Coffee polyphenols change the expression of STAT5b and ATF-2 modifying cyclin D1 levels in cancer cells

Background: Epidemiological studies suggest that coffee consumption reduces the risk of cancer, but the molecular mechanisms of its chemopreventive effects remain unknown. Objective: To identify differentially expressed genes upon incubation of HT29 colon cancer cells with instant caffeinated coffee (ICC) or caffeic acid (CA) using whole genome microarrays. Results: ICC incubation of HT29 cells caused the overexpression of 57 genes and the underexpression of 161, while CA incubation induced the overexpression of 12 genes and the underexpression of 32. Using Venn-Diagrams, we built a list of five overexpressed genes and twelve underexpressed genes in common between the two experimental conditions. This list was used to generate a biological association network in which STAT5B and ATF-2 appeared as highly interconnected nodes. STAT5B overexpression was confirmed at the mRNA and protein levels. For ATF-2, the changes in mRNA levels were confirmed for both ICC and CA, whereas the decrease in protein levels was only observed in CA-treated cells. The levels of cyclin D1, a target gene for both STAT5B and ATF-2, were dowregulated by CA in colon cancer cells and by ICC and CA in breast cancer cells. Conclusions: Coffee polyphenols are able to affect cyclin D1 expression in cancer cells through the modulation of STAT5B and ATF-2.

Alineamiento múltiple de secuencias con T-Coffee: una aproximación paralela

Las aplicaciones de alineamiento múltiple de secuencias son prototipos de aplicaciones que requieren elevada potencia de cómputo y memoria. Se destacan por la relevancia científica que tienen los resultados que brindan a investigaciones científicas en el campo de la biomedicina, genética y farmacología. Las aplicaciones de alineamiento múltiple tienen la limitante de que no son capaces de procesar miles de secuencias, por lo que se hace necesario crear un modelo para resolver la problemática. Analizando el volumen de datos que se manipulan en el área de las ciencias biológica y la complejidad de los algoritmos de alineamiento de secuencias, la única vía de solución del problema es a través de la utilización de entornos de cómputo paralelos y la computación de altas prestaciones. La investigación realizada por nosotros tiene como objetivo la creación de un modelo paralelo que le permita a los algoritmos de alineamiento múltiple aumentar el número de secuencias a procesar, tratando de mantener la calidad en los resultados para garantizar la precisión científica. El modelo que proponemos emplea como base la clusterización de las secuencias de entrada utilizando criterios biológicos que permiten mantener la calidad de los resultados. Además, el modelo se enfoca en la disminución del tiempo de cómputo y consumo de memoria. Para presentar y validar el modelo utilizamos T-Coffee, como plataforma de desarrollo e investigación. El modelo propuesto pudiera ser aplicado a cualquier otro algoritmo de alineamiento múltiple de secuencias.

Implicacions diagnòstiques del strem-1 (soluble triggering receptor expressed on myeloid cells) en malalts amb síndrom del distress respiratori agut (sdra) i patologia abdominal. estudi preliminar

Els pacients amb patologia abdominal aguda poden desenvolupar una insuficiència respiratòria secundària a la resposta inflamatòria generada o a una pneumònia nosocomial. El mesurament del “soluble *triggering receptor expressed on myeloid cells 1” (sTREM-1) en líquid alveolar, pleural, sinovial o cefalorraquidi ha demostrat la seva utilitat en el diagnòstic d'infecció. Es va determinar el sTREM-1 alveolar i peritoneal en pacients amb quadre abdominal agut més síndrom de distress respiratori agut (SDRA). Es va concloure que el sTREM-1 és útil per diagnosticar infeccions abdominals i pulmonars en aquests pacients i que la relació sTREM-1 alveolar/peritoneal podria ser útil per determinar el focus infecciós.

Developing and evaluating a pictogram-based Instant Messaging service for individuals with cognitive disabilities

Information and communication technologies pose accessibility problems to people with disabilities because its design fails to take into account their communication and usability requirements. The impossibility to access the services provided by these technologies creates a situation of exclusion that reduces the self-suficiency of disabled individuals and causes social isolation, which in turn diminishes their overall quality of life. Considering the importance of these technologies and services in our society, we have developed a pictogram-based Instant Messaging service for individuals with cognitive disabilities who have reading and writing problems. Along the paper we introduce and discuss the User Centred Design methodology that we have used to develop and evaluate the pictogram-based Instant Messaging service and client with individuals with cognitive disabilities taking into account their communication and usability requirements. From the results obtained in the evaluation process we can state that individuals with cognitive disabilities have been able to use the pictogram-based Instant Messaging service and client to communicate with their relatives and acquaintances, thus serving as a tool to help reducing their social and digital exclusion situation.

Improving the organisation and commercialisation of small coffee and cocoa producers in the Northern Amazon Region of Ecuador

Coffee and cocoa represent the main sources of income for small farmers in the Northern Amazon Region of Ecuador. The provinces of Orellana and Sucumbios, as border areas, have benefited from investments made by many public and private institutions. Many of the projects carried out in the area have been aimed at energising the production of coffee and cocoa, strengthening the producers’ associations and providing commercialisation infrastructure. Improving the quality of life of this population threatened by poverty and high migration flows mainly from Colombia is a significant challenge. This paper presents research highlighting the importance of associative commercialisation to raising income from coffee and cocoa. The research draws on primary information obtained during field work, and from official information from the Ministry of Agriculture. The study presents an overview of current organisational structures, initiatives of associative commercialisation, stockpiling of infrastructure and ownership regimes, as well as estimates for both ‘robusta’ coffee and national cocoa production and income. The analysis of the main constraints presents different alternatives for the implementation of public land policies. These policies are aimed at mitigating the problems associated with the organisational structure of the producers, with processes of commercialisation and with environmental aspects, among others.

A user-friendly web portal for T-Coffee on supercomputers

Background: Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers. Results: In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments. Conclusions: The PTC portal allows users to upload a large number of sequences to be aligned by the parallel version of TC that cannot be aligned by a single machine due to memory and execution time constraints. The web portal provides a user-friendly solution.

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

Soluble models in two-dimensional dilaton gravity

A one-parameter class of simple models of two-dimensional dilaton gravity, which can be exactly solved including back-reaction effects, is investigated at both classical and quantum levels. This family contains the RST model as a special case, and it continuously interpolates between models having a flat (Rindler) geometry and a constant curvature metric with a nontrivial dilaton field. The processes of formation of black hole singularities from collapsing matter and Hawking evaporation are considered in detail. Various physical aspects of these geometries are discussed, including the cosmological interpretation.

Lixiviacion de concentrados de cobre utilizando NaCl y el cobre soluble aportado por el propio concentrado.

Se ha estudiado la lixiviación de concentrados de cobre mediante cloro-complejos cúpricos, generados in situ por la reacción entre el Cu(II) procedente del cobre soluble del concentrado y cloruro de sodio en medio ácido. Se utilizaron concentrados de cobre provenientes de faenas mineras de Antofagasta, Chile. Se ha efectuado una caracterización química y mineralógica de los concentrados originales. Se ha estudiado el efecto de las siguientes variables, durante la lixiviación: concentración de cloruro, concentración de cobre soluble, tiempo de lixiviación, porcentaje de sólidos y temperatura. Se han caracterizado los residuos sólidos por DRX y microscopia electrónica. Los resultados experimentales indican que es posible obtener disoluciones con contenidos de cobre entre 15 y 35 g/l y de 2 a 5 g/l de acidez libre, con características adecuadas para entrar a la etapa de extracción por solventes. El procedimiento utiliza, solo, reactivos comunes y de muy bajo costo, como NaCl y ácido sulfúrico diluido. La ventaja de este procedimiento consiste en recuperar, a muy bajo coste, la totalidad del cobre soluble y entre 10 y 15% del cobre de sulfuros. El residuo final podría pasar a la pirometalurgia convencional