Hardware timestamping for image acquisition system based on FlexRIO and IEEE 1588 v2 Standard

Current fusion devices consist of multiple diagnostics and hundreds or even thousands of signals. This situation forces on multiple occasions to use distributed data acquisition systems as the best approach. In this type of distributed systems, one of the most important issues is the synchronization between signals, so that it is possible to have a temporal correlation as accurate as possible between the acquired samples of all channels. In last decades, many fusion devices use different types of video cameras to provide inside views of the vessel during operations and to monitor plasma behavior. The synchronization between each video frame and the rest of the different signals acquired from any other diagnostics is essential in order to know correctly the plasma evolution, since it is possible to analyze jointly all the information having accurate knowledge of their temporal correlation. The developed system described in this paper allows timestamping image frames in a real-time acquisition and processing system using 1588 clock distribution. The system has been implemented using FPGA based devices together with a 1588 synchronized timing card (see Fig.1). The solution is based on a previous system [1] that allows image acquisition and real-time image processing based on PXIe technology. This architecture is fully compatible with the ITER Fast Controllers [2] and offers integration with EPICS to control and monitor the entire system. However, this set-up is not able to timestamp the frames acquired since the frame grabber module does not present any type of timing input (IRIG-B, GPS, PTP). To solve this lack, an IEEE1588 PXI timing device its used to provide an accurate way to synchronize distributed data acquisition systems using the Precision Time Protocol (PTP) IEEE 1588 2008 standard. This local timing device can be connected to a master clock device for global synchronization. The timing device has a buffer timestamp for each PXI trigger line and requires tha- a software application assigns each frame the corresponding timestamp. The previous action is critical and cannot be achieved if the frame rate is high. To solve this problem, it has been designed a solution that distributes the clock from the IEEE 1588 timing card to all FlexRIO devices [3]. This solution uses two PXI trigger lines that provide the capacity to assign timestamps to every frame acquired and register events by hardware in a deterministic way. The system provides a solution for timestamping frames to synchronize them with the rest of the different signals.

Integral energy behaviour of photovoltaic semi-transparent glazing elements for building integration

La hipótesis general que esta tesis quiere demostrar es que la integración arquitectónica de sistemas fotovoltaicos semitransparentes (STPV) puede contribuir a mejorar la eficiencia energética de los edificios. Por lo tanto, la investigación se centra en el desarrollo de una metodología capaz de cuantificar la reducción de la demanda energética del edificio proporcionada por estas novedosas soluciones constructivas. Al mismo tiempo, los parámetros de diseño de las soluciones STPV se han analizado para establecer cuales presentan el mayor impacto sobre el balance energético global del edificio y por lo tanto tienen que ser cuidadosamente definidos a la hora de optimizar el comportamiento energético del mismo. A la luz de estos objetivos, la metodología de estudio se ha centrado en tres puntos principales:  Caracterizar el comportamiento energético global de sistemas STPV en condiciones de operación realistas, similares a las que se darían en un sistema real;  Caracterizar el comportamiento energético global de sistemas STPV en condiciones controladas, con el objetivo de estudiar la variación del comportamiento del los elementos en función de parámetro de diseño y operación;  Evaluar el potencial de ahorro energético global de los sistemas STPV en comparación con soluciones acristaladas convencionales al variar de las condiciones de contorno constituidas por los parámetros de diseño (como el grado de transparencia), las características arquitectónicas (como el ratio entre superficie acristalada y superficie opaca en la fachada del edificio) y las condiciones climáticas (cubriendo en particular la climatología europea). En síntesis, este trabajo intenta contribuir a comprender la interacción que existe entre los sistemas STPV y el edificio, proporcionando tanto a los fabricantes de los componentes como a los profesionales de la construcción información valiosa sobre el potencial de ahorro energético asociado a estos nuevos sistemas constructivos. Asimismo el estudio define los parámetros de diseño adecuados para lograr soluciones eficientes tanto en proyectos nuevos como de rehabilitación. ABSTRACT The general hypothesis this work seeks to demonstrate is that the architectural integration of Semi-Transparent Photovoltaic (STPV) systems can contribute to improving the energy efficiency of buildings. Accordingly, the research has focused on developing a methodology able to quantify the building energy demand reduction provided by these novel constructive solutions. At the same time, the design parameters of the STPV solution have been analysed to establish which of them have the greatest impact on the global energy balance of the building, and therefore which have to be carefully defined in order to optimize the building operation. In the light of these goals, the study methodology has focused on three main points:  To characterise the global energy behaviour of STPV systems in realistic operating conditions, similar to those in which a real system will operate;  To characterise the global energy behaviour of STPV systems in controlled conditions in order to study how the performance varies depending on the design and operating parameters;  To assess the global energy saving potential of STPV systems in comparison with conventional glazing solutions by varying the boundary conditions, including design parameters (such as the degree of transparency), architectural characteristics (such as the Window to Wall Ratio) and climatic conditions (covering the European climatic conditions). In summary, this work has sought to contribute to the understanding of the interaction between STPV systems and the building, providing both components manufacturers and construction technicians, valuable information on the energy savings potential of these new construction systems and defining the appropriate design parameters to achieve efficient solutions in both new and retrofitting projects.

Integration of embedded data processing algorithms inside PAMELA devices

PAMELA (Phased Array Monitoring for Enhanced Life Assessment) SHMTM System is an integrated embedded ultrasonic guided waves based system consisting of several electronic devices and one system manager controller. The data collected by all PAMELA devices in the system must be transmitted to the controller, who will be responsible for carrying out the advanced signal processing to obtain SHM maps. PAMELA devices consist of hardware based on a Virtex 5 FPGA with a PowerPC 440 running an embedded Linux distribution. Therefore, PAMELA devices, in addition to the capability of performing tests and transmitting the collected data to the controller, have the capability of perform local data processing or pre-processing (reduction, normalization, pattern recognition, feature extraction, etc.). Local data processing decreases the data traffic over the network and allows CPU load of the external computer to be reduced. Even it is possible that PAMELA devices are running autonomously performing scheduled tests, and only communicates with the controller in case of detection of structural damages or when programmed. Each PAMELA device integrates a software management application (SMA) that allows to the developer downloading his own algorithm code and adding the new data processing algorithm to the device. The development of the SMA is done in a virtual machine with an Ubuntu Linux distribution including all necessary software tools to perform the entire cycle of development. Eclipse IDE (Integrated Development Environment) is used to develop the SMA project and to write the code of each data processing algorithm. This paper presents the developed software architecture and describes the necessary steps to add new data processing algorithms to SMA in order to increase the processing capabilities of PAMELA devices.An example of basic damage index estimation using delay and sum algorithm is provided.

Engineering analysis of ITER In-Vessel Viewing System guide tube

The In Vessel Viewing System (IVVS) will be one of the essential machine diagnostic systems at ITER to provide information about the status of in-vessel and plasma facing components and to evaluate the dust inside the Vacuum Vessel. The current design consists of six scanning probes and their deployment systems, which are placed in dedicated ports at the divertor level. These units are located in resident guiding tubes 10 m long, which allow the IVVS probes to go from their storage location to the scanning position by means of a simple straight translation. Moreover, each resident tube is supported inside the corresponding Vacuum Vessel and Cryostat port extensions, which are part of the primary confinement barrier. As the Vacuum Vessel and the Cryostat will move with respect to each other during operation (especially during baking) and during incidents and accidents (disruptions, vertical displacement events, seismic events), the structural integrity of the resident tube and the surrounding vacuum boundaries would be compromised if the required flexibility and supports are not appropriately assured. This paper focuses on the integration of the present design of the IVVS into the Vacuum Vessel and Cryostat environment. It presents the adopted strategy to withstand all the main interfacing loads without damaging the confinement barriers and the corresponding analysis supporting it.

Embedded Linux integration using Linuxlink tool and peripheral driver development for Zedboard

This project is divided into two main parts: The first part shows the integration of an Embedded Linux operating system on a development hardware platform named Zedboard. This platform contains a Zynq-7000 System on Chip (Soc) which is composed by two dual core ARM Cortex-A9 processors and a FPGA Artix-7. The Embedded Linux is built with Linuxlink, a Timesys tool. Meanwhile, the platform hardware configuration is done with Xilinx Vivado. The system is loaded with an SD card which requires to have every files needed for the booting process and for the operation. Some of these files are generated with Xilinx SDK software. The second part starts up from the system already built to integrate a peripheral in the Zynq-7000 FPGA. Also the drivers for controlling the peripheral from the operating system are developed. Finally, a user space program is created to test both of them. RESUMEN. Este proyecto consta de dos partes: La primera muestra la integración de un sistema operativo Linux embebido en una plataforma de desarrollo hardware llamada Zedboard. Esta plataforma utiliza un System on Chip (SoC) Zynq-7000 que está formado por dos procesadores ARM Cortex-A9 de doble núcleo y una FPGA Artix-7. El Linux embebido se construye utilizando la herramienta Linuxlink de Timesys, mientras que el hardware de la plataforma de desarrollo se configura con Vivado de Xilinx. El sistema se carga en una tarjeta SD que debe tener todos los archivos necesarios para completar el arranque y hacer funcionar el sistema. Algunos de esos archivos se generan con la herramienta SDK de Xilinx. En la segunda parte se utiliza el sistema construido para integrar un periférico en la FPGA del Zynq-7000, haciendo uso de Vivado, y se desarrollan los drivers necesarios para utilizarlo mediante el sistema operativo. Para probar esta última parte se desarrolla un programa de espacio de usuario.

Design and evaluation of a dehumidifying plaster panel for passive architecture integration

Buildings Indoor Air Quality requires a control in the Relative Humidity parameter. In passive architecture in humid climates relative humidity is even more important for human comfort and difficult to control. Therefore, nowadays, there is a research on dehumidifying systems. The present article shows an innovative dehumidifying panel composed of a plaster and Calcium Chloride salt. Laboratory tests are carried out to establish its viability as an indoor air moister regulator integrated in common plaster building interior coatings. There are two types of tests that have been carried out in two consecutive empirical phases: in the first phase, the tests of characterization of the Calcium Chloride as a desiccant are carried out; in a second phase, the dehumidifying panel as a whole is tested. Finally, both types of empirical tests show the efficiency and viability as an air moisture passive control system.

Pre-investigation of water electrolysis for flexible energy storage at large scales: the case of the Spanish power system

This report analyzes the basis of hydrogen and power integration strategies, by using water electrolysis processes as a means of flexible energy storage at large scales. It is a prospective study, where the scope is to describe the characteristics of current power systems (like the generation technologies, load curves and grid constraints), and define future scenarios of hydrogen for balancing the electrical grids, considering the efficiency, economy and easiness of operations. We focus in the "Spanish case", which is a good example for planning the transition from a power system holding large reserve capacities, high penetration of renewable energies and limited interconnections, to a more sustainable energy system being capable to optimize the volumes, the regulation modes, the utilization ratios and the impacts of the installations. Thus, we explore a novel aspect of the "hydrogen economy" which is based in the potentials of existing power systems and the properties of hydrogen as energy carrier, by considering the electricity generation and demand globally and determining the optimal size and operation of the hydrogen production processes along the country; e.g. the cost production of hydrogen becomes viable for a base-load scenario with 58 TWh/year of power surplus at 0.025 V/kWh, and large number electrolyzer plants (50 MW) running in variable mode (1-12 kA/m2)

Feature integration in pattern perception

The human visual system is able to effortlessly integrate local features to form our rich perception of patterns, despite the fact that visual information is discretely sampled by the retina and cortex. By using a novel perturbation technique, we show that the mechanisms by which features are integrated into coherent percepts are scale-invariant and nonlinear (phase and contrast polarity independent). They appear to operate by assigning position labels or “place tags” to each feature. Specifically, in the first series of experiments, we show that the positional tolerance of these place tags in foveal, and peripheral vision is about half the separation of the features, suggesting that the neural mechanisms that bind features into forms are quite robust to topographical jitter. In the second series of experiment, we asked how many stimulus samples are required for pattern identification by human and ideal observers. In human foveal vision, only about half the features are needed for reliable pattern interpolation. In this regard, human vision is quite efficient (ratio of ideal to real ≈ 0.75). Peripheral vision, on the other hand is rather inefficient, requiring more features, suggesting that the stimulus may be relatively underrepresented at the stage of feature integration.

A Cell-free System to Study Regulation of Focal Adhesions and of the Connected Actin Cytoskeleton

Assembly and modulation of focal adhesions during dynamic adhesive processes are poorly understood. We describe here the use of ventral plasma membranes from adherent fibroblasts to explore mechanisms regulating integrin distribution and function in a system that preserves the integration of these receptors into the plasma membrane. We find that partial disruption of the cellular organization responsible for the maintenance of organized adhesive sites allows modulation of integrin distribution by divalent cations. High Ca2+ concentrations induce quasi-reversible diffusion of β1 integrins out of focal adhesions, whereas low Ca2+ concentrations induce irreversible recruitment of β1 receptors along extracellular matrix fibrils, as shown by immunofluorescence and electron microscopy. Both effects are independent from the presence of actin stress fibers in this system. Experiments with cells expressing truncated β1 receptors show that the cytoplasmic portion of β1 is required for low Ca2+-induced recruitment of the receptors to matrix fibrils. Analysis with function-modulating antibodies indicates that divalent cation-mediated receptor distribution within the membrane correlates with changes in the functional state of the receptors. Moreover, reconstitution experiments show that purified α-actinin colocalizes and redistributes with β1 receptors on ventral plasma membranes depleted of actin, implicating binding of α-actinin to the receptors. Finally, we found that recruitment of exogenous actin is specifically restricted to focal adhesions under conditions in which new actin polymerization is inhibited. Our data show that the described system can be exploited to investigate the mechanisms of integrin function in an experimental setup that permits receptor redistribution. The possibility to uncouple, under cell-free conditions, events involved in focal adhesion and actin cytoskeleton assembly should facilitate the comprehension of the underlying molecular mechanisms.

“Agrolistic” transformation of plant cells: Integration of T-strands generated in planta

We describe a novel plant transformation technique, termed “agrolistic,” that combines the advantages of the Agrobacterium transformation system with the high efficiency of biolistic DNA delivery. Agrolistic transformation allows integration of the gene of interest without undesired vector sequence. The virulence genes virD1 and virD2 from Agrobacterium tumefaciens that are required in bacteria for excision of T-strands from the tumor-inducing plasmid were placed under the control of the CaMV35S promoter and codelivered with a target plasmid containing border sequences flanking the gene of interest. Transient expression assays in tobacco and in maize cells indicated that vir gene products caused strand-specific nicking in planta at the right border sequence, similar to VirD1/VirD2-catalyzed T-strand excision observed in Agrobacterium. Agrolistically transformed tobacco calli were obtained after codelivery of virD1 and virD2 genes together with a selectable marker flanked by border sequences. Some inserts exhibited right junctions with plant DNA that corresponded precisely to the sequence expected for T-DNA (portion of the tumor-inducing plasmid that is transferred to plant cells) insertion events. We designate these as “agrolistic” inserts, as distinguished from “biolistic” inserts. Both types of inserts were found in some transformed lines. The frequency of agrolistic inserts was 20% that of biolistic inserts.

Integration of circadian and phototransduction pathways in the network controlling CAB gene transcription in Arabidopsis

The transcription of CAB genes, encoding the chlorophyll a/b-binding proteins, is rapidly induced in dark-grown Arabidopsis seedlings following a light pulse. The transient induction is followed by several cycles of a circadian rhythm. Seedlings transferred to continuous light are known to exhibit a robust circadian rhythm of CAB expression. The precise waveform of CAB expression in light–dark cycles, however, reflects a regulatory network that integrates information from photoreceptors, from the circadian clock and possibly from a developmental program. We have used the luciferase reporter system to investigate CAB expression with high time resolution. We demonstrate that CAB expression in light-grown plants exhibits a transient induction following light onset, similar to the response in dark-grown seedlings. The circadian rhythm modulates the magnitude and the kinetics of the response to light, such that the CAB promoter is not light responsive during the subjective night. A signaling pathway from the circadian oscillator must therefore antagonize the phototransduction pathways controlling the CAB promoter. We have further demonstrated that the phase of maximal CAB expression is delayed in light–dark cycles with long photoperiods, due to the entrainment of the circadian oscillator. Under short photoperiods, this pattern of entrainment ensures that dawn coincides with a phase of high light responsiveness, whereas under long photoperiods, the light response at dawn is reduced.

PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the finite parts list of folds from an expanding number of perspectives. We have developed a new resource, called PartsList, that lets one dynamically perform these comparative fold surveys. It is available on the web at http://bioinfo.mbb.yale.edu/partslist and http://www.partslist.org. The system is based on the existing fold classifications and functions as a form of companion annotation for them, providing ‘global views’ of many already completed fold surveys. The central idea in the system is that of comparison through ranking; PartsList will rank the approximately 420 folds based on more than 180 attributes. These include: (i) occurrence in a number of completely sequenced genomes (e.g. it will show the most common folds in the worm versus yeast); (ii) occurrence in the structure databank (e.g. most common folds in the PDB); (iii) both absolute and relative gene expression information (e.g. most changing folds in expression over the cell cycle); (iv) protein–protein interactions, based on experimental data in yeast and comprehensive PDB surveys (e.g. most interacting fold); (v) sensitivity to inserted transposons; (vi) the number of functions associated with the fold (e.g. most multi-functional folds); (vii) amino acid composition (e.g. most Cys-rich folds); (viii) protein motions (e.g. most mobile folds); and (ix) the level of similarity based on a comprehensive set of structural alignments (e.g. most structurally variable folds). The integration of whole-genome expression and protein–protein interaction data with structural information is a particularly novel feature of our system. We provide three ways of visualizing the rankings: a profiler emphasizing the progression of high and low ranks across many pre-selected attributes, a dynamic comparer for custom comparisons and a numerical rankings correlator. These allow one to directly compare very different attributes of a fold (e.g. expression level, genome occurrence and maximum motion) in the uniform numerical format of ranks. This uniform framework, in turn, highlights the way that the frequency of many of the attributes falls off with approximate power-law behavior (i.e. according to V–b, for attribute value V and constant exponent b), with a few folds having large values and most having small values.

Provirus integration into a gene encoding a ubiquitin-conjugating enzyme results in a placental defect and embryonic lethality.

Ubiquitin-conjugating enzymes (E2 or Ubc) constitute a family of conserved proteins that play a key role in ubiquitin-dependent degradation of proteins in eukaryotes. We describe here a transgenic mouse strain where retrovirus integration into an Ubc gene, designated UbcM4, results in a recessive-lethal mutation. UbcM4 is the mouse homologue of the previously described human UbcH7 that is involved in the in vitro ubiquitination of several proteins including the tumor suppressor protein p53. The provirus is located in the first intron of the gene. When both alleles are mutated the level of steady-state mRNA is reduced by about 70%. About a third of homozygous mutant embryos die around day 11.5 of gestation. Embryos that survive that stage are growth retarded and die perinatally. The lethal phenotype is most likely caused by impairment of placenta development as this is the only organ that consistently showed pathological defects. The placental labyrinth is drastically reduced in size and vascularization is disturbed. The UbcM4 mouse mutant represents the first example in mammals of a mutation in a gene involved in ubiquitin conjugation. Its recessive-lethal phenotype demonstrates that the ubiquitin system plays an essential role during mouse development.

Site-specific integration by adeno-associated virus.

Adeno-associated virus (AAV) has attracted considerable interest as a potential vector for gene delivery. Wild-type virus is notable for the lack of association with any human disease and the ability to stably integrate its genome in a site-specific manner in a locus on human chromosome 19 (AAVS1). Use of a functional model system for AAV DNA integration into AAVS1 has allowed us to conclude that the recombination event is directed by cellular DNA sequences. Recombinant junctions isolated from our integration assay were analyzed and showed characteristics similar to those found in latently infected cell lines. The minimal DNA signals within AAVS1 required for targeted integration were identified and shown to contain functional motifs of the viral origin of replication. A replication mediated model of AAV DNA integration is proposed.

Homeologous recombination and mismatch repair during transformation in Streptococcus pneumoniae: saturation of the Hex mismatch repair system.

The ability of the Hex generalized mismatch repair system to prevent recombination between partially divergent (also called homeologous) sequences during transformation in Streptococcus pneumoniae was investigated. By using as donor in transformation cloned fragments 1.7-17.5% divergent in DNA sequence from the recipient, it was observed that the Hex system prevents chromosomal integration of the least and the most divergent fragments but frequently fails to do so for other fragments. In the latter case, the Hex system becomes saturated (inhibited) due to an excess of mismatches: it is unable to repair a single mismatch located elsewhere on the chromosome. Further investigation with chromosomal donor DNA, carrying only one genetically marked divergent region, revealed that a single divergent fragment can lead to saturation of the Hex system. Increase in cellular concentration of either HexA, the MutS homologue that binds mismatches, or HexB, the MutL homologue for which the essential role in repair as yet remains obscure, was shown to restore repair ability in previously saturating conditions. Investigation of heterospecific transformation by chromosomal DNA from two related streptococcal species, Streptococcus oralis and Streptococcus mitis, also revealed complete saturation of the Hex system. Therefore the Hex system is not a barrier to interspecies recombination in S. pneumoniae. These results are discussed in light of those described for the Mut system of Escherichia coli.