Arquitetura multiprocessada e reconfigurável para a síntese de redes de Petri em hardware

Uma arquitetura reconfigurável e multiprocessada para a implementação física de Redes de Petri foi desenvolvida em VHDL e mapeada sobre um FPGA. Convencionalmente, as Redes de Petri são transformadas em uma linguagem de descrição de hardware no nível de transferências entre registradores e um processo de síntese de alto nível é utilizado para gerar as funções booleanas e tabelas de transição de estado para que se possa, finalmente, mapeá-las num FPGA (Morris et al., 2000) (Soto and Pereira, 2001). A arquitetura proposta possui blocos lógicos reconfiguráveis desenvolvidos exclusivamente para a implementação dos lugares e das transições da rede, não sendo necessária a descrição da rede em níveis de abstração intermediários e nem a utilização de um processo de síntese para realizar o mapeamento da rede na arquitetura. A arquitetura permite o mapeamento de modelos de Redes de Petri com diferenciação entre as marcas e associação de tempo no disparo das transições, sendo composta por um arranjo de processadores reconfiguráveis, cada um dos quais representando o comportamento de uma transição da Rede de Petri a ser mapeada e por um sistema de comunicação, implementado por um conjunto de roteadores que são capazes de enviar pacotes de dados de um processador reconfigurável a outro. A arquitetura proposta foi validada num FPGA de 10.570 elementos lógicos com uma topologia que permitiu a implementação de Redes de Petri de até 9 transições e 36 lugares, atingindo uma latência de 15,4ns e uma vazão de até 17,12GB/s com uma freqüência de operação de 64,58MHz.

MS2SV: Tradução de modelos em Simulink para VHDL-AMS

This paper presents a methodology and a tool for projects involving analogue and digital signals. A sub-systems group was developed to translation a Matlab/Simulink model in the correspondent structural model described in VHDL-AMS. The developed translation tool, named of MS(2)SV, can reads a file containing a Simulink model translating it in the correspondent VHDL-AMS structural code. The tool also creates the directories structure and necessary files to simulate the model translated in System Vision environment. Three models of D/A converters available commercially that use R-2R ladder network were studied. This work considers some of challenges set by the electronic industry for the further development of simulation methodologies and tools in the field of mixed-signal technology. Although the objective of the studies has been the D/A converter, the developed methodology has potentiality to be extended to consider control systems and mechatronic systems.

Desenvolvimento de uma arquitetura multiprocessada e reconfigurável para a síntese de redes de Petri em hardware

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Generation of a Chinese Hamster Ovary Cell Line Producing Recombinant Human Glucocerebrosidase

Impaired activity of the lysosomal enzyme glucocerebrosidase (GCR) results in the inherited metabolic disorder known as Gaucher disease. Current treatment consists of enzyme replacement therapy by administration of exogenous GCR. Although effective, it is exceptionally expensive, and patients worldwide have a limited access to this medicine. In Brazil, the public healthcare system provides the drug free of charge for all Gaucher's patients, which reaches the order of $ 84million per year. However, the production of GCR by public institutions in Brazil would reduce significantly the therapy costs. Here, we describe a robust protocol for the generation of a cell line producing recombinant human GCR. The protein was expressed in CHO-DXB11 (dhfr(-)) cells after stable transfection and gene amplification with methotrexate. As expected, glycosylated GCR was detected by immunoblotting assay both as cell-associated (similar to 64 and 59 kDa) and secreted (63-69 kDa) form. Analysis of subclones allowed the selection of stable CHO cells producing a secreted functional enzyme, with a calculated productivity of 5.14 pg/cell/day for the highest producer. Although being laborious, traditionalmethods of screening high-producing recombinant cellsmay represent a valuable alternative to generate expensive biopharmaceuticals in countries with limited resources.

Análisis de las herramientas ORCC y Vivado HLS para la Síntesis de Modelos de Flujo de Datos RVC-CAL

En este Proyecto Fin de Grado se ha realizado un estudio de cómo generar, a partir de modelos de flujo de datos en RVC-CAL (Reconfigurable Video Coding – CAL Actor Language), modelos VHDL (Versatile Hardware Description Language) mediante Vivado HLS (Vivado High Level Synthesis), incluida en las herramientas disponibles en Vivado de Xilinx. Una vez conseguido el modelo VHDL resultante, la intención es que mediante las herramientas de Xilinx se programe en una FPGA (Field Programmable Gate Array) o el dispositivo Zynq también desarrollado por Xilinx. RVC-CAL es un lenguaje de flujo de datos que describe la funcionalidad de bloques funcionales, denominados actores. Las funcionalidades que desarrolla un actor se definen como acciones, las cuales pueden ser diferentes en un mismo actor. Los actores pueden comunicarse entre sí y formar una red de actores o network. Con Vivado HLS podemos obtener un diseño VHDL a partir de un modelo en lenguaje C. Por lo que la generación de modelos en VHDL a partir de otros en RVC-CAL, requiere una fase previa en la que los modelos en RVC-CAL serán compilados para conseguir su equivalente en lenguaje C. El compilador ORCC (Open RVC-CAL Compiler) es la herramienta que nos permite lograr diseños en lenguaje C partiendo de modelos en RVC-CAL. ORCC no crea directamente el código ejecutable, sino que genera un código fuente disponible para ser compilado por otra herramienta, en el caso de este proyecto, el compilador GCC (Gnu C Compiler) de Linux. En resumen en este proyecto nos encontramos con tres puntos de estudio bien diferenciados, los cuales son: 1. Partimos de modelos de flujo de datos en RVC-CAL, los cuales son compilados por ORCC para alcanzar su traducción en lenguaje C. 2. Una vez conseguidos los diseños equivalentes en lenguaje C, son sintetizados en Vivado HLS para conseguir los modelos en VHDL. 3. Los modelos VHDL resultantes serian manipulados por las herramientas de Xilinx para producir el bitstream que sea programado en una FPGA o en el dispositivo Zynq. En el estudio del segundo punto, nos encontramos con una serie de elementos conflictivos que afectan a la síntesis en Vivado HLS de los diseños en lenguaje C generados por ORCC. Estos elementos están relacionados con la manera que se encuentra estructurada la especificación en C generada por ORCC y que Vivado HLS no puede soportar en determinados momentos de la síntesis. De esta manera se ha propuesto una transformación “manual” de los diseños generados por ORCC que afecto lo menos posible a los modelos originales para poder realizar la síntesis con Vivado HLS y crear el fichero VHDL correcto. De esta forma este documento se estructura siguiendo el modelo de un trabajo de investigación. En primer lugar, se exponen las motivaciones y objetivos que apoyan y se esperan lograr en este trabajo. Seguidamente, se pone de manifiesto un análisis del estado del arte de los elementos necesarios para el desarrollo del mismo, proporcionando los conceptos básicos para la correcta comprensión y estudio del documento. Se realiza una descripción de los lenguajes RVC-CAL y VHDL, además de una introducción de las herramientas ORCC y Vivado, analizando las bondades y características principales de ambas. Una vez conocido el comportamiento de ambas herramientas, se describen las soluciones desarrolladas en nuestro estudio de la síntesis de modelos en RVC-CAL, poniéndose de manifiesto los puntos conflictivos anteriormente señalados que Vivado HLS no puede soportar en la síntesis de los diseños en lenguaje C generados por el compilador ORCC. A continuación se presentan las soluciones propuestas a estos errores acontecidos durante la síntesis, con las cuales se pretende alcanzar una especificación en C más óptima para una correcta síntesis en Vivado HLS y alcanzar de esta forma los modelos VHDL adecuados. Por último, como resultado final de este trabajo se extraen un conjunto de conclusiones sobre todos los análisis y desarrollos acontecidos en el mismo. Al mismo tiempo se proponen una serie de líneas futuras de trabajo con las que se podría continuar el estudio y completar la investigación desarrollada en este documento. ABSTRACT. In this Project it has made a study of how to generate, from data flow models in RVC-CAL (Reconfigurable Video Coding - Actor CAL Language), VHDL models (Versatile Hardware Description Language) by Vivado HLS (Vivado High Level Synthesis), included in the tools available in Vivado of Xilinx. Once achieved the resulting VHDL model, the intention is that by the Xilinx tools programmed in FPGA or Zynq device also developed by Xilinx. RVC-CAL is a dataflow language that describes the functionality of functional blocks, called actors. The functionalities developed by an actor are defined as actions, which may be different in the same actor. Actors can communicate with each other and form a network of actors. With Vivado HLS we can get a VHDL design from a model in C. So the generation of models in VHDL from others in RVC-CAL requires a preliminary phase in which the models RVC-CAL will be compiled to get its equivalent in C. The compiler ORCC (Open RVC-CAL Compiler) is the tool that allows us to achieve designs in C language models based on RVC-CAL. ORCC not directly create the executable code but generates an available source code to be compiled by another tool, in the case of this project, the GCC compiler (GNU C Compiler) of Linux. In short, in this project we find three well-defined points of study, which are: 1. We start from data flow models in RVC-CAL, which are compiled by ORCC to achieve its translation in C. 2. Once you realize the equivalent designs in C, they are synthesized in Vivado HLS for VHDL models. 3. The resulting models VHDL would be manipulated by Xilinx tools to produce the bitstream that is programmed into an FPGA or Zynq device. In the study of the second point, we find a number of conflicting elements that affect the synthesis Vivado HLS designs in C generated by ORCC. These elements are related to the way it is structured specification in C generated ORCC and Vivado HLS cannot hold at certain times of the synthesis. Thus it has proposed a "manual" transformation of designs generated by ORCC that affected as little as possible to the original in order to perform the synthesis Vivado HLS and create the correct file VHDL models. Thus this document is structured along the lines of a research. First, the motivations and objectives that support and hope to reach in this work are presented. Then it shows an analysis the state of the art of the elements necessary for its development, providing the basics for a correct understanding and study of the document. A description of the RVC-CAL and VHDL languages is made, in addition an introduction of the ORCC and Vivado tools, analyzing the advantages and main features of both. Once you know the behavior of both tools, the solutions developed in our study of the synthesis of RVC-CAL models, introducing the conflicting points mentioned above are described that Vivado HLS cannot stand in the synthesis of design in C language generated by ORCC compiler. Below the proposed solutions to these errors occurred during synthesis, with which it is intended to achieve optimum C specification for proper synthesis Vivado HLS and thus create the appropriate VHDL models are presented. Finally, as the end result of this work a set of conclusions on all analyzes and developments occurred in the same are removed. At the same time a series of future lines of work which could continue to study and complete the research developed in this document are proposed.

Sistema di visione stereo su architettura ZYNQ

Lo scopo della tesi è creare un’architettura in FPGA in grado di ricavare informazioni 3D da una coppia di sensori stereo. La pipeline è stata realizzata utilizzando il System-on-Chip Zynq, che permette una stretta interazione tra la parte hardware realizzata in FPGA e la CPU. Dopo uno studio preliminare degli strumenti hardware e software, è stata realizzata l’architettura base per la scrittura e la lettura di immagini nella memoria DDR dello Zynq. In seguito l’attenzione si è spostata sull’implementazione di algoritmi stereo (rettificazione e stereo matching) su FPGA e nella realizzazione di una pipeline in grado di ricavare accurate mappe di disparità in tempo reale acquisendo le immagini da una camera stereo.

A review of time-motion analysis and combat development in mixed martial arts matches at regional level tournaments

Mixed martial arts (MMA) have become a fast-growing worldwide expansion of martial arts competition, requiring high level of skill, physical conditioning, and strategy, and involving a synthesis of combat while standing or on the ground. This study quantified the effort-pause ratio (EP), and classified effort segments of stand-up or groundwork development to identify the number of actions performed per round in MMA matches. 52 MMA athletes participated in the study (M age = 24 yr., SD = 5; average experience in MMA = 5 yr., SD = 3). A one-way analysis of variance with repeated measurements was conducted to compare the type of action across the rounds. A chi-squared test was applied across the percentages to compare proportions of different events. Only one significant difference (p < .05) was observed among rounds: time in groundwork of low intensity was longer in the second compared to the third round. When the interval between rounds was not considered, the EP ratio (between high-intensity effort to low-intensity effort plus pauses) WE S 1:2 to 1:4. This ratio is between ratios typical for judo, wrestling, karate, and taekwondo and reflects the combination of ground and standup techniques. Most of the matches ended in the third round, involving high-intensity actions, predominantly executed during groundwork combat.

Highly inducible synthesis of heterologous proteins in epithelial cells carrying a glucocorticoid-responsive vector.

A glucocorticoid-responsive vector is described which allows for the highly inducible expression of complementary DNAs (cDNAs) in stably transfected mammalian cell lines. This vector, pLK-neo, composed of a variant mouse mammary tumor virus long terminal repeat promoter, containing a hormone regulatory element, a Geneticin resistance-encoding gene in a simian virus 40 transcription unit, and a polylinker insertion site for heterologous cDNAs, was used to express the polymeric immunoglobulin (poly-Ig) receptor and the thymocyte marker, Thy-1, in Madin-Darby canine kidney (MDCK) cells and in murine fibroblast L cells. A high level of poly-Ig receptor or Thy-1 mRNA accumulation was observed in MDCK cells in response to dexamethasone with a parallel ten- to 200-fold increase in protein synthesis depending on the recombinant protein and the transfected cell clone.

Pathways for the synthesis of polyesters in plants; cutin, suberin, and polyhydroxyalkanoates

Plants naturally produce the lipid-derived polyester cutin, which is found in the plant cuticle that is deposited at the outermost extracellular matrix of the epidermis covering nearly all aboveground tissues. Being at the interface between the cell and the external environment, cutin and the cuticle play important roles in the protection of plants from several stresses. A number of enzymes involved in the synthesis of cutin monomers have recently been identified, including several P450s and one acyl-CoA synthetase, thus representing the first steps toward the understanding of polyester formation and, potentially, polyester engineering to improve the tolerance of plants to stresses, such as drought, and for industrial applications. However, numerous processes underlying cutin synthesis, such as a controlled polymerization, still remain elusive. Suberin is a second polyester found in the extracellular matrix, most often synthesized in root tissues and during secondary growth. Similar to cutin, the function of suberin is to seal off the respective tissue to inhibit water loss and contribute to resistance to pathogen attack. Being the main constituent of cork, suberin is a plant polyester that has already been industrially exploited. Genetic engineering may be worth exploring in order to change the polyester properties for either different applications or to increase cork production in other species. Polyhydroxyalkanoates (PHAs) are attractive polyesters of 3-hydroxyacids because of their properties as bioplastics and elastomers. Although PHAs are naturally found in a wide variety of bacteria, biotechnology has aimed at producing these polymers in plants as a source of cheap and renewable biodegradable plastics. Synthesis of PHA containing various monomers has been demonstrated in the cytosol, plastids, and peroxisomes of plants. Several biochemical pathways have been modified in order to achieve this, including the isoprenoid pathway, the fatty acid biosynthetic pathway, and the fatty acid β-oxidation pathway. PHA synthesis has been demonstrated in a number of plants, including monocots and dicots, and up to 40% PHA per gram dry weight has been demonstrated in Arabidopsis thaliana. Despite some successes, production of PHA in crop plants remains a challenging project. PHA synthesis at high level in vegetative tissues, such as leaves, is associated with chlorosis and reduced growth. The challenge for the future is to succeed in synthesis of PHA copolymers with a narrow range of monomer compositions, at levels that do not compromise plant productivity. This goal will undoubtedly require a deeper understanding of plant biochemical pathways and how carbon fluxes through these pathways can be manipulated, areas where plant "omics" can bring very valuable contributions.

GPS-signal Source Based on Direct Digital Synthesis

This thesis presents the design and implementation of a GPS-signal source suitable for receiver measurements. The developed signal source is based on direct digital synthesis which generates the intermediate frequency. The intermediate frequency is transfered to the final frequency with the aid of an Inphase/Quadrature modulator. The modulating GPS-data was generated with MATLAB. The signal source was duplicated to form a multi channel source. It was shown that, GPS-signals ment for civil navigation are easy to generate in the laboratory. The hardware does not need to be technically advanced if navigation with high level of accuracy is not needed. It was also shown that, the Inphase/Quadrature modulator can function as a single side band upconverter even with a high intermediate frequency. This concept reduces the demands required for output filtering.

Vulnerability of stream biota to climate change in mediterranean climate regions: a synthesis of ecological responses and conservation challenges

Freshwater species worldwide are experiencing dramatic declines partly attributable to ongoing climate change. It is expected that the future effects of climate change could be particularly severe in mediterranean climate (med-) regions, which host many endemic species already under great stress from the high level of human development. In this article, we review the climate and climate-induced changes in streams of med-regions and the responses of stream biota, focusing on both observed and anticipated ecological responses. We also discuss current knowledge gaps and conservation challenges. Expected climate alterations have already been observed in the last decades, and include: increased annual average air temperatures; decreased annual average precipitation; hydrologic alterations; and an increase in frequency, intensity and duration of extreme events, such as floods, droughts and fires. Recent observations, which are concordant with forecasts built, show stream biota of med-regions when facing climate changes tend to be displaced towards higher elevations and upper latitudes, communities tend to change their composition and homogenize, while some life-history traits seem to provide biota with resilience and resistance to adapt to the new conditions (as being short-lived, small, and resistant to low streamflow and desiccation). Nevertheless, such responses may be insufficient to cope with current and future environmental changes. Accurate forecasts of biotic changes and possible adaptations are difficult to obtain in med-regions mainly because of the difficulty of distinguishing disturbances due to natural variability from the effects of climate change, particularly regarding hydrology. Long-term studies are needed to disentangle such variability and improve knowledge regarding the ecological responses and the detection of early warning signals to climate change. Investments should focus on taxa beyond fish and macroinvertebrates, and in covering the less studied regions of Chile and South Africa. Scientists, policy makers and water managers must be involved in the climate change dialogue because the freshwater conservation concerns are huge.

A duplicated nitrotienyl derivative with antimycobacterial activity: synthesis, X-ray crystallography, biological and mutagenic activity tests

A duplicated nitrotienyl derivative was obtained as a by-product from the synthesis of a proposed molecular hybrid of a nitrotienyl derivative and isoniazid with an expected dual antimycobacteria mechanism. The structure was shown to be the 5,5'-dinitro-2(2,3-diaza-4-(2'-tienyl)buta-1,3-dienyl)tiophene by X-ray crystallography. The minimal inhibitory concentration (MIC) determination of this compound proved to be promising against Mycobacterium pathogenic strains such as M. avium and M. kansasei, although it had a high level of mutagenicity, as observed in mutagenic activity tests. (c) 2006 Elsevier Masson SAS. All rights reserved.

Synthesis and characterization of silver nanoparticles impregnated into bacterial cellulose

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Protein-energy status and 15N-glycine kinetic study of child a cirrhotic patients fed low- to high-protein energy diets

In five male cirrhotic patients (Child A) and in four age- and sex-matched healthy control subjects, whole-body protein turnover was measured using a single oral dose of N-15-glycine as a tracer and urinary ammonia as end product. Subjects were studied in the fasting and feeding state, with different levels of protein and energy intake. The patients were underweight and presented lower plasma transthyretin and retinol-binding protein levels. When compared with controls, the kinetic studies showed patients to be hypometabolic in the fasting (Do) state and with the control diet [D-1 = (0.85 g of protein/154 kJ). kg(-1). day(-1)]. However, when corrected by body weight, the kinetic differences between groups disappeared, whereas the N-retention in the feeding state showed better results for the patients due mainly to their efficient breakdown decrease. When fed high-level protein or energy diets [D-2 = (0.9 g protein/195 kJ) and D-3 = (1.56 g protein/158 kJ). kg(-1). day(-1)], the patients showed D-0 = D-1 = D-2 < D-3 for N-flux and (D-0 = D-1) < D-3 (D-2 is intermediary) for protein synthesis. Thus, the present data suggest that the remaining mass of the undernourished mild cirrhotic patients has fairly good protein synthesis activity and also that protein, rather than energy intake, would be the limiting factor for increasing their whole-body protein synthesis.

Assessment of the high-dose concept and level of control provided by MON 87701 x MON 89788 soybean against Anticarsia gemmatalis and Pseudoplusia includens (Lepidoptera: Noctuidae) in Brazil

BACKGROUND: Genetically modified MON 87701 X MON 89788 soybean (Glycine max), which expresses the Cry1Ac and EPSP-synthase proteins, has been registered for commercial use in Brazil. To develop an Insect Resistance Management (IRM) program for this event, laboratory and field studies were conducted to assess the high-dose concept and level of control it provides against Anticarsia gemmatalis and Pseudoplusia includens. RESULTS: The purified Cry1Ac protein was more active against A. gemmatalis [LC50 (FL 95%) = 0.23 (0.150.34) mu g Cry1Ac mL-1 diet] than P. includens [LC50 (FL 95%) = 3.72 (2.654.86) mu g Cry1Ac mL-1 diet]. In bioassays with freeze-dried MON 87701X MON 89788 soybean tissue diluted 25 times in an artificial diet, there was 100% mortality of A. gemmatalis and up to 95.79% mortality for P. includens. In leaf-disc bioassays and under conditions of high artificial infestation in the greenhouse and natural infestation in the field, MON 87701X MON 89788 soybean showed a high level of efficacy against both target pests. CONCLUSIONS: The MON 87701X MON 89788 soybean provides a high level of control against A. gemmatalis and P. includes, but a high-dose event only to A. gemmatalis. Copyright (c) 2012 Society of Chemical Industry