RIN of 1.4. Gene expression of G6PD could be measured in all samples, old and recent, using RT-PCR primers designed for RNA fragments up to 151 bp. RNA quality from ten year old FFPE samples was similar to that extracted from months old samples, but quantity and success rate were generally higher for the months old group. We preferred the magnetic bead-based protocol because of its speed and higher quantity of extracted RNA, although it produced similar quality RNA to other protocols. If a chosen protocol fails to extract biologically useful RNA from a given sample in a first attempt, another attempt and then another protocol should be tried before excluding the case from molecular analysis.

A Java-based simulation environment for networks of simplified neuron models

ACR is supported by a research grant from CNPq.

Desarrollo de un videojuego multiplataforma en Java

[ES] El trabajo consistirá en abordar el desarrollo de un videojuego utilizando el lenguaje de programación Java y una librería especializada en desarrollo de videojuegos. Crearemos un videojuego del género plataformas. Para ello utilizaremos una vista en dos dimensiones, el jugador controlará un personaje humanoide con el que deberá atravesar una serie de niveles. Los niveles estarán agrupados en mundos con distintas temáticas (nieve, espacio, etc.) y en ellos el jugador se encontrará con múltiples obstáculos y enemigos. Los mundos se definen como agrupaciones de diez niveles en las que en el décimo nivel de cada mundo (nivel final) el jugador se enfrenta a un enemigo con una complejidad mayor al resto. Un ejemplo de videojuego de plataformas similar al que se va a desarrollar sería: "Super Mario Bros.". La librería que utilizaremos permite el desarrollo de videojuegos de escritorio y para móviles utilizando el mismo código. Es multiplataforma y soporta Windows, Linux, Mac OS X, Android, iOS, y navegadores con soporte WebGL.

MWRegEx : monitor web de expresiones regulares

[ES] El Trabajo de Fin de Grado, Monitor Web de Expresiones Regulares (MWRegEx), es una herramienta basada en tecnologías web, desarrollada usando el entorno Visual Studio. El objetivo principal de la aplicación es dar apoyo a la docencia de expresiones regulares, en el marco de la enseñanza del manejo de ristras de caracteres en las asignaturas de programación del Grado en Ingeniería Informática.  La aplicación permite obtener el dibujo de un autómata de una expresión regular, facilitando su comprensión; además, permite aplicar la expresión a diferentes ristras de caracteres, mostrando las coincidencias encontradas, y ofrece una versión de la expresión adaptada a su uso en literales string de lenguajes como Java y otros. La herramienta se ha implementado en dos partes: un servicio web, escrito en C#, donde se realizan todos los análisis de las expresiones regulares y las ristras a contrastar; y un cliente web, implementado usando tecnología asp.net, con JavaScript y JQuery, que gestiona la interfaz de usuario y muestra los resultados. Esta separación permite que el servicio web pueda ser reutilizado con otras aplicaciones cliente. El autómata que representa una expresión regular esta dibujado usando la librería Raphaël JavaScript que permite manejar los elementos SVG. Cada elemento de la expresión regular tiene un dibujo diferente y único para así diferenciarlo. Toda la interfaz gráfica de usuario está internacionalizada de manera tal que pueda adaptarse a diferentes idiomas y regiones sin la necesidad de realizar cambios de ingeniería ni en el código. Tanto el servicio web como la parte cliente están estructurados para que se puedan agregar nuevas modificaciones sin que esto genere una onda expansiva a lo largo de las diversas clases existentes.

JavaFMI una librería Java para el estándar Functional Mockup Interface

[ES] El estándar Functional Mockup Interface (FMI), es un estándar abierto e independiente de cualquier aplicación o herramienta que permite compartir modelos de sistemas dinámicos entre aplicaciones. Provee una interfaz escrita en lenguaje C que ha de ser implementada por las distintas herramientas exportadoras y pone en común un conjunto de funciones para manipular los modelos.
JavaFMI es una herramienta que permite utilizar simulaciones que cumplen con el estándar FMI en aplicaciones Java de una manera muy simple, limpia y eficiente. Es un proyecto open source con licencia LGPL V2.1H y su código fuente se encuentra disponible para ser clonado en la pagina del proyecto. El proyecto se encuentra alojado en www.bitbucket.org/siani/javafmi y cuenta con una página de bienvenida donde se explica como se usa la librería, una página para reportar incidencias o solicitar que se implementen nuevas historias y una página donde se listan todas las versiones que hay disponibles para descargar. JavaFMI se distribuye como un fichero zip que contiene el .jar con el código compilado de la librería una carpeta lib con las dos dependencias que tiene con librerías externas y una copia de la licencia. Comparada con JFMI, con menos lineas de código, una API limpia, expresiva y auto documentada, y un rendimiento que es un 66 % mejor, JavaFMI es objetivamente la mejor herramienta Java que existe para manipular FMUs de la versión 1.0 y 2.0 del estándar FMI.

Automatic code generation: from process algebraic architectural descriptions to multithreaded java programs

Process algebraic architectural description languages provide a formal means for modeling software systems and assessing their properties. In order to bridge the gap between system modeling and system im- plementation, in this thesis an approach is proposed for automatically generating multithreaded object-oriented code from process algebraic architectural descriptions, in a way that preserves – under certain assumptions – the properties proved at the architectural level. The approach is divided into three phases, which are illustrated by means of a running example based on an audio processing system. First, we develop an architecture-driven technique for thread coordination management, which is completely automated through a suitable package. Second, we address the translation of the algebraically-specified behavior of the individual software units into thread templates, which will have to be filled in by the software developer according to certain guidelines. Third, we discuss performance issues related to the suitability of synthesizing monitors rather than threads from software unit descriptions that satisfy specific constraints. In addition to the running example, we present two case studies about a video animation repainting system and the implementation of a leader election algorithm, in order to summarize the whole approach. The outcome of this thesis is the implementation of the proposed approach in a translator called PADL2Java and its integration in the architecture-centric verification tool TwoTowers.

Food safety in wine: optimization of analytical controls and evaluation of production technologies

This PhD thesis has been proposed to validate and then apply innovative analytical methodologies for the determination of compounds with harmful impact on human health, such as biogenic amines and ochratoxin A in wines. Therefore, the influence of production technology (pH, amino acids precursor and use of different malolactic starters) on biogenic amines content in wines was evaluated. An HPLC method for simultaneous determination of amino acids and amines with precolumnderivatization with 9-Fluorenyl-methoxycarbonyl chloride (FMOC-Cl) and UV detection was developed. Initially, the influence of pH, time of derivatization, gradient profile were studied. In order to improve the separation of amino acids and amines and reduce the time of analysis, it was decided to study the influence of different flows and the use of different columns in the chromatographic method. Firstly, a C18 Luna column was used and later two monolithic columns Chromolith in series. It appeared to be suitable for an easy, precise and accurate determination of a relatively large number of amino acids and amines in wines. This method was then applied on different wines produced in the Emilia Romagna region. The investigation permitted to discriminate between red and white wines. Amino acids content is related to the winemaking process. Biogenic amines content in these wines does not represent a possible toxicological problem for human health. The results of the study of influence of technologies and wine composition demonstrated that pH of wines and amino acids content are the most important factors. Particularly wines with pH > 3,5 show higher concentration of biogenic amines than wines with lower pH. The enrichment of wines by nutrients also influences the content of some biogenic amines that are higher in wines added with amino acids precursors. In this study, amino acids and biogenic amines are not statistically affected by strain of lactic acid bacteria inoculated as a starter for malolactic fermentation. An evaluation of different clean-up (SPE-MycoSep; IACs and LLE) and determination methods (HPLC and ELISA) of ochratoxin A was carried out. The results obtained proved that the SPE clean-up are reliable at the same level while the LLE procedures shows lowest recovery. The ELISA method gave a lower determination and a low reproducibility than HPLC method.

New lightweight optimization method applied in parts made by selective laser sintering and polyjet technologies

[EN]The continuous evolution of materials and technologies of Additive Manufacturing (AM) has led to a competitive production process even for functional parts. The capabilities of these technologies for manufacturing complex geometries allow the definition of new designs that cannot be obtained with any other manufacturing processes. An application where this capability can be exploited is the lightening of parts using internal structures. This allows to obtain more efficient parts and, at the same time, reduce the costs of material and manufacturing time. A new lightweight optimization method to optimize the design of these structures and minimize weight while keeping the minimal mechanical properties is presented in this paper.

Copper(I) phenanthroline complexes and supramolecular systems containing fullerenes: Photophysics, photochemistry and potential applications in sustainable energy technologies.

Chemistry can contribute, in many different ways to solve the challenges we are facing to modify our inefficient and fossil-fuel based energy system. The present work was motivated by the search for efficient photoactive materials to be employed in the context of the energy problem: materials to be utilized in energy efficient devices and in the production of renewable electricity and fuels. We presented a new class of copper complexes, that could find application in lighting techhnologies, by serving as luminescent materials in LEC, OLED, WOLED devices. These technologies may provide substantial energy savings in the lighting sector. Moreover, recently, copper complexes have been used as light harvesting compounds in dye sensitized photoelectrochemical solar cells, which offer a viable alternative to silicon-based photovoltaic technologies. We presented also a few supramolecular systems containing fullerene, e.g. dendrimers, dyads and triads.The most complex among these arrays, which contain porphyrin moieties, are presented in the final chapter. They undergo photoinduced energy- and electron transfer processes also with long-lived charge separated states, i.e. the fundamental processes to power artificial photosynthetic systems.