Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.

Mapping sub-flows to p2mp LSPs

In previous work we proposed a multi-objective traffic engineering scheme (MHDB-S model) using different distribution trees to multicast several flows. In this paper, we propose a heuristic algorithm to create multiple point-to-multipoint (p2mp) LSPs based on the optimum sub-flow values obtained with our MHDB-S model. Moreover, a general problem for supporting multicasting in MPLS networks is the lack of labels. To reduce the number of labels used, a label space reduction algorithm solution is also considered

Las entidades sub-nacionales en Norteamérica y la lucha contra el cambio climático: desarrollo normativo y vinculación de sistemas de comercio de derechos de emisión

[spa] Mientras que en Europa la interdependencia y la dimensión transfronteriza de las cuestiones ligadas al cambio climático ha facilitado una cierta"continentalización" de la gestión de este fenómeno, favorecida por el carácter intergubernamental de las medidas que se adoptan en el marco de la Unión Europea, al otro lado del Atlántico la transversalidad de este mismo fenómeno explica la necesidad de que, ante las limitaciones del marco regional, se pongan en marcha mecanismos que faciliten la intervención no sólo estatal sino también de las entidades sub-nacionales. En este sentido, la ausencia de la acción federal tanto en Estados Unidos como en Canadá ha comportado un mayor desarrollo de la acción de las entidades sub-nacionales, que han tomado el liderazgo en la lucha contra el cambio climático. Son estas medidas las que se han visualizado en el escenario internacional. Ello ha favorecido el establecimiento de mecanismos de coordinación de la acción de estas entidades sub-nacionales en el seno de redes transnacionales, que han ido adquiriendo una mayor relevancia en la implementación del Convenio Marco sobre el Cambio Climático y del Protocolo de Kyoto, particularmente en relación a uno de sus instrumentos, el comercio de los derechos de emisión de gases de efecto invernadero. En este contexto, la futura vinculación de los sistemas de comercio de derechos de emisión de gases de efecto invernadero en Norteamérica con el sistema de la Unión Europea presenta diversos retos de carácter material y formal.

Forming efficient networks

In this paper, we suggest a simple sequential mechanism whose subgame perfect equilibria give rise to efficient networks. Moreover, the payoffs received by the agents coincide with their Shapley value in an appropriately defined cooperative game.

Knowledge, networks of cities and growth in regional urban systems

The objective of this paper is to measure the impact of different kinds of knowledge and external economies on urban growth in an intraregional context. The main hypothesis is that knowledge leads to growth, and that this knowledge is related to the existence of agglomeration and network externalities in cities. We develop a three-tage methodology: first, we measure the amount and growth of knowledge in cities using the OCDE (2003) classification and employment data; second, we identify the spatial structure of the area of analysis (networks of cities); third, we combine the Glaeser - Henderson - De Lucio models with spatial econometric specifications in order to contrast the existence of spatially static (agglomeration) and spatially dynamic (network) external economies in an urban growth model. Results suggest that higher growth rates are associated to higher levels of technology and knowledge. The growth of the different kinds of knowledge is related to local and spatial factors (agglomeration and network externalities) and each knowledge intensity shows a particular response to these factors. These results have implications for policy design, since we can forecast and intervene on local knowledge development paths.

Cooperative Transmission and Radio Resources Management for Wireless Networks

Report for the scientific sojourn at the Multimedia Communications Laboratory, University of Texas at Dallas, USA, from September to December 2005. The cooperative transmission has been analyzed taking a broadcast relay channel which assumes a scenario with one source and multiple destinations. Moreover, in order to improve the performance in terms of mutual information, it has been considered that for each destination there is another nearby terminal (called relay) which will help to improve the performance of the destination. This scheme combines different types of channels considered in the information theory, such as the relay channel, broadcast channel and interference channel (if the relays transmit information intended only to its associated destination). In this work, the author has studied the optimal way to encode the signals for the different users, known as capacity region (i.e. related to radio resources management ), of the broadcast relay channel.

The Evolution of roommate networks: a comment on Jackson and Watts JET (2002)

We extend Jackson and Watts's (2002) result on the coincidence of S-stochastically stable and core stable networks from marriage problems to roommate problems. In particular, we show that the existence of a side-optimal core stable network, on which the proof of Jackson and Watts (2002) hinges, is not crucial for their result.

Convergence of the mass-transport steepest descent scheme for the sub-critical Patlak-Keller-Segel model

Variational steepest descent approximation schemes for the modified Patlak-Keller-Segel equation with a logarithmic interaction kernel in any dimension are considered. We prove the convergence of the suitably interpolated in time implicit Euler scheme, defined in terms of the Euclidean Wasserstein distance, associated to this equation for sub-critical masses. As a consequence, we recover the recent result about the global in time existence of weak-solutions to the modified Patlak-Keller-Segel equation for the logarithmic interaction kernel in any dimension in the sub-critical case. Moreover, we show how this method performs numerically in one dimension. In this particular case, this numerical scheme corresponds to a standard implicit Euler method for the pseudo-inverse of the cumulative distribution function. We demonstrate its capabilities to reproduce easily without the need of mesh-refinement the blow-up of solutions for super-critical masses.

The Difficult and tortuous path of agricultural cooperative networks in spain, 1890-1935

The rural associationism developed from the last decades of the XIX century could be consider as an answer of the agriculturists to the increasing integration of agriculture in the market, and to the effects of the Great Depression. In the case of Spain, the initiatives in this sense arose with certain delay in relation to the countries of Western Europe. The beginning of the Spanish cooperativism is closely bound to the Law of 1906. It granted the agrarian cooperatives with fiscal exemptions and other types of supports to the associates, although the process did not really accelerate until the promulgation of the law regulation in 1908.

A relative double commutant theorem for hereditary sub-C*-algebras

We prove a double commutant theorem for hereditary subalgebras of a large class of C*-algebras, partially resolving a problem posed by Pedersen[8]. Double commutant theorems originated with von Neumann, whose seminal result evolved into an entire field now called von Neumann algebra theory. Voiculescu proved a C*-algebraic double commutant theorem for separable subalgebras of the Calkin algebra. We prove a similar result for hereditary subalgebras which holds for arbitrary corona C*-algebras. (It is not clear how generally Voiculescu's double commutant theorem holds.)

Information networks and worker recruitment

This paper studies experimentally how the existence of social information networks affects the ways in which firms recruit new personnel. Through such networks firms learn about prospective employees' performance in previous jobs. Assuming individualistic preferences social networks are predicted not to affect overall labor market behavior, while with social preferences the prediction is that when bilaterally negotiated: (i) wages will be higher and (ii) that workers in jobs with incomplete contracts will respond with higher effort. Our experimental results are consistent with the social preferences view, both for the case of excess demand and excess supply of labor. In particular, the presence of information networks leads to more efficient allocations.

Preliminary study of cooperation in hybrid ad-hoc networks

In this paper, we present a first approach to evolve a cooperative behavior in ad hoc networks. Since wireless nodes are energy constrained, it may not be in the best interest of a node to always accept relay requests. On the other hand, if all nodes decide not to expend energy in relaying, then network throughput will drop dramatically. Both these extreme scenarios are unfavorable to the interests of a user. In this paper we deal with the issue of user cooperation in ad hoc networks by developing the algorithm called Generous Tit-For-Tat. We assume that nodes are rational, i.e., their actions are strictly determined by self-interest, and that each node is associated with a minimum lifetime constraint. Given these lifetime constraints and the assumption of rational behavior, we study the added behavior of the network.

Diseño de filtros con topología apilada mediante resonadores FBAR

Els continguts de la memòria es divideixen en dues parts fonamentals, precedides d’una breu explicació on s’introdueix al lector en el tema; primer s’exposen les bases d’un ressonador simple FBAR, d’on s’obtenen equacions de control vitals, i seguidament es plantegen les bases per a un ressonador apilat SCR, derivades de l’estudi previ d’un ressonador simple. La primera part fonamental del treball es centra en l’anàlisi d’un ressonador SCR. Aquest anàlisi es recolza sobre el punt de vista teòric dels paràmetres imatge, el nostre punt de sortida. Aquesta primera part és la més teòrica: obtenció i aplicació dels paràmetres imatge i obtenció dels elements discrets que conformen el circuit equivalent SCR, una xarxa de dos ports. Posteriorment, s’analitza què succeeix modificant els valors dels elements discrets sense variar determinats paràmetres imatge i finalment, es proposa una aproximació per a controlar determinades especificacions de disseny, com són l’ample de banda de transmissió de la xarxa i el factor de qualitat, en funció de les modificacions dels elements discrets. En la segona part s’analitzen, de forma qualitativa, xarxes compostes per diferents ressonadors apilats connectats en cascada. Aquest segon estudi es divideix en dues subparts. En la primera connectem N ressonadors idèntics, plantegem algunes equacions de control i analitzem les respostes. En la segona, es planteja la connexió de dos (N=2) ressonadors diferents amb freqüències de ressonància properes. Aquest segon anàlisi es també totalment qualitatiu, però ens aporta informació que amb la unió de N ressonadors iguals no aconseguíem. Finalitzant aquesta segona part, es planteja l’optimització dels resultats obtinguts per a N=2, mitjançant estructures N=3 ressonadors.

Wealth constraints, skill prices or networks: what determines emigrant selection?

The productive characteristics of migrating individuals, emigrant selection, affect welfare. The empirical estimation of the degree of selection suffers from a lack of complete and nationally representative data. This paper uses a new and better dataset to address both issues: the ENET (Mexican Labor Survey), which identifies emigrants right before they leave and allows a direct comparison to non-migrants. This dataset presents a relevant dichotomy: it shows on average negative selection for Mexican emigrants to the United States for the period 2000-2004 together with positive selection in Mexican emigration out of rural Mexico to the United States in the same period. Three theories that could explain this dichotomy are tested. Whereas higher skill prices in Mexico than in the US are enough to explain negative selection in urban Mexico, its combination with network effects and wealth constraints is required to account for positive selection in rural Mexico.

QoS support in satellite and wireless networks: study under the network simulator (NS-2)

Aquest projecte es basa en l'estudi de l'oferiment de qualitat de servei en xarxes wireless i satel·litals. Per això l'estudi de les tècniques de cross-layer i del IEEE 802.11e ha sigut el punt clau per al desenvolupament teòric d’aquest estudi. Usant el simulador de xarxes network simulator, a la part de simulacions es plantegen tres situacions: l'estudi de la xarxa satel·lital, l'estudi del mètode d'accés HCCA i la interconnexió de la xarxa satel·lital amb la wireless. Encara que aquest últim punt, incomplet en aquest projecte, ha de ser la continuació per a futures investigacions.