Networking of differentially expressed genes in human cancer cells resistant to methotrexate

BACKGROUND: The need for an integrated view of data obtained from high-throughput technologies gave rise to network analyses. These are especially useful to rationalize how external perturbations propagate through the expression of genes. To address this issue in the case of drug resistance, we constructed biological association networks of genes differentially expressed in cell lines resistant to methotrexate (MTX). METHODS: Seven cell lines representative of different types of cancer, including colon cancer (HT29 and Caco2), breast cancer (MCF-7 and MDA-MB-468), pancreatic cancer (MIA PaCa-2), erythroblastic leukemia (K562) and osteosarcoma (Saos-2), were used. The differential expression pattern between sensitive and MTX-resistant cells was determined by whole human genome microarrays and analyzed with the GeneSpring GX software package. Genes deregulated in common between the different cancer cell lines served to generate biological association networks using the Pathway Architect software. RESULTS: Dikkopf homolog-1 (DKK1) is a highly interconnected node in the network generated with genes in common between the two colon cancer cell lines, and functional validations of this target using small interfering RNAs (siRNAs) showed a chemosensitization toward MTX. Members of the UDP-glucuronosyltransferase 1A (UGT1A) family formed a network of genes differentially expressed in the two breast cancer cell lines. siRNA treatment against UGT1A also showed an increase in MTX sensitivity. Eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) was overexpressed among the pancreatic cancer, leukemia and osteosarcoma cell lines, and siRNA treatment against EEF1A1 produced a chemosensitization toward MTX. CONCLUSIONS: Biological association networks identified DKK1, UGT1As and EEF1A1 as important gene nodes in MTX-resistance. Treatments using siRNA technology against these three genes showed chemosensitization toward MTX.

The transcriptional network activated by Cln3 cyclin at the G1-to-S transition of the yeast cell cycle

Background: The G1-to-S transition of the cell cycle in the yeast Saccharomyces cerevisiae involves an extensive transcriptional program driven by transcription factors SBF (Swi4-Swi6) and MBF (Mbp1-Swi6). Activation of these factors ultimately depends on the G1 cyclin Cln3. Results: To determine the transcriptional targets of Cln3 and their dependence on SBF or MBF, we first have used DNA microarrays to interrogate gene expression upon Cln3 overexpression in synchronized cultures of strains lacking components of SBF and/or MBF. Secondly, we have integrated this expression dataset together with other heterogeneous data sources into a single probabilistic model based on Bayesian statistics. Our analysis has produced more than 200 transcription factor-target assignments, validated by ChIP assays and by functional enrichment. Our predictions show higher internal coherence and predictive power than previous classifications. Our results support a model whereby SBF and MBF may be differentially activated by Cln3. Conclusions: Integration of heterogeneous genome-wide datasets is key to building accurate transcriptional networks. By such integration, we provide here a reliable transcriptional network at the G1-to-S transition in the budding yeast cell cycle. Our results suggest that to improve the reliability of predictions we need to feed our models with more informative experimental data.

Protective effects of social networks on disability among older adults in Spain

The loss of autonomy at advanced ages is not only associated with ageing, but also with the characteristics of the physical and social environment. Recent investigations have shown that social networks, social engagement and participation act like predictors of disability among the elderly. The aim of this study is to determine whether social networks are related to the development and progression of disability in the early years of old age. The source of data is the first wave of the survey "Processes of Vulnerability among Spanish Elderly", carried out in 2005 to a sample of 1 244 individuals. The population object of study is the cohort aged 70 to 74 years in metropolitan areas (Madrid and Barcelona) and not institutionalized. Disability is measured by the development of basic activities of daily life (ADL), and instrumental activities of daily life (IADL). The structural aspects of the social relationships are measured through the diversity of social networks and participation. We used the social network index (SNI). For each point over the SNI, the risk of developing any type of disability decreased by 49% (HR = 0.51, 95%CI = 0.31-0.82). The SNI was a decisive factor in all forecasting models constructed with some hazard ratios (HR) that ranged from 0.29 (95%CI = 0.14-0.59) in the first model to 0.43 (95%CI 0.20-0.90) in the full model. The results of the present study showed a strong association between an active social life, emotional support provided by friends and confidents and disability. These findings suggest a protective effect of social networks on disability. Also, these results indicate that some family and emotional ties have a significant effect on both the prevalence and the incidence of disability.

Generalization transitions in Hidden-Layer neural networks for third-order feature discrimination

Stochastic learning processes for a specific feature detector are studied. This technique is applied to nonsmooth multilayer neural networks requested to perform a discrimination task of order 3 based on the ssT-block¿ssC-block problem. Our system proves to be capable of achieving perfect generalization, after presenting finite numbers of examples, by undergoing a phase transition. The corresponding annealed theory, which involves the Ising model under external field, shows good agreement with Monte Carlo simulations.

Identification of Paintings from Camera-Phone Images

Peer-reviewed

PhD Students’ Research Group Networks: a Qualitative Approach

This article examines the networks within the research groups where Spanish PhD students are pursuing their doctorate. Capó et al. (2007) used quantitative data to predict PhD students’ publishing performance from their background, attitudes, supervisors’ performance and research group networks. Variables related to the research group network had a negligible explanatory power on student performance once the remaining variables had been accounted for. In this article, a qualitative follow up of the same students is carried out using extreme case sampling and indepth interviews. The qualitative research shows networking as important for students. Out of the 115 aspects that students mention in the interviews as relevant to publishing in the qualitative research, 92 have to do with their supervisors, their research group or their network as a whole. Similarly, out of the 50 hindrances mentioned, 20 have to do with the networks or relations. The most commonly mentioned network-related topics are research group members pushing PhD students to publish, meeting researchers outside the research group, existence of other PhD students in the group, help with the PhD from group members, supervisor’s interest in the thesis, the possibility of discussing with experts on the PhD’s topic and frequent contact with the supervisor and research group members. Some of these characteristics were not, however, measured in the conventional quantitative social network survey

Combined dielectrophoretic and impedance system for on-chip controlled bacteria concentration: Application to Escherichia coli

The present paper reports a bacteria autonomous controlled concentrator prototype with a user-friendly interface for bench-top applications. It is based on a micro-fluidic lab-on-a-chip and its associated custom instrumentation, which consists in a dielectrophoretic actuator, to pre-concentrate the sample, and an impedance analyser, to measure concentrated bacteria levels. The system is composed by a single micro-fluidic chamber with interdigitated electrodes and a instrumentation with custom electronics. The prototype is supported by a real-time platform connected to a remote computer, which automatically controls the system and displays impedance data used to monitor the status of bacteria accumulation on-chip. The system automates the whole concentrating operation. Performance has been studied for controlled volumes of Escherichia coli (E. coli) samples injected into the micro-fluidic chip at constant flow rate of 10 μL/min. A media conductivity correcting protocol has been developed, as the preliminary results showed distortion of the impedance analyser measurement produced by bacterial media conductivity variations through time. With the correcting protocol, the measured impedance values were related to the quantity of bacteria concentrated with a correlation of 0.988 and a coefficient of variation of 3.1%. Feasibility of E. coli on-chip automated concentration, using the miniaturized system, has been demonstrated. Furthermore, the impedance monitoring protocol had been adjusted and optimized, to handle changes in the electrical properties of the bacteria media over time.

Dealing with Tyranny: International Sanctions and Autocrats’ Duration

This paper enquires into whether economic sanctions are effective in destabilizing authoritarian rulers. We argue that this effect is mediated by the type of authoritarian regime against which sanctions are imposed. Thus, personalist regimes and monarchies, which are more dependent on aid and resource rents to maintain their patronage networks, are more likely to be affected by sanctions. In contrast, single-party and military regimes are able to maintain (and even increase) their tax revenues and to reallocate their expenditures and so increase their levels of cooptation. Data on sanction episodes, authoritarian rulers and regimes covering the period 1946–2000 have allowed us to test our hypotheses. To do so, duration models have been run, and the results confirm that personalist autocrats are more vulnerable to foreign pressure. Concretely, the analysis of the modes of exit reveals that sanctions increase the likelihood of an irregular change of ruler, such as a coup. Sanctions are basically ineffective when targeting single-party or military regimes.

Integración de empresas: planificación y gestión del cambio

Este proyecto nace de la necesidad de realizar una integración de los sistemas informáticos de una empresa en una multinacional; las empresas disponen de servicios de outsourcing en sistemas de información. Al tratarse de una integración operativa, sólo trataremos de trasladar los servicios de centro de atención al usuario, soporte local y ofimática desde un outsourcing de servicios a otro, añadiendo los cambios de procesos necesarios para disponer de un único entorno de trabajo. El cambio de entorno de trabajo se ha de realizar sin perdida de disponibilidad ni de información.

Agrupación de antenas microstrip para un receptor SAR biestático

El objetivo de este proyecto es el diseño de las antenas para el receptor de un radar de apertura sintética biestáticos (SAR). Estas antenas tendrán que maximizar la ganancia con la restricción de maximizar también el campo de visión del radar. Esto quiere decir, que la antena tendrá que tener un ancho de banda relativamente grande en uno de sus planos principales y relativamente estrecho en el otro plano. Con el propósito de diseñar una agrupación de antenas para un receptor SAR biestático, en este documento se analiza la tecnología microstrip orientada a las antenas y la teoría de las agrupaciones de antenas, se diseñan antenas de doble polarización, se estudian agrupaciones de antenas microstrip que cumplan con las especificaciones, se presentan redes de alimentaciones para dichas agrupaciones y se fabrica y mide una agrupación de antenas con doble polarización.

Estudi òptic dels minerals

El Grup Consolidat d’Innovació Docent de Mineralogia i òptica cristal·lina de la Universitat de Barcelona ha desenvolupat un CD interactiu que simula el funcionament d’un microscopi petrogràfic, per tal de facilitar a l’alumne un material d’autoaprenentatge, ha de servir per a reforçar els coneixements dels minerals formadors de roques en làmina prima. Aquest material te tres entrades diferents, en català, castellà i anglès. Cada mineral té una fitxa general amb les seves propietats òptiques i una complementaria amb les característiques cristal·logràfiques, camp d’estabilitat, diagrames de fases i característiques morfològiques del mineral a observar, les quals marquen els trets determinatius d’aquell mineral per tal de facilitar el seu reconeixement. Per tal de complementar les dades s’han introduït links directes amb la planes web: “webmineral” i “mindat” on hi ha les corresponents estructures i morfologies “interactives” de cadascun dels minerals que apareixen en el programa. En l’aplicació informàtica hi ha 169 filmacions corresponents a 43 dels principals minerals que formen les roques, una filmació correspon a la imatge només amb el polaritzador, i l'altre a la imatge amb el polaritzador més l'analitzador. Cadascuna d'aquestes imatges es presenta amb un gir de 360º; es pot aturar i després continuar girant, simulant el que veuríem al microscopi. D'aquesta manera es pot determinar el pleocroisme, la presència de macles, el color d'interferència i l'angle d'extinció.. S’ha intentat sempre que hi hagués diferents exemples d’un mateix mineral en diverses paragènesis. També s'incorpora una fitxa que l'usuari pot omplir amb les característiques texturals i òptiques del mineral agrupades segons les observacions que es fan, bé amb el polaritzador, amb el polaritzador i l'analitzador o bé amb les condicions específiques per veure la figura d'interferència i el signe òptic. Aquesta fitxa, un cop plena, es pot imprimir. En tot moment hi ha un menú d’ajuda on l’usuari pot remetre i fer la consulta adient per poder continuar.

Xarxes tolerants a endarreriments i interrupcions: desenvolupament d'un scheduler d'agents mòbils

En aquest projecte es proposa i s’implementa una nova forma de crear xarxes DTN (Delay-Tolerant Networks) mitjançant agents mòbils. Aquestes xarxes tenen la peculiaritat de ser tolerants a endarreriments i interrupcions, podent ser utilitzades en entorns on les xarxes actuals no es poden aplicar. Hem dissenyat mecanismes que permeten prendre decisions d’encaminament a nivell d’aplicació i mecanismes de priorització d’agents mitjançant informació d’alt nivell. Aquests mecanismes milloren les DTN fent-les més flexibles i efectives.

Casa Museu Lluís Domènech i Montaner : Recurs electrònic

Treball de recerca que té com a principal objectiu elaborar una guia electrònica (pàgina web) de la Casa Museu Lluís Domènech i Montaner. Aquest treball està inscrit dins un aprenentatge museístic i informàtic. Serà un aprenentatge museístic per tot el que comporta la lectura de les sales i els materials que s'hi exposen, i informàtic perquè es tracta de dissenyar i elaborar un recurs electrònic que ha de permetre una presentació agradable, fàcil de progrés, harmoniosa i, alhora, concreta.

Gestió de xarxes Internet basada en SNMP

El treball es divideix en dos grans parts, una primera eminentment teòrica en la que s'estudia SNMP, i una segona íntegrament pràctica en la que s'implementa el protocol. Per a cada part es defineix una metodologia ben diferenciada.

Plan de actualización informática de las oficinas de la Mutua

Aquest projecte ha procurat reflectir les diferents opcions que té la Mútua a l'hora d'actualitzar el seu sistema informàtic. Després d'estudiar la viabilitat de les diferents opcions proposa solucions per a tots els aspectes plantejats.