Development of Biomarkers Based on Diet-Dependent Metabolic Serotypes: Practical Issues in Development of Expert System-Based Classification Models in Metabolomic Studies

This is the publisher's official version, also available electronically from: http://online.liebertpub.com/doi/pdfplus/10.1089/omi.2004.8.197Dietary restriction (DR)-induced changes in the serum metabolome may be biomarkers for physiological status (e.g., relative risk of developing age-related diseases such as cancer). Megavariate analysis (unsupervised hierarchical cluster analysis IHCAJ; principal components analysis [PCAJ) of serum metabolites reproducibly distinguish DR from ad libitum fed rats. Component-based approaches (i.e., PCA) consistently perform as well as or better than distance-based metrics (i.e., HCA). We therefore tested the following: (A) Do identified subsets of serum metabolites contain sufficient information to construct mathematical models of class membership (i.e., expert systems)? (B) Do component-based metrics out-perform distance-based metrics? Testing was conducted using KNN (k-nearest neighbors, supervised HCA) and SIMCA (soft independent modeling of class analogy, supervised PCA). Models were built with single cohorts, combined cohorts or mixed samples from previously studied cohorts as training sets. Both algorithms over-fit models based on single cohort training sets. KNN models had >85% accuracy within training/test sets, but were unstable (i.e., values of k could not be accurately set in advance). SIMCA models had 100% accuracy within all training sets, 89% accuracy in test sets, did not appear to over-fit mixed cohort training sets, and did not require post-hoc modeling adjustments. These data indicate that (i) previously defined metabolites are robust enough to construct classification models (expert systems) with SIMCA that can predict unknowns by dietary category; (ii) component-based analyses outperformed distance-based metrics; (iii) use of over-fitting controls is essential; and (iv) subtle inter-cohort variability may be a critical issue for high data density biomarker studies that lack state markers

Development of Biomarkers Based on Diet-Dependent Metabolic Serotypes: Characteristics of Component-Based Models of Metabolic Serotypes

This is the publisher's version, also available electronically from: http://online.liebertpub.com/doi/pdfplus/10.1089/omi.2004Our research seeks to identify a scrum profile, or serotype, that reflects the systemic physiologic modifications resultant from dietary restriction (DR), in part such that this knowledge can be applied for biomarker studies. Direct comparison suggests that component-based classification algorithms consistently out-perform distance-based metrics for studies of nutritional modulation of metabolic serotype, but are subject to over-fitting concerns. Intercohort differences in the sera metabolome could partially obscure the effects of DR. Further analysis now shows that implementation of component-based approaches (also called projection methods) optimized for class separation and controlled for over-fitting have >97% accuracy for distinguishing sera from control or DR rats. DR's effect on the metabolome is shown to be robust across cohorts, but differs in males and females (although some metabolites are affected in both). We demonstrate the utility of projection-based methods for both sample and variable diagnostics, including identification of critical metabolites and samples that are atypical with respect to both class and variable models. Inclusion of non-statistically different variables enhances classification models. Variables that contribute to these models are sharply dependent on mathematical processing techniques; some variables that do not contribute under one paradigm arc powerful under alternative mathematical paradigms. In practical terms, this information may find purpose in other endeavors, such as mechanistic studies of DR. Application of these approaches confirms the utility of megavariate data analysis techniques for optimal generation of biomarkers based on nutritional modulation of physiological processes

Experiment scenarios, prototypes and report - Iteration 1

The task of WP6 is to evaluate the CONNECT technologies under realistic situations. To achieve this goal, WP6 concentrated its effort in the development of a main scenario in the context of the GMES, which required the connection of two very different and independently build systems provided by the industry partners. The first one is a video-surveillance system provided by Thales; the second one, is an implementation of the GSMA Rich Communication Suite provided by DOCOMO. The resulting scenario allows to verify the validity of some of the CONNECT claims and to investigate with the introduction of some of the CONNECT technologies in the context of the integration of real systems. In addition, WP6 started the work of evaluating how the overall CONNECT work cycle can be introduced in the context of industrial prototype development

Intermediate CONNECT Architecture

Interoperability remains a fundamental challenge when connecting heterogeneous systems which encounter and spontaneously communicate with one another in pervasive computing environments. This challenge is exasperated by the highly heterogeneous technologies employed by each of the interacting parties, i.e., in terms of hardware, operating system, middleware protocols, and application protocols. The key aim of the CONNECT project is to drop this heterogeneity barrier and achieve universal interoperability. Here we report on the activities of WP1 into developing the CONNECT architecture that will underpin this solution. In this respect, we present the following key contributions from the second year. Firstly, the intermediary CONNECT architecture that presents a more concrete view of the technologies and principles employed to enable interoperability between heterogeneous networked systems. Secondly, the design and implementation of the discovery enabler with emphasis on the approaches taken to match compatible networked systems. Thirdly, the realisation of CONNECTors that can be deployed in the environment; we provide domain specific language solutions to generate and translate between middleware protocols. Fourthly, we highlight the role of ontologies within CONNECT and demonstrate how ontologies crosscut all functionality within the CONNECT architecture

Utility-Based Mechanism for Structural Self-Organization in Service-Oriented MAS

Structural relations established among agents influence the performance of decentralized service discovery process in multiagent systems. Moreover, distributed systems should be able to adapt their structural relations to changes in environmental conditions. In this article, we present a service-oriented multiagent systems, where agents initially self-organize their structural relations based on the similarity of their services. During the service discovery process, agents integrate a mechanism that facilitates the self-organization of their structural relations to adapt the structure of the system to the service demand. This mechanism facilitates the task of decentralized service discovery and improves its performance. Each agent has local knowledge about its direct neighbors and the queries received during discovery processes. With this information, an agent is able to analyze its structural relations and decide when it is more appropriate to modify its direct neighbors and select the most suitable acquaintances to replace them. The experimental evaluation shows how this self-organization mechanism improves the overall performance of the service discovery process in the system when the service demand changesThis work is partially supported by the Spanish Ministry of Science and Innovation through grants CSD2007-0022 (CONSOLIDER-INGENIO 2010), TIN2012-36586-C03-01, TIN2012-36586-C03-01, TIN2012-36586-C03-02, PROMETEOII/2013/019, and FPU grant AP-2008-00601 awarded to E. Del Val.Del Val Noguera, E.; Rebollo Pedruelo, M.; Vasirani, M.; Fernández, A. (2014). Utility-Based Mechanism for Structural Self-Organization in Service-Oriented MAS. ACM Transactions on Autonomous and Adaptive Systems. 9(3):1-24. https://doi.org/10.1145/2651423S12493Sherief Abdallah and Victor Lesser. 2007. Multiagent reinforcement learning and self-organization in a network of agents. In Proceedings of the 6th International Conference on Autonomous Agents and Multiagent Systems. 172--179.Lada A. Adamic and Bernardo A. Huberman. 2002. Zipf’s law and the Internet. Glottometrics 3, 143--150.Muntasir Al-Asfoor, Brendan Neville, and Maria Fasli. 2012. Heuristic resource search in a self-organised distributed multi agent system. In Proceedings of the 6th International Workshop on Self-Organizing Systems. 84--89.Mathieu Aquin, Salman Elahi, and Enrico Motta. 2010. Personal monitoring of Web information exchange: Towards Web lifelogging. In Proceedings of the Web Science Conference.Ulrich Basters and Matthias Klusch. 2006. RS2D: Fast adaptive search for semantic Web services in unstructured p2p networks. In Proceedings of the International Semantic Web Conference. 87--100.Umesh Bellur and Roshan Kulkarni. 2007. Improved matchmaking algorithm for semantic Web services based on bipartite graph matching. In Proceedings of the International Semantic Web Conference. 86--93.Devis Bianchini, Valeria De Antonellis, and Michele Melchiori. 2009. Service-based semantic search in p2p systems. In Proceedings of the European Conference on Web Services. 7--16.Bartosz Biskupski, Jim Dowling, and Jan Sacha. 2007. Properties and mechanisms of self-organizing MANET and P2P systems. ACM Transactions on Autonomous and Adaptive Systems 2, 1, 1--34.Alberto Blanc, Yi-Kai Liu, and Amin Vahdat. 2005. Designing incentives for peer-to-peer routing. In Proceedings of the 24th Annual Joint Conference of the IEEE Computer and Communications Societies. 374--385.Michael Bowling and Manuela Veloso. 2002. Multiagent learning using a variable learning rate. Artificial Intelligence 136, 215--250.Frances M. T. Brazier, Jeffrey O. Kephart, H. Van Dyke Parunak, and Michael N. Huhns. 2009. Agents and service-oriented computing for autonomic computing: A research agenda. IEEE Internet Computing 13, 3, 82--87.Tyson Condie, Sepandar D. Kamvar, and Hector Garcia-Molina. 2004. Adaptive peer-to-peer topologies. In Proceedings of the 4th International Conference on Peer-to-Peer Computing. 53--62.Arturo Crespo and Hector Garcia-Molina. 2002. Routing indices for peer-to-peer systems. In Proceedings of the 22nd International Conference on Distributed Computing Systems. 23--32.Elena Del Val, Natalia Criado, Carlos Carrascosa, Vicente Julian, Miguel Rebollo, Estefania Argente, and Vicente Botti. 2010. THOMAS: A service-oriented framework for virtual organizations. In Proceedings of the 9th International Conference on Autonomous Agents and Multiagent Systems (AAMAS’10). 1631--1632.Elena Del Val, Miguel Rebollo, and Vicente Botti. 2011. Introducing homophily to improve semantic service search in a self-adaptive system. In Proceedings of the 10th International Conference on Autonomous Agents and Multiagent Systems. 1241--1242.Elena Del Val, Miguel Rebollo, and Vicente Botti. 2012a. Enhancing decentralized service discovery in open service-oriented multi-agent systems. Autonomous Agents and Multi-Agent Systems 28, 1, 1--30.Elena Del Val, Miguel Rebollo, and Vicente Botti. 2012b. Promoting cooperation in service-oriented MAS through social plasticity and incentives. Journal of Systems and Software 86, 2, 520--537.Gianni Di Caro, Frederick Ducatelle, and Luca Maria Gambardella. 2005. AntHocNet: An adaptive nature-inspired algorithm for routing in mobile ad hoc networks. European Transactions on Telecommunications 16, 443--455.Ding Ding, Lei Liu, and Hartmut Schmeck. 2010. Service discovery in self-organizing service-oriented environments. In Proceedings of the 2010 IEEE Asia-Pacific Services Computing Conference. 717--724.Sergey N. Dorogovtsev and Jose F. F. Mendes. 2003. Evolution of Networks: From Biological Nets to the Internet and WWW. Oxford University Press.Giovanna Di Marzo Serugendo, Marie-Pierre Gleizes, and Anthony Karageorgos. 2011. Self-Organizing Software: From Natural to Artificial Adaptation. Natural Computing Series.Erik Einhorn and Andreas Mitschele-Thiel. 2008. RLTE: Reinforcement learning for traffic-engineering. In Proceedings of the 2nd International Conference on Autonomous Infrastructure, Management, and Security. 120--133.Nelson Fernandez, Carlos Maldonado, and Carlos Gershenson. 2014. Information measures of complexity, emergence, self-organization, homeostasis, and autopoiesis. In Guided Self-Organization: Inception. Emergence, Complexity and Computation, Vol. 9. Springer, 19--51. DOI: http://dx.doi.org/10.1007/978-3-642-53734-9_2Jose Luis Fernandez-Marquez, Josep Lluis Arcos, and Giovanna Di Marzo Serugendo. 2012. A decentralized approach for detecting dynamically changing diffuse event sources in noisy WSN environments. Applied Artificial Intelligence 26, 4, 376--397. DOI: http://dx.doi.org/10.1080/08839514.2012.653659Agostino Forestiero, Carlo Mastroianni, and Michela Meo. 2009. Self-Chord: A bio-inspired algorithm for structured P2P systems. In Proceedings of the 9th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing. 44--51.Matthew E. Gaston and Marie des Jardins. 2005. Agent-organized networks for multi-agent production and exchange. In Proceedings of the 20th AAAI Conference on Artificial Intelligence. 77--82.Nathan Griffiths and Michael Luck. 2010. Changing neighbours: Improving tag-based cooperation. In Proceedings of the 9th International Conference on Autonomous Agents and Multiagent Systems. 249--256.Peter Haase, Ronny Siebes, and Frank van Harmelen. 2008. Expertise-based peer selection in peer-to-peer networks. Knowledge and Information Systems 15, 1, 75--107.Philip N. Howard, Lee Rainee, and Steve Jones. 2001. Days and nights on the Internet. American Behavioural Scientist, 383--404.Bernardo A. Huberman and Lada A. Adamic. 2000. The nature of markets in the WWW. Quarterly Journal of Electronic Commerce 1, 5--12.Michael N. Huhns et al. 2005. Research directions for service-oriented multiagent systems. IEEE Internet Computing 9, 6, 65--70.Tomoko Itao, Tatsuya Suda, Tetsuya Nakamura, Miyuki Imada, Masato Matsuo, and Tomonori Aoyama. 2001. Jack-in-the-Net: Adaptive networking architecture for service emergence. In Proceedings of the Asian-Pacific Conference on Communications. 9.Emily M. Jin, Michelle Girvan, and Mark E. J. Newman. 2001. Structure of growing social networks. Physical Review E 64, 4, 046132.Sachin Kamboj and Keith S. Decker. 2007. Organizational self-design in semi-dynamic environments. In Proceedings of the 6th International Joint Conference on Autonomous Agents and Multiagent Systems. 335--337.Rahamatullah Khondoker, S. M. Taslim Arif, Nathan Kerr, and Dennis Schwerdel. 2011. Self-organizing communication services in future network architectures. In Proceedings of the 5th International Workshop on Self-Organizing Systems.Matthias Klusch, Benedikt Fries, and Katia Sycara. 2009. OWLS-MX: A hybrid Semantic Web service matchmaker for OWL-S services. Web Semantics Science Services and Agents on the World Wide Web 7, 2, 121--133.Dionisis Kontominas, Paraskevi Raftopoulou, Christos Tryfonopoulos, and Euripides G. M. Petrakis. 2013. DS4: A distributed social and semantic search system. Advances in Information Retrieval 7814, 832--836.Ramachandra Kota, Nicholas Gibbins, and Nicholas R. Jennings. 2012. Decentralized approaches for self-adaptation in agent organizations. ACM Transactions on Autonomous and Adaptive Systems 7, 1, Article No. 1.Paul Lazarsfeld. 1954. Friendship as a social process: A substantive and methodological analysis. In Freedom and Control in Modern Society. Van Nostrand, New York, NY.Paulo Leito. 2013. Towards self-organized service-oriented multi-agent systems. In Service Orientation in Holonic and Multi Agent Manufacturing and Robotics. Studies in Computational Intelligence, Vol. 472. Springer, 41--56.W. Sabrina Lin, Hong Vikcy Zhao, and K. J. Ray Liu. 2009. Incentive cooperation strategies for peer-to-peer live multimedia streaming social networks. IEEE Transactions on Multimedia 11, 3, 396--412.Sheila A. McIlraith, Tran Cao Son, and Honglei Zeng. 2001. Semantic Web services. IEEE Intelligent Systems 16, 2, 46--53.Miller McPherson, Lynn Smith-Lovin, and James Cook. 2001. Birds of a feather: Homophily in social networks. Annual Review of Sociology 27, 415--444.Vivek Nallur and Rami Bahsoon. 2012. A decentralized self-adaptation mechanism for service-based applications in the cloud. IEEE Transactions on Software Engineering 99, 591--612.Aris Ouksel, Yair Babad, and Thomas Tesch. 2004. Matchmaking software agents in B2B markets. In Proceedings of the 37th Annual Hawaii International Conference on System Sciences. 1--9.Massimo Paolucci, Takahiro Kawamura, Terry R. Payne, and Katia P. Sycara. 2002. Semantic matching of Web services capabilities. In Proceedings of the 1st International Semantic Web Conference. 333--347.Leonid Peshkin and Virginia Savova. 2002. Reinforcement learning for adaptive routing. In Proceedings of the 2002 International Conference on Neural Networks (IJCNN’02). 1825--1830.Paraskevi Raftopoulou and Euripides G. M. Petrakis. 2008. iCluster: A self-organizing overlay network for P2P information retrieval. In Proceedings of the 30th European Conference on Advances in Information Retrieval (ECIR’08). 65--76.Sharmila Savarimuthu, Maryam Purvis, Martin Purvis, and Bastin Tony Roy Savarimuthu. 2011. Mechanisms for the self-organization of peer groups in agent societies. In Multi-Agent-Based Simulation XI. Lecture Notes in Computer Science, Vol. 6532. Springer, 93--107.Giovanna Di Marzo Serugendo, Marie-Pierre Gleizes, and Anthony Karageorgos. 2005. Self-organization in multi-agent systems. Knowledge Engineering Review 20, 2, 165--189.Abdul Khalique Shaikh, Saadat M. Alhashmi, and Rajendran Parthiban. 2012. A semantic impact in decentralized resource discovery mechanism for grid computing environments. In Algorithms and Architectures for Parallel Processing. Lecture Notes in Computer Science, Vol. 7440. Springer, 206--216.Qixiang Sun and Hector Garcia-Molina. 2004. SLIC: A selfish link-based incentive mechanism for unstructured peer-to-peer networks. In Proceedings of the 24th International Conference on Distributed Computing Systems (ICDCS’04). 506--515.Mirko Viroli and Franco Zambonelli. 2010. A biochemical approach to adaptive service ecosystems. Information Sciences 180, 10, 1876--1892. DOI: http://dx.doi.org/10.1016/j.ins.2009.11.021Li Wang. 2011. SoFA: An expert-driven, self-organization peer-to-peer semantic communities for network resource management. Expert Systems with Applications 38, 1, 94--105.Kevin Werbach. 2000. Syndication—the emerging model for business in the Internet era. Harvard Business Review 78, 3, 84--93, 214.Tom Wolf and Tom Holvoet. 2005. Emergence versus self-organisation: Different concepts but promising when combined. In Engineering Self-Organising Systems. Lecture Notes in Computer Science, Vol. 3464. Springer, 1--15.Haizheng Zhang, W. Bruce Croft, Brian Levine, and Victor Lesser. 2004. A multi-agent approach for peer-to-peer based information retrieval system. In Proceedings of the 3rd International Conference on Autonomous Agents and Multiagent Systems, Vol. 1. 456--463.Ming Zhong. 2006. Popularity-biased random walks for peer-to-peer search under the square-root principle. In Proceedings of the 5th International Workshop on Peer-to-Peer Systems

Initial CONNECT Architecture

Interoperability remains a fundamental challenge when connecting heterogeneous systems which encounter and spontaneously communicate with one another in pervasive computing environments. This challenge is exasperated by the highly heterogeneous technologies employed by each of the interacting parties, i.e., in terms of hardware, operating system, middleware protocols, and application protocols. The key aim of the CONNECT project is to drop this heterogeneity barrier and achieve universal interoperability. Here we report on the development of the overall CONNECT architecture that will underpin this solution; in this respect, we present the following contributions: i) an elicitation of interoperability requirements from a set of pervasive computing scenarios, ii) a survey of existing solutions to interoperability, iii) an initial view of the CONNECT architecture, and iv) a series of experiments to provide initial validation of the architecture

Measurement of W Polarisation at LEP

The three different helicity states of W bosons produced in the reaction e+ e- -> W+ W- -> l nu q q~ at LEP are studied using leptonic and hadronic W decays. Data at centre-of-mass energies \sqrt s = 183-209 GeV are used to measure the polarisation of W bosons, and its dependence on the W boson production angle. The fraction of longitudinally polarised W bosons is measured to be 0.218 \pm 0.027 \pm 0.016 where the first uncertainty is statistical and the second systematic, in agreement with the Standard Model expectation

Search for Branons at LEP

We search, in the context of extra-dimension scenarios, for the possible existence of brane fluctuations, called branons. Events with a single photon or a single Z-boson and missing energy and momentum collected with the L3 detector in e^+ e^- collisions at centre-of-mass energies sqrt{s}=189-209$ GeV are analysed. No excess over the Standard Model expectations is found and a lower limit at 95% confidence level of 103 GeV is derived for the mass of branons, for a scenario with small brane tensions. Alternatively, under the assumption of a light branon, brane tensions below 180 GeV are excluded

Bose-Einstein Correlations of Neutral and Charged Pions in Hadronic Z Decays

Bose-Einstein correlations of both neutral and like-sign charged pion pairs are measured in a sample of 2 million hadronic Z decays collected with the L3 detector at LEP. The analysis is performed in the four-momentum difference range 300 MeV < Q < 2 GeV. The radius of the neutral pion source is found to be smaller than that of charged pions. This result is in qualitative agreement with the string fragmentation model

Study of Spin and Decay-Plane Correlations of W Bosons in the e+e- -> W+W- Process at LEP

Data collected at LEP at centre-of-mass energies \sqrt(s) = 189 - 209 GeV are used to study correlations of the spin of W bosons using e+e- -> W+W- -> lnqq~ events. Spin correlations are favoured by data, and found to agree with the Standard Model predictions. In addition, correlations between the W-boson decay planes are studied in e+e- -> W+W- -> lnqq~ and e+e- -> W+W- -> qq~qq~ events. Decay-plane correlations, consistent with zero and with the Standard Model predictions, are measured