A Pattern Approach to Modeling the Provider Selection Problem

This article introduces the notion of agreement patterns, which provide a framework for modelling reusable problem solution descriptions for agreement fulfilment. In particular, the Provider Selection pattern has been identified for modelling the common problem of selecting a provider by a service consumer. The article presents the pattern structure as well as the reusable domain model and cognitive structures. Agreement patterns aim at providing reusable patterns useful for developers in multidisciplinary areas, such as Agent Technology and Service Oriented Computing

An Ontology for Formalising Agreement Patterns in Auction Markets

Knowledge and best practices on auction systems are cur- rently disseminated across the research literature, which limits its access, reuse, evaluation and feedback by practitioners. This article presents a systematic approach to collect this knowledge as design patterns, in order to provide assistance to software developers. An ontology has been de- _ned for formalising design patterns in auction systems, with the aim of improving its searchability by software developers. Finally, a case study illustrates how the proposed pattern ontology provides assistance in the development of a dynamic pricing model for an e-commerce servic

Automatización del Despliegue de Recursos en Bases de Datos

En una arquitectura SOA, los servicios presentan dependencias con otros servicios y recursos ya desplegados, necesitando comunicarse con la base de datos para que les provea de información y donde almacenen los datos obtenidos. Una arquitectura telemática que gestione la configuración y el despliegue de tales servicios se hace esencial y dentro de esta, un sistema que gestione los recursos de bases de datos. Las tareas relacionadas con base de datos suponen una actividad ardua y compleja que es realizada de forma manual por administradores especializados. Rompiendo con esta idea y siguiendo la línea de investigación actual, el sistema desarrollado pretende gestionar automáticamente los recursos en el proceso de despliegue dando un soporte integral al DBA, facilitando considerablemente su trabajo y colocándole a un nivel superior de validación y optimización. El sistema se puede separar en dos: una herramienta de generación de unidades de despliegue y otra para realizar el despliegue en base de datos

ArchDB 2014:Structural classification of loops in proteins

The function of a protein is determined by its three-dimensional structure, which is formed by regular (i.e. β-strands and α-helices) and non-periodic structural units such as loops. Compared to regular structural elements, non-periodic, non-repetitive conformational units enclose a much higher degree of variability—raising difficulties in the identification of regularities, and yet represent an important part of the structure of a protein. Indeed, loops often play a pivotal role in the function of a protein and different aspects of protein folding and dynamics. Therefore, the structural classification of protein loops is an important subject with clear applications in homology modelling, protein structure prediction, protein design (e.g. enzyme design and catalytic loops) and function prediction. ArchDB, the database presented here (freely available at http://sbi.imim.es/archdb), represents such a resource and has been an important asset for the scientific community throughout the years. In this article, we present a completely reworked and updated version of ArchDB. The new version of ArchDB features a novel, fast and user-friendly web-based interface, and a novel graph-based, computationally efficient, clustering algorithm. The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses

Seasonal impact of biogenic very short-lived bromocarbons on lowermost stratospheric ozone between 60° N and 60° S during the 21st century

Biogenic very short-lived bromocarbons (VSLBr) currently represent ∼25 % of the total stratospheric bromine loading. Owing to their much shorter lifetime compared to anthropogenic long-lived bromine (e.g. halons) and chlorine (e.g. chlorofluorocarbons), the impact of VSLBr on ozone peaks in the lowermost stratosphere, which is a key climatic and radiative atmospheric region. Here we present a modelling study of the evolution of stratospheric ozone and its chemical loss within the tropics and at mid-latitudes during the 21st century. Two different experiments are explored: considering and neglecting the additional stratospheric injection of 5 ppt biogenic bromine naturally released from the ocean. Our analysis shows that the inclusion of VSLBr results in a realistic stratospheric bromine loading and improves the agreement between the model and satellite observations of the total ozone column (TOC) for the 1980?2015 period at mid-latitudes. We show that the overall ozone response to VSLBr at mid-latitudes follows the stratospheric evolution of long-lived inorganic chlorine and bromine throughout the 21st century. Additional ozone loss due to VSLBr is maximized during the present-day period (1990?2010), with TOC differences of −8 DU (−3 %) and −5.5 DU (−2 %) for the Southern Hemisphere and Northern Hemisphere mid-latitudes (SH-MLs and NH-MLs), respectively. Moreover, the projected TOC differences at the end of the 21st century are ∼50 % lower than the values found for the present-day period.We find that seasonal VSLBr impact on lowermost stratospheric ozone at mid-latitude is influenced by the seasonality of the heterogeneous inorganic-chlorine reactivation processes on ice crystals. Indeed, due to the more efficient reactivation of chlorine reservoirs (mainly ClONO2 and HCl) within the colder SH-ML lowermost stratosphere, the seasonal VSLBr impact shows a small but persistent hemispheric asymmetry through the whole modelled period. Our results indicate that, although the overall VSLBr-driven ozone destruction is greatest during spring, the halogen-mediated (Halogx-Loss) ozone loss cycle in the mid-latitude lowermost stratosphere during winter is comparatively more efficient than the HOx cycle with respect to other seasons. Indeed, when VSLBr are considered, Halogx-Loss dominates wintertime lowermost stratospheric ozone loss at SH-MLs between 1985 and 2020, with a contribution of inter-halogen ClOx?BrOx cycles to Halogx-Loss of ∼50 %.Within the tropics, a small (<−2.5 DU) and relatively constant (∼−1 %) ozone depletion mediated by VSLBr is closely related to their fixed emissions throughout the modelled period. By including the VSLBr sources, the seasonal Halogx-Loss contribution to lowermost stratospheric ozone loss is practically dominated by the BrOx cycle, reflecting the low sensitivity of very short-lived (VSL) bromine to background halogen abundances to drive tropical stratospheric ozone depletion. We conclude that the link between biogenic bromine sources and seasonal changes in heterogeneous chlorine reactivation is a key feature for future projections of mid-latitude lowermost stratospheric ozone during the 21st century.Fil: Barrera, Javier Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Interdisciplinario de Ciencias Básicas. - Universidad Nacional de Cuyo. Instituto Interdisciplinario de Ciencias Básicas; ArgentinaFil: Fernandez, Rafael Pedro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Interdisciplinario de Ciencias Básicas. - Universidad Nacional de Cuyo. Instituto Interdisciplinario de Ciencias Básicas; Argentina. Consejo Superior de Investigaciones Científicas; España. Universidad Tecnológica Nacional; ArgentinaFil: Iglesias Suarez, Fernando. Consejo Superior de Investigaciones Científicas; EspañaFil: Cuevas, Carlos Alberto. Consejo Superior de Investigaciones Científicas; EspañaFil: Lamarque, Jean Francois. National Center for Atmospheric Research; Estados UnidosFil: Saiz-lopez, Alfonso. Consejo Superior de Investigaciones Científicas; Españ

On the mechanisms of protein interactions : predicting their affinity from unbound tertiary structures

Motivation: The characterization of the protein–protein association mechanisms is crucial to understanding how biological processes occur. It has been previously shown that the early formation of non-specific encounters enhances the realization of the stereospecific (i.e. native) complex by reducing the dimensionality of the search process. The association rate for the formation of such complex plays a crucial role in the cell biology and depends on how the partners diffuse to be close to each other. Predicting the binding free energy of proteins provides new opportunities to modulate and control protein–protein interactions. However, existing methods require the 3D structure of the complex to predict its affinity, severely limiting their application to interactions with known structures. Results: We present a new approach that relies on the unbound protein structures and protein docking to predict protein–protein binding affinities. Through the study of the docking space (i.e. decoys), the method predicts the binding affinity of the query proteins when the actual structure of the complex itself is unknown. We tested our approach on a set of globular and soluble proteins of the newest affinity benchmark, obtaining accuracy values comparable to other state-of-art methods: a 0.4 correlation coefficient between the experimental and predicted values of ΔG and an error < 3 Kcal/mol. Availability and implementation: The binding affinity predictor is implemented and available at http://sbi.upf.edu/BADock and https://github.com/badocksbi/BADock

InteractoMIX:A suite of computational tools to exploit interactomes in biological and clinical research

Virtually all the biological processes that occur inside or outside cells are mediated by protein–protein interactions (PPIs). Hence, the charting and description of the PPI network, initially in organisms, the interactome, but more recently in specific tissues, is essential to fully understand cellular processes both in health and disease. The study of PPIs is also at the heart of renewed efforts in the medical and biotechnological arena in the quest of new therapeutic targets and drugs. Here, we present a mini review of 11 computational tools and resources tools developed by us to address different aspects of PPIs: from interactome level to their atomic 3D structural details. We provided details on each specific resource, aims and purpose and compare with equivalent tools in the literature. All the tools are presented in a centralized, one-stop, web site: InteractoMIX (http://interactomix.com)

MEP pathway products allosterically promote monomerization of deoxy-D-xylulose-5-phosphate synthase to feedback-regulate their supply

Isoprenoids are a very large and diverse family of metabolites required by all living organisms. All isoprenoids derive from the double-bond isomers isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are produced by the methylerythritol 4-phosphate (MEP) pathway in bacteria and plant plastids. It has been reported that IPP and DMAPP feedback-regulate the activity of deoxyxylulose 5-phosphate synthase (DXS), a dimeric enzyme that catalyzes the main flux-controlling step of the MEP pathway. Here we provide experimental insights into the underlying mechanism. Isothermal titration calorimetry and dynamic light scattering approaches showed that IPP and DMAPP can allosterically bind to DXS in vitro, causing a size shift. In silico ligand binding site analysis and docking calculations identified a potential allosteric site in the contact region between the two monomers of the active DXS dimer. Modulation of IPP and DMAPP contents in vivo followed by immunoblot analyses confirmed that high IPP/DMAPP levels resulted in monomerization and eventual aggregation of the enzyme in bacterial and plant cells. Loss of the enzymatically active dimeric conformation allows a fast and reversible reduction of DXS activity in response to a sudden increase or decrease in IPP/DMAPP supply, whereas aggregation and subsequent removal of monomers that would otherwise be available for dimerization appears to be a more drastic response in the case of persistent IPP/DMAPP overabundance (e.g., by a blockage in their conversion to downstream isoprenoids). Our results represent an important step toward understanding the regulation of the MEP pathway and rational design of biotechnological endeavors aimed at increasing isoprenoid contents in microbial and plant systems

MAYORISTAPE. APP

El proyecto se enfoca en cubrir la necesidad de dos segmentos de clientes que son interdependientes entre si según el modelo de negocio. El primero está conformado por los clientes mayoristas y el segundo por clientes del segmento de bodegas (canal tradicional). En este proyecto el cual se ha bautizado como MayoristaPe. se busca cubrir las necesidades de ambos segmentos a través del uso de la aplicación desde donde las bodegas podrán realizar y gestionar sus compras para abastecer sus comercios, y los mayoristas cuenten con la posibilidad incrementar sus ventas, publicar ofertas y generar valor para sus clientes, logrando crear eficiencia en tiempos y costos en sus comercios. Inicialmente MayoristaPe. se enfocará en la Ciudad de Lima y Callao, donde se ubican la mayor concentración de mercados mayoristas y bodegas, a futuro buscará ampliar a otros puntos estratégicos. Las fuentes de ingreso se generarán a través de un cobro de membresía mensual y/o a través de un porcentaje sobre las ventas, lo que dependerá del segmento en donde se encuentre cada uno.The project focuses on meeting the need of two customer segments that are interdependent with each other according to the business model. The first is made up of wholesale clients and the second by clients of the winery segment (traditional channel). In this project which has been baptized as MayoristaPe. It seeks to meet the needs of both segments through the use of the application from where wineries can make and manage their purchases to supply their stores, and wholesalers have the possibility to increase their sales, publish offers and generate value for their customers, managing to create time and cost efficiency in their businesses. Initially MayoristaPe. will focus on the City of Lima and Callao, where the largest concentration of wholesale markets and warehouses are located, in the future it will seek to expand to other strategic points. The sources of income will be generated through a monthly membership charge and / or through a percentage of sales, which will depend on the segment where each one is located.Trabajo de investigació