A core ontological model for semantic sensor web infrastructures

Semantic Sensor Web infrastructures use ontology-based models to represent the data that they manage; however, up to now, these ontological models do not allow representing all the characteristics of distributed, heterogeneous, and web-accessible sensor data. This paper describes a core ontological model for Semantic Sensor Web infrastructures that covers these characteristics and that has been built with a focus on reusability. This ontological model is composed of different modules that deal, on the one hand, with infrastructure data and, on the other hand, with data from a specific domain, that is, the coastal flood emergency planning domain. The paper also presents a set of guidelines, followed during the ontological model development, to satisfy a common set of requirements related to modelling domain-specific features of interest and properties. In addition, the paper includes the results obtained after an exhaustive evaluation of the developed ontologies along different aspects (i.e., vocabulary, syntax, structure, semantics, representation, and context).

Memory isolation in many-core embedded systems

The current approach to developing mixed-criticality sys- tems is by partitioning the hardware resources (processors, memory and I/O devices) among the different applications. Partitions are isolated from each other both in the temporal and the spatial domain, so that low-criticality applications cannot compromise other applications with a higher level of criticality in case of misbehaviour. New architectures based on many-core processors open the way to highly parallel systems in which each partition can be allocated to a set of dedicated proces- sor cores, thus simplifying partition scheduling and temporal separation. Moreover, spatial isolation can also benefit from many-core architectures, by using simpler hardware mechanisms to protect the address spaces of different applications. This paper describes an architecture for many- core embedded partitioned systems, together with some implementation advice for spatial isolation.

CompactRIO: advanced data acquisition systems integration in CODAC Core System

Las herramientas de configuración basadas en lenguajes de alto nivel como LabVIEW permiten el desarrollo de sistemas de adquisición de datos basados en hardware reconfigurable FPGA muy complejos en un breve periodo de tiempo. La estandarización del ciclo de diseño hardware/software y la utilización de herramientas como EPICS facilita su integración con la plataforma de adquisición y control ITER CODAC CORE SYSTEM (CCS) basada en Linux. En este proyecto se propondrá una metodología que simplificará el ciclo completo de integración de plataformas novedosas, como cRIO, en las que el funcionamiento del hardware de adquisición puede ser modificado por el usuario para que éste se amolde a sus requisitos específicos. El objetivo principal de este proyecto fin de master es realizar la integración de un sistema cRIO NI9159 y diferentes módulos de E/S analógica y digital en EPICS y en CODAC CORE SYSTEM (CCS). Este último consiste en un conjunto de herramientas software que simplifican la integración de los sistemas de instrumentación y control del experimento ITER. Para cumplir el objetivo se realizarán las siguientes tareas: • Desarrollo de un sistema de adquisición de datos basado en FPGA con la plataforma hardware CompactRIO. En esta tarea se realizará la configuración del sistema y la implementación en LabVIEW para FPGA del hardware necesario para comunicarse con los módulos: NI9205, NI9264, NI9401.NI9477, NI9426, NI9425 y NI9476 • Implementación de un driver software utilizando la metodología de AsynDriver para integración del cRIO con EPICS. Esta tarea requiere definir todos los records necesarios que exige EPICS y crear las interfaces adecuadas que permitirán comunicarse con el hardware. • Implementar la descripción del sistema cRIO y del driver EPICS en el sistema de descripción de plantas de ITER llamado SDD. Esto automatiza la creación de las aplicaciones de EPICS que se denominan IOCs. SUMMARY The configuration tools based in high-level programing languages like LabVIEW allows the development of high complex data acquisition systems based on reconfigurable hardware FPGA in a short time period. The standardization of the hardware/software design cycle and the use of tools like EPICS ease the integration with the data acquisition and control platform of ITER, the CODAC Core System based on Linux. In this project a methodology is proposed in order to simplify the full integration cycle of new platforms like CompactRIO (cRIO), in which the data acquisition functionality can be reconfigured by the user to fits its concrete requirements. The main objective of this MSc final project is to develop the integration of a cRIO NI-9159 and its different analog and digital Input/Output modules with EPICS in a CCS. The CCS consists of a set of software tools that simplifies the integration of instrumentation and control systems in the International Thermonuclear Reactor (ITER) experiment. To achieve such goal the following tasks are carried out: • Development of a DAQ system based on FPGA using the cRIO hardware platform. This task comprehends the configuration of the system and the implementation of the mandatory hardware to communicate to the I/O adapter modules NI9205, NI9264, NI9401, NI9477, NI9426, NI9425 y NI9476 using LabVIEW for FPGA. • Implementation of a software driver using the asynDriver methodology to integrate such cRIO system with EPICS. This task requires the definition of the necessary EPICS records and the creation of the appropriate interfaces that allow the communication with the hardware. • Develop the cRIO system’s description and the EPICS driver in the ITER plant description tool named SDD. This development will automate the creation of EPICS applications, called IOCs.

Thermodynamic stability of wild-type and mutant p53 core domain

Some 50% of human cancers are associated with mutations in the core domain of the tumor suppressor p53. Many mutations are thought just to destabilize the protein. To assess this and the possibility of rescue, we have set up a system to analyze the stability of the core domain and its mutants. The use of differential scanning calorimetry or spectroscopy to measure its melting temperature leads to irreversible denaturation and aggregation and so is useful as only a qualitative guide to stability. There are excellent two-state denaturation curves on the addition of urea that may be analyzed quantitatively. One Zn2+ ion remains tightly bound in the holo-form of p53 throughout the denaturation curve. The stability of wild type is 6.0 kcal (1 kcal = 4.18 kJ)/mol at 25°C and 9.8 kcal/mol at 10°C. The oncogenic mutants R175H, C242S, R248Q, R249S, and R273H are destabilized by 3.0, 2.9, 1.9, 1.9, and 0.4 kcal/mol, respectively. Under certain denaturing conditions, the wild-type domain forms an aggregate that is relatively highly fluorescent at 340 nm on excitation at 280 nm. The destabilized mutants give this fluorescence under milder denaturation conditions.

Proteolytic Processing and Ca2+-binding Activity of Dense-Core Vesicle Polypeptides in Tetrahymena

Formation and discharge of dense-core secretory vesicles depend on controlled rearrangement of the core proteins during their assembly and dispersal. The ciliate Tetrahymena thermophila offers a simple system in which the mechanisms may be studied. Here we show that most of the core consists of a set of polypeptides derived proteolytically from five precursors. These share little overall amino acid identity but are nonetheless predicted to have structural similarity. In addition, sites of proteolytic processing are notably conserved and suggest that specific endoproteases as well as carboxypeptidase are involved in core maturation. In vitro binding studies and sequence analysis suggest that the polypeptides bind calcium in vivo. Core assembly and postexocytic dispersal are compartment-specific events. Two likely regulatory factors are proteolytic processing and exposure to calcium. We asked whether these might directly influence the conformations of core proteins. Results using an in vitro chymotrypsin accessibility assay suggest that these factors can induce sequential structural rearrangements. Such progressive changes in polypeptide folding may underlie the mechanisms of assembly and of rapid postexocytic release. The parallels between dense-core vesicles in different systems suggest that similar mechanisms are widespread in this class of organelles.

Phosphorylation of synaptic vesicle proteins: modulation of the alpha SNAP interaction with the core complex.

We analyzed whether synaptic membrane trafficking proteins are substrates for casein kinase II, calcium/calmodulin-dependent protein kinase II, and cAMP-dependent protein kinase (PKA), three kinases implicated in the modulation of synaptic transmission. Each kinase phosphorylates a specific set of the vesicle proteins syntaxin 1A, N-ethylmaleimide-sensitive factor (NSF), vesicle-associated membrane protein (VAMP), synaptosome-associated 25-kDa protein (SNAP-25), n-sec1, alpha soluble NSF attachment protein (alpha SNAP), and synaptotagmin. VAMP is phosphorylated by calcium/calmodulin-dependent protein kinase II on serine 61. alpha SNAP is phosphorylated by PKA; however, the beta SNAP isoform is phosphorylated only 20% as efficiently. alpha SNAP phosphorylated by PKA binds to the core docking and fusion complex 10 times weaker than the dephosphorylated form. These studies provide a first glimpse at regulatory events that may be important in modulating neurotransmitter release during learning and memory.