Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

Background: The arrangement of regulatory motifs in gene promoters, or promoterarchitecture, is the result of mutation and selection processes that have operated over manymillions of years. In mammals, tissue-specific transcriptional regulation is related to the presence ofspecific protein-interacting DNA motifs in gene promoters. However, little is known about therelative location and spacing of these motifs. To fill this gap, we have performed a systematic searchfor motifs that show significant bias at specific promoter locations in a large collection ofhousekeeping and tissue-specific genes.Results: We observe that promoters driving housekeeping gene expression are enriched inparticular motifs with strong positional bias, such as YY1, which are of little relevance in promotersdriving tissue-specific expression. We also identify a large number of motifs that show positionalbias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specificmotifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis,as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictionsfor 559 tissue-specific motifs in mouse gene promoters.Conclusion: The study shows that motif positional bias is an important feature of mammalianproximal promoters and that it affects both general and tissue-specific motifs. Motif positionalconstraints define very distinct promoter architectures depending on breadth of expression andtype of tissue.

Deciphering the global organization of clustering in real complex networks

We uncover the global organization of clustering in real complex networks. To this end, we ask whether triangles in real networks organize as in maximally random graphs with given degree and clustering distributions, or as in maximally ordered graph models where triangles are forced into modules. The answer comes by way of exploring m-core landscapes, where the m-core is defined, akin to the k-core, as the maximal subgraph with edges participating in at least m triangles. This property defines a set of nested subgraphs that, contrarily to k-cores, is able to distinguish between hierarchical and modular architectures. We find that the clustering organization in real networks is neither completely random nor ordered although, surprisingly, it is more random than modular. This supports the idea that the structure of real networks may in fact be the outcome of self-organized processes based on local optimization rules, in contrast to global optimization principles.

Neural networks complemented with genetic algorithms and fuzzy systems for predicting nitrogenous effluent variables in wastewater treatment plants

This work focuses on the prediction of the two main nitrogenous variables that describe the water quality at the effluent of a Wastewater Treatment Plant. We have developed two kind of Neural Networks architectures based on considering only one output or, in the other hand, the usual five effluent variables that define the water quality: suspended solids, biochemical organic matter, chemical organic matter, total nitrogen and total Kjedhal nitrogen. Two learning techniques based on a classical adaptative gradient and a Kalman filter have been implemented. In order to try to improve generalization and performance we have selected variables by means genetic algorithms and fuzzy systems. The training, testing and validation sets show that the final networks are able to learn enough well the simulated available data specially for the total nitrogen

Bootstrapping a statistical speech translator from a rule-based one

We describe a series of experiments in which we start with English to French and English to Japanese versions of an Open Source rule-based speech translation system for a medical domain, and bootstrap correspondign statistical systems. Comparative evaluation reveals that the rule-based systems are still significantly better than the statistical ones, despite the fact that considerable effort has been invested in tuning both the recognition and translation components; also, a hybrid system only marginally improved recall at the cost of a los in precision. The result suggests that rule-based architectures may still be preferable to statistical ones for safety-critical speech translation tasks.

Enhanced MDIR receiver for space-time dispersive channels

A particular property of the matched desiredimpulse response receiver is introduced in this paper, namely,the fact that full exploitation of the diversity is obtained withmultiple beamformers when the channel is spatially and timelydispersive. This particularity makes the receiver specially suitablefor mobile and underwater communications. The new structureprovides better performance than conventional and weightedVRAKE receivers, and a diversity gain with no needs of additionalradio frequency equipment. The baseband hardware neededfor this new receiver may be obtained through reconfigurabilityof the RAKE architectures available at the base station. Theproposed receiver is tested through simulations assuming UTRAfrequency-division-duplexing mode.

Smart antennas in software radio base stations

The application of adaptive antenna techniques to fixed-architecture base stations has been shown to offer wide-ranging benefits, including interference rejection capabilities or increased coverage and spectral efficiency.Unfortunately, the actual implementation ofthese techniques to mobile communication scenarios has traditionally been set back by two fundamental reasons. On one hand, the lack of flexibility of current transceiver architectures does not allow for the introduction of advanced add-on functionalities. On the other hand, theoften oversimplified models for the spatiotemporal characteristics of the radio communications channel generally give rise toperformance predictions that are, in practice, too optimistic. The advent of software radio architectures represents a big step toward theintroduction of advanced receive/transmitcapabilities. Thanks to their inherent flexibilityand robustness, software radio architecturesare the appropriate enabling technology for theimplementation of array processing techniques.Moreover, given the exponential progression ofcommunication standards in coexistence andtheir constant evolution, software reconfigurabilitywill probably soon become the only costefficientalternative for the transceiverupgrade. This article analyzes the requirementsfor the introduction of software radio techniquesand array processing architectures inmultistandard scenarios. It basically summarizesthe conclusions and results obtained withinthe ACTS project SUNBEAM,1 proposingalgorithms and analyzing the feasibility ofimplementation of innovative and softwarereconfigurablearray processing architectures inmultistandard settings.

Evolution based on domain combinations: the case of glutaredoxins

Background: Protein domains represent the basic units in the evolution of proteins. Domain duplication and shuffling by recombination and fusion, followed by divergence are the most common mechanisms in this process. Such domain fusion and recombination events are predicted to occur only once for a given multidomain architecture. However, other scenarios may be relevant in the evolution of specific proteins, such as convergent evolution of multidomain architectures. With this in mind, we study glutaredoxin (GRX) domains, because these domains of approximately one hundred amino acids are widespread in archaea, bacteria and eukaryotes and participate in fusion proteins. GRXs are responsible for the reduction of protein disulfides or glutathione-protein mixed disulfides and are involved in cellular redox regulation, although their specific roles and targets are often unclear. Results: In this work we analyze the distribution and evolution of GRX proteins in archaea,bacteria and eukaryotes. We study over one thousand GRX proteins, each containing at least one GRX domain, from hundreds of different organisms and trace the origin and evolution of the GRX domain within the tree of life. Conclusion: Our results suggest that single domain GRX proteins of the CGFS and CPYC classes have, each, evolved through duplication and divergence from one initial gene that was present in the last common ancestor of all organisms. Remarkably, we identify a case of convergent evolution in domain architecture that involves the GRX domain. Two independent recombination events of a TRX domain to a GRX domain are likely to have occurred, which is an exception to the dominant mechanism of domain architecture evolution.

Modeling and manufacturability assessment of bistable quantum-dot cells

We have investigated the behavior of bistable cells made up of four quantum dots and occupied by two electrons, in the presence of realistic confinement potentials produced by depletion gates on top of a GaAs/AlGaAs heterostructure. Such a cell represents the basic building block for logic architectures based on the concept of quantum cellular automata (QCA) and of ground state computation, which have been proposed as an alternative to traditional transistor-based logic circuits. We have focused on the robustness of the operation of such cells with respect to asymmetries derived from fabrication tolerances. We have developed a two-dimensional model for the calculation of the electron density in a driven cell in response to the polarization state of a driver cell. Our method is based on the one-shot configuration-interaction technique, adapted from molecular chemistry. From the results of our simulations, we conclude that an implementation of QCA logic based on simple ¿hole arrays¿ is not feasible, because of the extreme sensitivity to fabrication tolerances. As an alternative, we propose cells defined by multiple gates, where geometrical asymmetries can be compensated for by adjusting the bias voltages. Even though not immediately applicable to the implementation of logic gates and not suitable for large scale integration, the proposed cell layout should allow an experimental demonstration of a chain of QCA cells.

Straightforward synthesis of cyclic and bicyclic peptides

Cyclic peptide architectures can be easily synthesized from cysteine-containing peptides with appending maleimides, free or protected, through an intramolecular Michael-type reaction. After peptide assembly, the peptide can cyclize either during the trifluoroacetic acid treatment, if the maleimide is not protected, or upon deprotection of the maleimide. The combination of free and protected maleimide moieties and two orthogonally protected cysteines gives access to structurally different bicyclic peptides with isolated or fused cycles.

Variable-stiffness composite panels: Defect tolerance under in-plane tensile loading

Automated Fiber Placement is being extensively used in the production of major composite components for the aircraft industry. This technology enables the production of tow-steered panels, which have been proven to greatly improve the structural efficiency of composites by means of in-plane stiffness variation and load redistribution. However, traditional straight-fiber architectures are still preferred. One of the reasons behind this is related to the uncertainties, as a result of process-induced defects, in the mechanical performance of the laminates. This experimental work investigates the effect of the fiber angle discontinuities between different tow courses in a ply on the un-notched and open-hole tensile strength of the laminate. The influence of several manufacturing parameters are studied in detail. The results reveal that 'ply staggering' and '0% gap coverage' is an effective combination in reducing the influence of defects in these laminates

Generación de Agentes Móviles Seguros a partir de Itinerarios y Arquitecturas Criptográficas

En este trabajo presentamos un esquema para la creación de agentes móviles seguros a partir de una representación del itinerario que deben seguir, el código a ejecutar, y una especificación de la arquitectura criptográfica con la que estarán protegidos. Este tipo de agentes es muy útil en aplicaciones seguras, pero su programación resulta muy complicada. El esquema propuesto facilita enormemente esta tarea, automatizando el proceso a partir de especificaciones concretas. En la práctica hemos conseguido un sistema de generación de código de fácil utilización que permite, no sólo la programación de agentes móviles seguros, sino también la creación sencilla de nuevos esquemas criptográficos para la protección del código y los datos de los agentes. El sistema puede usarse para desarrollar aplicaciones de propósito general basadas en el framework de ejecución de agentes Jade.

Performance evaluation of MPEG-4 Video encoder on Adres

Actualment un típic embedded system (ex. telèfon mòbil) requereix alta qualitat per portar a terme tasques com codificar/descodificar a temps real; han de consumir poc energia per funcionar hores o dies utilitzant bateries lleugeres; han de ser el suficientment flexibles per integrar múltiples aplicacions i estàndards en un sol aparell; han de ser dissenyats i verificats en un període de temps curt tot i l’augment de la complexitat. Els dissenyadors lluiten contra aquestes adversitats, que demanen noves innovacions en arquitectures i metodologies de disseny. Coarse-grained reconfigurable architectures (CGRAs) estan emergent com a candidats potencials per superar totes aquestes dificultats. Diferents tipus d’arquitectures han estat presentades en els últims anys. L’alta granularitat redueix molt el retard, l’àrea, el consum i el temps de configuració comparant amb les FPGAs. D’altra banda, en comparació amb els tradicionals processadors coarse-grained programables, els alts recursos computacionals els permet d’assolir un alt nivell de paral•lelisme i eficiència. No obstant, els CGRAs existents no estant sent aplicats principalment per les grans dificultats en la programació per arquitectures complexes. ADRES és una nova CGRA dissenyada per I’Interuniversity Micro-Electronics Center (IMEC). Combina un processador very-long instruction word (VLIW) i un coarse-grained array per tenir dues opcions diferents en un mateix dispositiu físic. Entre els seus avantatges destaquen l’alta qualitat, poca redundància en les comunicacions i la facilitat de programació. Finalment ADRES és un patró enlloc d’una arquitectura concreta. Amb l’ajuda del compilador DRESC (Dynamically Reconfigurable Embedded System Compile), és possible trobar millors arquitectures o arquitectures específiques segons l’aplicació. Aquest treball presenta la implementació d’un codificador MPEG-4 per l’ADRES. Mostra l’evolució del codi per obtenir una bona implementació per una arquitectura donada. També es presenten les característiques principals d’ADRES i el seu compilador (DRESC). Els objectius són de reduir al màxim el nombre de cicles (temps) per implementar el codificador de MPEG-4 i veure les diferents dificultats de treballar en l’entorn ADRES. Els resultats mostren que els cícles es redueixen en un 67% comparant el codi inicial i final en el mode VLIW i un 84% comparant el codi inicial en VLIW i el final en mode CGA.