From the Queue to the Quality of Service Policy: A Middleware Implementation

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-02481-8_61Quality of service policies in communications is one of the current trends in distributed systems based on middleware technology. To implement the QoS policies it is necessary to define some common parameters. The aim of the QoS policies is to optimize the user defined QoS parameters. This article describes how to obtain the common QoS parameters using message queues for the communications and control components of communication. The paper introduces the Queue-based Quality of Service Cycle concept for each middleware component. The QoS parameters are obtained directly from the queue parameters, and Quality of Service Policies controls directly the message queues to obtain the user-defined parameters values.The middleware architecture described in this article is a part of the coordinated project SIDIRELI: Distributed Systems with Limited Resources. Control Kernel and Coordination. Education and Science Department, Spanish Government. CICYT: MICINN: DPI2008-06737-C02-01/02.Poza-Lujan, J.; Posadas-Yagüe, J.; Simó Ten, JE. (2009). From the Queue to the Quality of Service Policy: A Middleware Implementation. En Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living. Springer Verlag (Germany). 432-437. doi:10.1007/978-3-642-02481-8_61S432437Aurrecoechea, C., Campbell, A.T., Hauw, L.: A Survey of QoS Architectures. Multimedia Systems Journal, Special Issue on QoS Architecture 6(3), 138–151 (1998)OMG. Data Distribution Service for Real-Time Systems, v1.1. Document formal/2005-12-04 (December 2005)Botts, M., Percivall, G., Reed, C., Davidson, J.: OGC®. Sensor Web Enablement: Overview And High Level Architecture, OpenGIS Consortium Inc (2006)Poza, J.L., Posadas, J.I., Simó, J.E.: QoS-based middleware architecture for distributed control systems. In: International Symposium on Distributed Computing and Artificial Intelligence, Salamanca (2008)Vogel, A., Kerherve, B., von Bochmann, G., Gecsei, J.: Distributed Multi-media and QoS: A Survey 2(2), 10–19 (1995)Crawley, E., Nair, R., Rajagopalan, B.: RFC 2386: A Framework for QoS-based Routing in the Internet, pp. 1–37, XP002219363 (August 1998)ITU-T Recommendation E.800 (0894). Terms and Definitions Related to Quality of Service and Network Performance Including Dependability (1994)Stuck, B.W., Arthurs, E.: A Computer & Communications Network Performance Analysis Primer. Prentice Hall, Englewood Cliffs (1984)Jain, R.: The art of Computer Systems Performance Analysis. John Wiley & Sons Inc., New york (1991)Coulouris, G., Dollimore, J., Kindberg, T.: Distributed Systems. Concepts and Design, 3rd edn. Addison Wesley, Madrid (2001)Jung, J.-l.: Quality of Service in Telecommunications Part II: Translation of QoS Pa-rameters into ATM Performance Parameters in B-ISDN. IEEE Comm. Mag., pp. 112–117 (August 1996)Wohlstadter, E., Tai, S., Mikalsen, T., Rouvellou, I., Devanbu, P.: GlueQoS: Middleware to Sweeten Quality-of-Service Policy Interactions. In: ICSE, 26th International Conference on Software Engineering (ICSE 2004) (2004

Multi-Agent Architecture with Support to Quality of Service and Quality of Control

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-15381-5_17Multi Agent Systems (MAS) are one of the most suitable frameworks for the implementation of intelligent distributed control system. Agents provide suitable flexibility to give support to implied heterogeneity in cyber-physical systems. Quality of Service (QoS) and Quality of Control (QoC) parameters are commonly utilized to evaluate the efficiency of the communications and the control loop. Agents can use the quality measures to take a wide range of decisions, like suitable placement on the control node or to change the workload to save energy. This article describes the architecture of a multi agent system that provides support to QoS and QoC parameters to optimize de system. The architecture uses a Publish-Subscriber model, based on Data Distribution Service (DDS) to send the control messages. Due to the nature of the Publish-Subscribe model, the architecture is suitable to implement event-based control (EBC) systems. The architecture has been called FSACtrlThe architecture described in this article is a part of the coordinated project SIDIRELI: Distributed Systems with Limited Resources. Control Kernel and Coordination. Education and Science Department, Spanish Government and FEDER funds.Poza-Lujan, J.; Posadas-Yagüe, J.; Simó Ten, JE. (2010). Multi-Agent Architecture with Support to Quality of Service and Quality of Control. En Intelligent Data Engineering and Automated Learning – IDEAL 2010. Springer Verlag (Germany). 137-144. doi:10.1007/978-3-642-15381-5_17S137144Lee, E.A.: Cyber Physical Systems: Design Challenges. In: 11th IEEE Symposium on Object Oriented Real-Time Distributed Computing, pp. 363–369 (2008)Siegel, J.: CORBA 3: Fundamentals and Programming. OMG (2000)FIPA. FIPA-QoS (2002), http://www.fipa.org/specs/fipa00094Object Management Group (OMG): Data Distribution Service for Real-Time Systems, v1.1. Document formal (2005-12-04)Posadas, J.L., Poza, J.L., Simó, J.E., Benet, G., Blanes, F.: Agent Based Distributed Architecture for Mobile Robot Control. Engineering Applications of Artificial Intelligence 21(6), 805–823 (2008)Aurrecoechea, C., Campbell, A.T., Hauw, L.: A Survey of QoS Architectures. Multimedia Systems Journal, Special Issue on QoS Architecture 6(3), 138–151 (1998)Pardo-Castellote, G.: OMG Data-Distribution Service: architectural overview. In: Proceedings of 23rd International Conference on Distributed Computing Systems Workshops, Providence, USA, vol. 19(22), pp. 200–206 (2003)International Telecommunication Union (ITU). Terms and Definitions Related to Quality of Service and Network Performance Including Dependability. ITU-T Recommendation E.800 (0894) (1994)Sánchez, J., Guarnes, M.Á., Dormido, S.: On the Application of Different Event-Based Sampling Strategies to the Control of a Simple Industrial Process. Sensors 9, 6795–6818 (2009)Dorf, R.C., Bishop, R.H.: Modern Control Systems, 11th edn. Prentice Hall, Englewood Cliffs (2008)Poza, J.L., Posadas, J.L., Simó, J.E.: Middleware with QoS Support to Control Intelligent Systems. In: 2th International Conference on Advanced Engineering Computing and Applications in Sciences, ADVCOMP, pp. 211–216 (2008)Poza, J.L., Posadas, J.L., Simó, J.E.: From the Queue to the Quality of Service Policy: A Middleware Implementation. In: Omatu, S., Rocha, M.P., Bravo, J., Fernández, F., Corchado, E., Bustillo, A., Corchado, J.M. (eds.) IWANN 2009. LNCS, vol. 5518, pp. 432–437. Springer, Heidelberg (2009

Quality of service and quality of control based protocol to distribute agents

The final publication is available at Springer via http://dx.doi.org/10.1007/978-3-642-14883-5_10This paper describes an agent s movement protocol. Additionally, a distributed architecture to implement such protocol is presented. The architecture allows the agents to move in accordance with their requirements. The protocol is based on division and fusion of the agents in their basic components called Logical Sensors. The movement of the agents is based on the quality of services (QoS) and quality of control (QoC) parameters that the system can provides. The protocol is used to know the impact that the movement of the agents may have on the system and obtain the equilibrium points where the impact is minimal.The architecture described in this article is a part of the coordinated project SIDIRELI: Distributed Systems with Limited Resources. Control Kernel and Coordination. Education and Science Department, Spanish Government. CICYT: MICINN: DPI2008-06737-C02-01/02.Poza-Lujan, J.; Posadas-Yagüe, J.; Simó Ten, JE. (2010). Quality of service and quality of control based protocol to distribute agents. En Distributed Computing and Artificial Intelligence: 7th International Symposium. Springer. 73-80. doi:10.1007/978-3-642-14883-5_10S7380Posadas, J.L., Poza, J.L., Simó, J.E., Benet, G., Blanes, F.: Agent Based Distributed Architecture for Mobile Robot Control. In: Engineering Applications of Artificial Intelligence, vol. 21(6), pp. 805–823. Pergamon Press Ltd., Oxford (2008)Object Management Group (OMG): Data Distribution Service for Real-Time Systems, v1.1. Document formal / 2005-12-04 (2005)Odum, E.P.: Fundamentals of Ecology, 3rd edn. W.B. Saunders Company, Philadelphia (1971)Aurrecoechea, C., Campbell, A.T., Hauw, L.: A Survey of QoS Architectures. ACM/Springer Verlag Multimedia Systems Journal, Special Issue on QoS Architecture 6(3), 138–151 (1998)Pardo-Castellote, G.O.: Data-Distribution Service: architectural overview. In: Proceedings of 23rd International Conference on Distributed Computing Systems Workshops, vol. 19-22, pp. 200–206 (2003)International Telecommunication Union (ITU). Terms and Definitions Related to Quality of Service and Network Performance Including Dependability. ITU-T Recommendation E.800 (0894) (1994)Foundation for Intelligent Physical Agents. FIPA Quality of Service Ontology Specification, Experimental Doc: XC00094 (2002)Dorf, R.C., Bishop, R.H.: Modern Control Systems, 11th edn. Prentice Hall, Englewood Cliffs (2008)Poza, J.L., Posadas, J.L., Simó, J.E.: Middleware with QoS Support to Control Intelligent Systems. In: 2nd International Conference on Advanced Engineering Computing and Applications in Sciences, ADVCOMP, pp. 211–216 (2008)Bellifemine, F., Poggi, A., Rimassa, G.: Jade: A FIPA-compliant agent framework. In: Proceedings of PAAM 1999, pp. 97–108 (1999)Poza, J.L., Posadas, J.L., Simó, J.E.: From the Queue to the Quality of Service Policy: A Middleware Implementation. In: Omatu, S., Rocha, M.P., Bravo, J., Fernández, F., Corchado, E., Bustillo, A., Corchado, J.M. (eds.) IWANN 2009. Part II. LNCS, vol. 5518, pp. 432–437. Springer, Heidelberg (2009)Foundation for Intelligent Physical Agents. FIPA Agent Management Specification, Doc: FIPA00023 (2000)Jeong, B., Cho, H., Kulvatunyou, B., Jones, A.: A Multi-Criteria Web Services Composition Problem. In: Proceedings of the IEEE International Conference on Information Reuse and Integration, 2007 (IRI 2007), pp. 379–384. IEEE, Los Alamitos (2007)Poza, J.L., Posadas, J.L., Simó, J.E., Benet, G.: Distributed Agent Specification for an Intelligent control Architecture. In: 6th International Workshop on Practical Applications of Agents and Multiagent Systems. IWPAAMS (2007) ISBN 978-84-611-8858-

The invasive cell coat at the microsporidian Trachipleistophora hominis-host cell interface contains secreted hexokinases

Funding: Wellcome Trust (Grant Number: 089803/D/09/Z), 600th anniversary studentship from the University of St Andrews.Microsporidia are obligate intracellular parasites causing significant disease in humans and economically important animals. In parallel to their extreme genetic reduction, Microsporidia have evolved novel mechanisms for exploiting host metabolism. A number of microsporidians confer secretion of otherwise cytosolic proteins by coding for signal peptides that direct entry into the endoplasmic reticulum. The human pathogen Trachipleistophora hominis encodes for four hexokinases, three of which have signal peptides at the N‐terminus. Here, we localized hexokinase 2 and hexokinase 3 through developmental stages of T. hominis using light and electron microscopy. Both proteins were concentrated in an extracellular coat previously termed the plaque matrix (PQM). The PQM (containing hexokinases) was morphologically dynamic, infiltrating the host cytoplasm predominantly during replicative stages. Throughout development the PQM interacted closely with endoplasmic reticulum that was demonstrated to be active in membrane protein biosynthesis and export. The impact of hexokinase on the host metabolism was probed using the fluorescent analog of glucose, 2‐NBDG, which displayed spatially restricted increases in signal intensity at the parasite/vacuole surface, coincident with hexokinase/PQM distribution. Gross metabolic aberrations, measured using metabolic profiling with the Seahorse XF Analyzer, were not detectable in mixed stage cocultures. Overall, these results highlight a role for the extended cell coat of T. hominis in host–parasite interactions, within which secreted hexokinases may work as part of a metabolic machine to increase glycolytic capacity or ATP generation close to the parasite surface.Publisher PDFPeer reviewe

The Plasmodium falciparum, Nima-related kinase Pfnek-4: a marker for asexual parasites committed to sexual differentiation

<b>Background</b> Malaria parasites undergo, in the vertebrate host, a developmental switch from asexual replication to sexual differentiation leading to the formation of gametocytes, the only form able to survive in the mosquito vector. Regulation of the onset of the sexual phase remains largely unknown and represents an important gap in the understanding of the parasite's complex biology. <b>Methods:</b> The expression and function of the Nima-related kinase Pfnek-4 during the early sexual development of the human malaria parasite Plasmodium falciparum were investigated, using three types of transgenic Plasmodium falciparum 3D7 lines: (i) episomally expressing a Pfnek-4-GFP fusion protein under the control of its cognate pfnek-4 promoter; (ii) episomally expressing negative or positive selectable markers, yeast cytosine deaminase-uridyl phosphoribosyl transferase, or human dihydrofolate reductase, under the control of the pfnek-4 promoter; and (iii) lacking a functional pfnek-4 gene. Parasite transfectants were analysed by fluorescence microscopy and flow cytometry. In vitro growth rate and gametocyte formation were determined by Giemsa-stained blood smears. <b>Results:</b> The Pfnek-4-GFP protein was found to be expressed in stage II to V gametocytes and, unexpectedly, in a subset of asexual-stage parasites undergoing schizogony. Culture conditions stimulating gametocyte formation resulted in significant increase of this schizont subpopulation. Moreover, sorted asexual parasites expressing the Pfnek-4-GFP protein displayed elevated gametocyte formation when returned to in vitro culture in presence of fresh red blood cells, when compared to GFP- parasites from the same initial population. Negative selection of asexual parasites expressing pfnek-4 showed a marginal reduction in growth rate, whereas positive selection caused a marked reduction in parasitaemia, but was not sufficient to completely abolish proliferation. Pfnek-4- clones are not affected in their asexual growth and produced normal numbers of stage V gametocytes. <b>Conclusions:</b> The results indicate that Pfnek-4 is not strictly gametocyte-specific, and is expressed in a small subset of asexual parasites displaying high rate conversion to sexual development. Pfnek-4 is not required for erythrocytic schizogony and gametocytogenesis. This is the first study to report the use of a molecular marker for the sorting of sexually-committed schizont stage P. falciparum parasites, which opens the way to molecular characterization of this pre-differentiated subpopulation

The strategies WDK: a graphical search interface and web development kit for functional genomics databases

Web sites associated with the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) have recently introduced a graphical user interface, the Strategies WDK, intended to make advanced searching and set and interval operations easy and accessible to all users. With a design guided by usability studies, the system helps motivate researchers to perform dynamic computational experiments and explore relationships across data sets. For example, PlasmoDB users seeking novel therapeutic targets may wish to locate putative enzymes that distinguish pathogens from their hosts, and that are expressed during appropriate developmental stages. When a researcher runs one of the approximately 100 searches available on the site, the search is presented as a first step in a strategy. The strategy is extended by running additional searches, which are combined with set operators (union, intersect or minus), or genomic interval operators (overlap, contains). A graphical display uses Venn diagrams to make the strategy’s flow obvious. The interface facilitates interactive adjustment of the component searches with changes propagating forward through the strategy. Users may save their strategies, creating protocols that can be shared with colleagues. The strategy system has now been deployed on all EuPathDB databases, and successfully deployed by other projects. The Strategies WDK uses a configurable MVC architecture that is compatible with most genomics and biological warehouse databases, and is available for download at code.google.com/p/strategies-wdk

Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism.

Plasmodium knowlesi is a newly described zoonosis that causes malaria in the human population that can be severe and fatal. The study of P. knowlesi parasites from human clinical isolates is relatively new and, in order to obtain maximum information from patient sample collections, we explored the possibility of generating P. knowlesi genome sequences from archived clinical isolates. Our patient sample collection consisted of frozen whole blood samples that contained excessive human DNA contamination and, in that form, were not suitable for parasite genome sequencing. We developed a method to reduce the amount of human DNA in the thawed blood samples in preparation for high throughput parasite genome sequencing using Illumina HiSeq and MiSeq sequencing platforms. Seven of fifteen samples processed had sufficiently pure P. knowlesi DNA for whole genome sequencing. The reads were mapped to the P. knowlesi H strain reference genome and an average mapping of 90% was obtained. Genes with low coverage were removed leaving 4623 genes for subsequent analyses. Previously we identified a DNA sequence dimorphism on a small fragment of the P. knowlesi normocyte binding protein xa gene on chromosome 14. We used the genome data to assemble full-length Pknbpxa sequences and discovered that the dimorphism extended along the gene. An in-house algorithm was developed to detect SNP sites co-associating with the dimorphism. More than half of the P. knowlesi genome was dimorphic, involving genes on all chromosomes and suggesting that two distinct types of P. knowlesi infect the human population in Sarawak, Malaysian Borneo. We use P. knowlesi clinical samples to demonstrate that Plasmodium DNA from archived patient samples can produce high quality genome data. We show that analyses, of even small numbers of difficult clinical malaria isolates, can generate comprehensive genomic information that will improve our understanding of malaria parasite diversity and pathobiology

Disease progression in Plasmodium knowlesi malaria is linked to variation in invasion gene family members.

Emerging pathogens undermine initiatives to control the global health impact of infectious diseases. Zoonotic malaria is no exception. Plasmodium knowlesi, a malaria parasite of Southeast Asian macaques, has entered the human population. P. knowlesi, like Plasmodium falciparum, can reach high parasitaemia in human infections, and the World Health Organization guidelines for severe malaria list hyperparasitaemia among the measures of severe malaria in both infections. Not all patients with P. knowlesi infections develop hyperparasitaemia, and it is important to determine why. Between isolate variability in erythrocyte invasion, efficiency seems key. Here we investigate the idea that particular alleles of two P. knowlesi erythrocyte invasion genes, P. knowlesi normocyte binding protein Pknbpxa and Pknbpxb, influence parasitaemia and human disease progression. Pknbpxa and Pknbpxb reference DNA sequences were generated from five geographically and temporally distinct P. knowlesi patient isolates. Polymorphic regions of each gene (approximately 800 bp) were identified by haplotyping 147 patient isolates at each locus. Parasitaemia in the study cohort was associated with markers of disease severity including liver and renal dysfunction, haemoglobin, platelets and lactate, (r = ≥ 0.34, p =  <0.0001 for all). Seventy-five and 51 Pknbpxa and Pknbpxb haplotypes were resolved in 138 (94%) and 134 (92%) patient isolates respectively. The haplotypes formed twelve Pknbpxa and two Pknbpxb allelic groups. Patients infected with parasites with particular Pknbpxa and Pknbpxb alleles within the groups had significantly higher parasitaemia and other markers of disease severity. Our study strongly suggests that P. knowlesi invasion gene variants contribute to parasite virulence. We focused on two invasion genes, and we anticipate that additional virulent loci will be identified in pathogen genome-wide studies. The multiple sustained entries of this diverse pathogen into the human population must give cause for concern to malaria elimination strategists in the Southeast Asian region

SpiroESTdb: a transcriptome database and online tool for sparganum expressed sequences tags

<p>Abstract</p> <p>Background</p> <p>Sparganum (plerocercoid of <it>Spirometra erinacei</it>) is a parasite that possesses the remarkable ability to survive by successfully modifying its physiology and morphology to suit various hosts and can be found in various tissues, even the nervous system. However, surprisingly little is known about the molecular function of genes that are expressed during the course of the parasite life cycle. To begin to decipher the molecular processes underlying gene function, we constructed a database of expressed sequence tags (ESTs) generated from sparganum.</p> <p>Findings</p> <p>SpiroESTdb is a web-based information resource that is built upon the annotation and curation of 5,655 ESTs data. SpiroESTdb provides an integrated platform for expressed sequence data, expression dynamics, functional genes, genetic markers including single nucleotide polymorphisms and tandem repeats, gene ontology and KEGG pathway information. Moreover, SpiroESTdb supports easy access to gene pages, such as (i) curation and query forms, (ii) <it>in </it><it>silico </it>expression profiling and (iii) BLAST search tools. Comprehensive descriptions of the sparganum content of all sequenced data are available, including summary reports. The contents of SpiroESTdb can be viewed and downloaded from the web (<url>http://pathod.cdc.go.kr/spiroestdb</url>).</p> <p>Conclusions</p> <p>This integrative web-based database of sequence data, functional annotations and expression profiling data will serve as a useful tool to help understand and expand the characterization of parasitic infections. It can also be used to identify potential industrial drug targets and vaccine candidate genes.</p

Modeling and Performance Analysis of Priority Queuing Systems

The paper presents the results of modeling and analysis of data performance on systems that support QoS (Quality of Service). In order to evaluate the performance of the modeled systems used were TPN (Timed Petri Nets). Studied were mechanisms of traffic shaping systems based on PQS (Priority Queuing System). Tested was the impact of the mechanism of generating traffic using TPN. Moreover, discussed were the basic mechanisms and queuing systems occurring in QoS structures. It is shown that models can be effectively used in the modeling and analysis of the performance of computer systems