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.

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.

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.

El marketing experiencial en espais i botigues de Barcelona

Des de la perspectiva del brand management, el present treball pretén demostrar que una incoherent aplicació del marketing experiencial en entorns espacials pot contribuir a malmetre la construcció de la marca. Per corroborar la hipòtesi, el treball consta d’una una part teòrica, on s’aborda des de la marca fins al marketing experiencial, i una part pràctica en què s’exposa l’anàlisi de cinc entorns espacials de la ciutat de Barcelona: Nespresso, IceBarcelona, Pans&Company, Sephora i Starbucks Coffee.

Anàlisi, disseny i implementació d'una aplicació fent servir l'arquitectura J2EE

L'objectiu general és l'anàlisi, el disseny i la implementació d'una 'Guia del viatger'. Es pretén separar clarament la presentació, la lògica de negoci i l'accés a les dades. Concretament, la presentació es preveu implementar amb la combinació de Servlets i JSP's, mentre que la lògica de negoci i la capa de dades amb Enterprise Java Beans (EJB's)

Gestió banc de temps

Aquest document, correspon a la memòria del Treball de Fi de Carrera (TFC), hi trobareu tota la documentació realitzada per a l'anàlisi, implementació i el disseny d'una aplicació informàtica basada en la gestió d'un banc de temps, desenvolupat utilitzant tecnologia Java JEE5.

Creencias sesgadas respecto al grado de "dureza" de algunas drogas en estudiantes universitarios

El objetivo de esta investigación es evaluar las creencias de los estudiantes universitarios respecto a la dureza de diez drogas: anfetaminas, café, heroína, barbitúricos, marihuana, ansiolíticos, tabaco, alcohol, cocaína y té. Ciento cincuenta y cinco estudiantes de Psicología debían indicar si creían que estas sustancias eran o no drogas duras. Los resultados indican que aunque existe consenso a la hora de clasificar como drogas duras a la heroína y la cocaína y como drogas blandas al tabaco, el café y el té, no existe acuerdo respecto a la clasificación de las otras sustancias. Asimismo se observa que aunque la OMS clasifica el alcohol como una droga altamente peligrosa, menos de la mitad de sujetos lo consideran una droga dura. En general los sujetos tienden a considerar las drogas legales como menos duras independientemente de si los efectos nocivos para la salud. Estos resultados adquieren relevancia cuando lo que se pone en juego es la fiabilidad y validez de los datos obtenidos en diferentes investigaciones que utilizan habitualmente esos conceptos

Projecte d'una indústria elaboradora de cafè situada al terme municipal de Celrà (Gironès)

Disseny i posada en marxa d’una indústria productora i envasadora de cafè torrat. La indústria s’ubicarà al polígon industrial del terme municipal de Celrà a la comarca del Gironès, en una propietat del promotor, dotada amb bones comunicacions de carretera, ferrocarril i avió, i a més es troba situada a prop de nuclis urbans importants com Girona i Barcelona. Per tant per la seva localització i les bones infrastructures existents hi haurà un bon accés per la recepció de les matèries primeres i per la distribució dels productes acabats.La indústria es dissenya per a garantir una capacitat productiva de 850 tones l’any de producte acabat, essent les necessitat anuals de cafè verd i cafè torrefacte de 961.404 kg i 48.875 kg respectivament. Es produirà cafè natural, cafè mescla (natural més torrefacte) i cafè descafeïnat, mòlt o en gra. El 90% d’aquesta producció es destinarà a l’hostaleria, on el paper de les multinacionals no és tant representatiu, fet que provoca que el mercat sigui més estable i atractiu per introduir els productes que elaborarà la indústria. El 10% restant es destinarà a les llars, bàsicament per donar a conèixer la marca de cafès de la indústria projectada

Disseny i implementació d'una aplicació web per a la reserva on-line de localitats d'espectacles

Aquest treball presenta un terminal de reserva d'espectacles. Es tracta d'una aplicació web que permet als seus usuaris registrats reservar localitats de diferents tipus d'espectacles a través d'internet i amb total llibertat d'horaris. L'aplicació s'ha dissenyat amb tecnologia Java (servlets, JSP, beans ...) i s'ha llicenciat com a aplicació de programari lliure amb la llicència GPL.

Sweet diversity: Colonial goods and the rise of European living standards after 1492

When did overseas trade start to matter for living standards? Traditional real-wage indices suggest that living standards in Europe stagnated before 1800. In this paper, we argue thatwelfare rose substantially, but surreptitiously, because of an influx of new goods as a result ofoverseas trade. Colonial luxuries such as tea, coffee, and sugar transformed European diets afterthe discovery of America and the rounding of the Cape of Good Hope. These goods became household items in many countries by the end of the 18th century. We use three different methodsto calculate welfare gains based on price data and the rate of adoption of these new colonialgoods. Our results suggest that by 1800, the average Englishman would have been willing to forego 10% or more of his income in order to maintain access to sugar and tea alone. These findings are robust to a wide range of alternative assumptions, data series, and valuation methods.

Polyphenol-rich foods in the Mediterranean diet are associated with better cognitive function in elderly subjects at high cardiovascular risk

Brain oxidative processes play a major role in age-related cognitive decline, thus consumption of antioxidant-rich foods might help preserve cognition. Our aim was to assess whether consumption of antioxidant-rich foods in the Mediterranean diet relates to cognitive function in the elderly. In asymptomatic subjects at high cardiovascular risk (n = 447; 52% women; age 5580 y) enrolled in the PREDIMED study, a primary prevention dietary-intervention trial, we assessed food intake and cardiovascular risk profile, determined apolipoprotein E genotype, and used neuropsychological tests to evaluate cognitive function.We also measured urinary polyphenols as an objective biomarker of intake. Associations between energy-adjusted food consumption, urinary polyphenols, and cognitive scores were assessed by multiple linear regression models adjusted for potential confounders. Consumption of some foods was independently related to better cognitive function. The specific associations [regression coefficients (95% confidence intervals)] were: total olive oil with immediate verbal memory [0.755 (0.1511.358)]; virgin olive oil and coffee with delayed verbal memory [0.163 (0.0100.316) and 0.294 (0.0550.534), respectively];walnuts with working memory [1.191 (0.0612.322)]; and wine with Mini-Mental State Examination scores [0.252 (0.0060.496)]. Urinary polyphenols were associated with better scores in immediate verbal memory [1.208 (0.2362.180)]. Increased consumption of antioxidant-rich foods in general and of polyphenols in particular is associated with better cognitive performance in elderly subjects at high cardiovascular risk. The results reinforce the notion that Mediterranean diet components might counteract age-related cognitive decline.

The underestimation of compliance to direct help requests explained by adaptive sampling

Helping behavior is any intentional behavior that benefits another living being or group (Hogg & Vaughan, 2010). People tend to underestimate the probability that others will comply with their direct requests for help (Flynn & Lake, 2008). This implies that when they need help, they will assess the probability of getting it (De Paulo, 1982, cited in Flynn & Lake, 2008) and then they will tend to estimate one that is actually lower than the real chance, so they may not even consider worth asking for it. Existing explanations for this phenomenon attribute it to a mistaken cost computation by the help seeker, who will emphasize the instrumental cost of “saying yes”, ignoring that the potential helper also needs to take into account the social cost of saying “no”. And the truth is that, especially in face-to-face interactions, the discomfort caused by refusing to help can be very high. In short, help seekers tend to fail to realize that it might be more costly to refuse to comply with a help request rather than accepting. A similar effect has been observed when estimating trustworthiness of people. Fetchenhauer and Dunning (2010) showed that people also tend to underestimate it. This bias is reduced when, instead of asymmetric feedback (getting feedback only when deciding to trust the other person), symmetric feedback (always given) was provided. This cause could as well be applicable to help seeking as people only receive feedback when they actually make their request but not otherwise. Fazio, Shook, and Eiser (2004) studied something that could be reinforcing these outcomes: Learning asymmetries. By means of a computer game called BeanFest, they showed that people learn better about negatively valenced objects (beans in this case) than about positively valenced ones. This learning asymmetry esteemed from “information gain being contingent on approach behavior” (p. 293), which could be identified with what Fetchenhauer and Dunning mention as ‘asymmetric feedback’, and hence also with help requests. Fazio et al. also found a generalization asymmetry in favor of negative attitudes versus positive ones. They attributed it to a negativity bias that “weights resemblance to a known negative more heavily than resemblance to a positive” (p. 300). Applied to help seeking scenarios, this would mean that when facing an unknown situation, people would tend to generalize and infer that is more likely that they get a negative rather than a positive outcome from it, so, along with what it was said before, people will be more inclined to think that they will get a “no” when requesting help. Denrell and Le Mens (2011) present a different perspective when trying to explain judgment biases in general. They deviate from the classical inappropriate information processing (depicted among other by Fiske & Taylor, 2007, and Tversky & Kahneman, 1974) and explain this in terms of ‘adaptive sampling’. Adaptive sampling is a sampling mechanism in which the selection of sample items is conditioned by the values of the variable of interest previously observed (Thompson, 2011). Sampling adaptively allows individuals to safeguard themselves from experiences they went through once and turned out to lay negative outcomes. However, it also prevents them from giving a second chance to those experiences to get an updated outcome that could maybe turn into a positive one, a more positive one, or just one that regresses to the mean, whatever direction that implies. That, as Denrell and Le Mens (2011) explained, makes sense: If you go to a restaurant, and you did not like the food, you do not choose that restaurant again. This is what we think could be happening when asking for help: When we get a “no”, we stop asking. And here, we want to provide a complementary explanation for the underestimation of the probability that others comply with our direct help requests based on adaptive sampling. First, we will develop and explain a model that represents the theory. Later on, we will test it empirically by means of experiments, and will elaborate on the analysis of its results.

Implementación de una herramienta de gestión de cambios dentro del ERP eSengoⓇ, e introducción al ERP eSengoⓇ y al framework SherpaBeansⓇ

Esta memoria trata sobre la implementación de un gestor de peticiones de cambio, basado en los estándares definidos por ITIL. Este gestor se implementa dentro del ERP eSengo, desarrollado por Isencia S.L. También se hace una breve explicación sobre los submódulos que han sido necesarios y los estados de flujo de ejecución del gestor. Además se explican características sobre el ERP eSengo y sobre la plataforma basada en Java Beans, SherpaBeans, también desarrollada por Isencia, a parte de enumerar las tecnologías que esta plataforma utiliza.