A neural network model for constructing endophenotypes of common complex diseases: an application to male young-onset hypertension microarray data

Motivation: Identification of disease-related genes using high-throughput microarray data is more difficult for complex diseases as compared with monogenic ones. We hypothesized that an endophenotype derived from transcriptional data is associated with a set of genes corresponding to a pathway cluster. We assumed that a complex disease is associated with multiple endophenotypes and can be induced by their up/downregulated gene expression patterns. Thus, a neural network model was adopted to simulate the gene–endophenotype–disease relationship in which endophenotypes were represented by hidden nodes

Effective bootstrapping of Peer-to Peer networks over Mobile Ad-hoc networks

Mobile Ad-hoc Networks (MANETs) and Peer-to-Peer (P2P) networks are vigorous, revolutionary communication technologies in the 21st century. They lead the trend of decentralization. Decentralization will ultimately win clients over client/server model, because it gives ordinary network users more control, and stimulates their active participation. It is a determinant factor in shaping the future of networking. MANETs and P2P networks are very similar in nature. Both are dynamic, distributed. Both use multi-hop broadcast or multicast as major pattern of traffic. Both set up connection by self-organizing and maintain connection by self-healing. Embodying the slogan networking without networks, both abandoned traditional client/server model and disclaimed pre-existing infrastructure. However, their status quo levels of real world application are widely divergent. P2P networks are now accountable for about 50 ~ 70% internet traffic, while MANETs are still primarily in the laboratory. The interesting and confusing phenomenon has sparked considerable research effort to transplant successful approaches from P2P networks into MANETs. While most research in the synergy of P2P networks and MANETs focuses on routing, the network bootstrapping problem remains indispensable for any such transplantation to be realized. The most pivotal problems in bootstrapping are: (1) automatic configuration of nodes addresses and IDs, (2) topology discovery and transformation in different layers and name spaces. In this dissertation research, we have found novel solutions for these problems. The contributions of this dissertation are: (1) a non-IP, flat address automatic configuration scheme, which integrates lower layer addresses and P2P IDs in application layer and makes simple cryptographical assignment possible. A related paper entitled Pastry over Ad-Hoc Networks with Automatic Flat Address Configuration was submitted to Elsevier Journal of Ad Hoc Networks in May. (2) an effective ring topology construction algorithm which builds perfect ring in P2P ID space using only simplest multi-hop unicast or multicast. Upon this ring, popular structured P2P networks like Chord, Pastry could be built with great ease. A related paper entitled Chord Bootstrapping on MANETs - All Roads lead to Rome will be ready for submission after defense of the dissertation

Principles for optimal cooperativity in allosteric materials

Allosteric proteins transmit a mechanical signal induced by binding a ligand. However, understanding the nature of the information transmitted and the architectures optimizing such transmission remains a challenge. Here we show using an {\it in-silico} evolution scheme and theoretical arguments that architectures optimized to be cooperative, which propagate efficiently energy, {qualitatively} differ from previously investigated materials optimized to propagate strain. Although we observe a large diversity of functioning cooperative architectures (including shear, hinge and twist designs), they all obey the same principle {of displaying a {\it mechanism}, i.e. an extended {soft} mode}. We show that its optimal frequency decreases with the spatial extension $L$ of the system as $L^{-d/2}$, where $d$ is the spatial dimension. For these optimal designs, cooperativity decays logarithmically with $L$ for $d=2$ and does not decay for $d=3$. Overall our approach leads to a natural explanation for several observations in allosteric proteins, and { indicates an experimental path to test if allosteric proteins lie close to optimality}.Comment: 11 pages, 9 figures in the main text, 9 pages 9 figures in the supplemental materia

Redesigning hazard communication through technology: collaboration, co-production and coherence

Digital and virtual communication impacts increasingly upon the management of natural hazards in an uncertain world, challenging the boundaries between science and society. This study uses sociological theory to explore how technology reduces the mitigation failures and conflicts that scholars often disproportionately prioritise; it also evaluates the evolution of nodal points between communicating stakeholders in a complex hazard management network. Technical innovation has reshaped Iceland’s approach to mitigating risks associated with volcanic events; interconnections between stakeholders within the network evolve through technical innovation and the forming of collaborative engagements that renegotiate the roles and responsibilities of monitoring and response agencies. Interviews and participant observations, with agencies including the Icelandic Meteorological Office, evidence the impact of network evolution upon social media use, inter-agency trust, the expansion of crowdsourcing, and increasingly distributed decision-making frameworks.La communication numérique et virtuelle impacte de plus en plus la gestion des risques naturels dans un monde instable, défiant les frontières entre science et société. Notre étude étudie, sous l'angle de la sociologie, comment la technologie contribue à réduire les défaillances et les divergences en la matière, auxquels se réfèrent trop souvent les scientifiques. Nous analysons également l'évolution des points nodaux entre les acteurs de la communication à l'intérieur d'un réseau complexe de gestion des risques. En Islande les progrès technologiques ont remodelé l'approche de l'atténuation des risques associés aux événements volcaniques. Les interconnexions entre acteurs du réseau évoluent en fonction des innovations techniques et du développement d'engagements de collaboration qui renégocient les rôles et les responsabilités des organismes de contrôle et d'intervention. Les interviews et les observations des différents organismes, y compris l'Office météorologique d'Islande, démontrent l'impact de l'évolution du réseau sur l'utilisation des médias sociaux, la collaboration entre organismes, l'extension du "crowdsourcing", et la répartition croissante des cadres décisionnels