Gene expression databases and data mining.

The DNA microarray technology has arguably caught the attention of the worldwide life science community and is now systematically supporting major discoveries in many fields of study. The majority of the initial technical challenges of conducting experiments are being resolved, only to be replaced with new informatics hurdles, including statistical analysis, data visualization, interpretation, and storage. Two systems of databases, one containing expression data and one containing annotation data are quickly becoming essential knowledge repositories of the research community. This present paper surveys several databases, which are considered "pillars" of research and important nodes in the network. This paper focuses on a generalized workflow scheme typical for microarray experiments using two examples related to cancer research. The workflow is used to reference appropriate databases and tools for each step in the process of array experimentation. Additionally, benefits and drawbacks of current array databases are addressed, and suggestions are made for their improvement.

Young People's Health in Great Britain and Ireland: Findings from the Health Behaviour in School-Aged Children (HBSC)Survey, 2006.

This report presents data from the 2006 Health Behaviour in School-aged Children (HBSC) survey; a World Health Organization (WHO) collaborative cross-national study and focuses on data collected from young people in England, Ireland, Scotland and Wales. It expands on the findings from the international report Inequalities in Young People's Health (Currie et al, 2008), with additional variables and prevalence rates that allows more comprehensive and focussed comparisons to be made between the four countries.This resource was contributed by The National Documentation Centre on Drug Use.

Differentiated normalization and drug transitions among rural youth in Ireland.

Prevalence surveys in Ireland indicate an increased trend of youth drug use with rural areas reporting comparable drug availability and prevalence of use in urban settings (Currie, C., Nic Gabhainn, S., Godeau, E., Roberts, C., Smith, R., & Currie, D. (Eds.). (2008). Inequalities in young people's health: HBSC international report from the 2005/2006 survey. Copenhagen: WHO Regional Office for Europe). Few studies have explored the contexts and meaning of drug use on rural youth transitions in terms of increased drug prevalence, recent influx of rural drug activity, normative tolerance of recreational drug consumption and fragmentation of traditional rural communities. Qualitative interviews were conducted with 220 young people (15–17 years), and 78 service providers in a rural area of Ireland, in order to yield contextualized narratives of their experiences of drug use and achieve a wider exploration of processes, drug transitions and realities of rural youth. The thematic analysis of the research described varied pathways, attitudes and typologies of rural youth drug use, ranging from abstinent, recreational and moderated to maturing out. The research suggests support for a ‘differentiated’ normalization theory (Shildrick, T. (2002). Young people, illicit drug use and the question of normalisation theory. Journal of Youth Studies, 5, 35–48) in terms of consumerist and normative rural youth drug use transitions in their negotiation of risk within integrating rural and urban dichotomies. In conclusion, it is recommended that drug education programmes need to situate localized rural drug taking behaviours within a wider understanding of rural community life.This resource was contributed by The National Documentation Centre on Drug Use.

Standard Evaluation Framework (SEF) for weight management interventions Presentation

This presentation summaries the Standard Evaluation Framework which is designed to support high quality, consistent evaluation of weight management interventions in order to increase the evidence base.

Changes in the transcriptional profile of transporters in the intestine along the anterior-posterior and crypt-villus axes.

BACKGROUND: The purpose of this work was to characterize the expression of drug and nutrient carriers along the anterior-posterior and crypt-villus axes of the intestinal epithelium and to study the validity of utilizing whole gut tissue rather than purified epithelial cells to examine regional variations in gene expression. RESULTS: We have characterized the mRNA expression profiles of 76 % of all currently known transporters along the anterior-posterior axis of the gut. This is the first study to describe the expression profiles of the majority of all known transporters in the intestine. The expression profiles of transporters, as defined according to the Gene Ontology consortium, were measured in whole tissue of the murine duodenum, jejunum, ileum and colon using high-density microarrays. For nine transporters (Abca1, Abcc1, Abcc3, Abcg8, Slc10a2, Slc28a2, Slc2a1, Slc34a2 and Slc5a8), the mRNA profiles were further measured by RT-PCR in laser micro-dissected crypt and villus epithelial cells corresponding to the aforementioned intestinal regions. With respect to differentially regulated transporters, the colon had a distinct expression profile from small intestinal segments. The majority (59 % for p cutoff < or = 0.05) of transporter mRNA levels were constant across the intestinal sections studied. For the transporter subclass "carrier activity", which contains the majority of known carriers for biologically active compounds, a significant change (p < or = 0.05) along the anterior-posterior axis was observed. CONCLUSION: All nine transporters examined in laser-dissected material demonstrated good replication of the region-specific profiles revealed by microarray. Furthermore, we suggest that the distribution characteristics of Slc5a8 along the intestinal tract render it a suitable candidate carrier for monocarboxylate drugs in the posterior portion of the intestine. Our findings also predict that there is a significant difference in the absorption of carrier-mediated compounds in the different intestinal segments. The most pronounced differences can be expected between the adjoining segments ileum and colon, but the differences between the other adjoining segments are not negligible. Finally, for the examined genes, profiles measured in whole intestinal tissue extracts are representative of epithelial cell-only gene expression.

Vaccines against Toxoplasma gondii: challenges and opportunities

Development of vaccines against Toxoplasma gondii infection in humans is of high priority, given the high burden of disease in some areas of the world like South America, and the lack of effective drugs with few adverse effects. Rodent models have been used in research on vaccines against T. gondii over the past decades. However, regardless of the vaccine construct, the vaccines have not been able to induce protective immunity when the organism is challenged with T. gondii, either directly or via a vector. Only a few live, attenuated T. gondii strains used for immunization have been able to confer protective immunity, which is measured by a lack of tissue cysts after challenge. Furthermore, challenge with low virulence strains, especially strains with genotype II, will probably be insufficient to provide protection against the more virulent T. gondii strains, such as those with genotypes I or II, or those genotypes from South America not belonging to genotype I, II or III. Future studies should use animal models besides rodents, and challenges should be performed with at least one genotype II T. gondii and one of the more virulent genotypes. Endpoints like maternal-foetal transmission and prevention of eye disease are important in addition to the traditional endpoint of survival or reduction in numbers of brain cysts after challenge.

Análisis discursivo de ser y estar: aspectos de la periodización de sus usos y valores

En esta comunicación se presentan los resultados de un trabajo en curso cuyo objetivo es profundizar en la explicación de la naturaleza del cambio lingüístico que comporta la progresiva sustitución de ser por estar en castellano medieval y en la periodización de este cambio. La comunicación se organiza en cuatro apartados. El primero expone los aspectos generales del comportamiento de ser y estar en oraciones atributivas, pasivas resultativas y construcciones locativas. El segundo se centra en la descripción de la distribución de estos verbos en el Cantar de Myo Çid, obra en la que estar se atestigua únicamente en construcciones locativas. En el tercer apartado se examinan los datos del Calila e Dimna, los cuales ponen de manifiesto el avance de estar en detrimento de ser en oraciones atributivas cuyo predicado expresa estado, en algunas pasivas resultativas y en construcciones locativas. El último apartado presenta una propuesta de análisis en la línea de Roberts y Roussou (1999, 2002 y 2003) que es perfectamente compatible con las propuestas pragmáticas en la línea de la Teoría de la Relevancia

El proceso de codificación sintáctica de la causalidad en las lenguas románicas medievales

En esta comunicación vamos a examinar los patrones que sigue la codificación sintáctica en los conectores causales resultantes de procesos de gramaticalización. Tal como observó Givón (1979:107), la dirección de los procesos de codificación puede producirse desde el discurso a la sintaxis. Esta idea se ha retomado en teorías más recientes como, por ejemplo, la Teoría de la Relevancia, desarrollada en distintos trabajos de Sperber y Wilson, entre otros. La aplicación de esta teoría en el ámbito de los conectores discursivos ha sido llevada a cabo por distintos autores, entre los cuales destaca Blakemore. El propósito de nuestro trabajo residirá en integrar las ventajas de un análisis pragmático discursivo como la citada Teoría de la Relevancia con una teoría sintáctica formal de la gramaticalización, concretamente la que proponen dentro del marco de la gramática generativa Roberts y Roussou (2003). Esto permitirá profundizar, por un lado, en el tipo de codificación de las instruccions lingüísticas que aportan los conectores (información procedimental) y, por otro, en la relación lógico-discursiva entre las proposiciones y en la propia estructura del nexo

The BRAIN TRIAL: a randomised, placebo controlled trial of a Bradykinin B2 receptor antagonist (Anatibant) in patients with traumatic brain injury

BACKGROUND Cerebral oedema is associated with significant neurological damage in patients with traumatic brain injury. Bradykinin is an inflammatory mediator that may contribute to cerebral oedema by increasing the permeability of the blood-brain barrier. We evaluated the safety and effectiveness of the non-peptide bradykinin B2 receptor antagonist Anatibant in the treatment of patients with traumatic brain injury. During the course of the trial, funding was withdrawn by the sponsor. METHODS Adults with traumatic brain injury and a Glasgow Coma Scale score of 12 or less, who had a CT scan showing an intracranial abnormality consistent with trauma, and were within eight hours of their injury were randomly allocated to low, medium or high dose Anatibant or to placebo. Outcomes were Serious Adverse Events (SAE), mortality 15 days following injury and in-hospital morbidity assessed by the Glasgow Coma Scale (GCS), the Disability Rating Scale (DRS) and a modified version of the Oxford Handicap Scale (HIREOS). RESULTS 228 patients out of a planned sample size of 400 patients were randomised. The risk of experiencing one or more SAEs was 26.4% (43/163) in the combined Anatibant treated group, compared to 19.3% (11/57) in the placebo group (relative risk = 1.37; 95% CI 0.76 to 2.46). All cause mortality in the Anatibant treated group was 19% and in the placebo group 15.8% (relative risk 1.20, 95% CI 0.61 to 2.36). The mean GCS at discharge was 12.48 in the Anatibant treated group and 13.0 in the placebo group. Mean DRS was 11.18 Anatibant versus 9.73 placebo, and mean HIREOS was 3.94 Anatibant versus 3.54 placebo. The differences between the mean levels for GCS, DRS and HIREOS in the Anatibant and placebo groups, when adjusted for baseline GCS, showed a non-significant trend for worse outcomes in all three measures. CONCLUSION This trial did not reach the planned sample size of 400 patients and consequently, the study power to detect an increase in the risk of serious adverse events was reduced. This trial provides no reliable evidence of benefit or harm and a larger trial would be needed to establish safety and effectiveness. TRIAL REGISTRATION This study is registered as an International Standard Randomised Controlled Trial, number ISRCTN23625128.

Blood pressure loci identified with a gene-centric array.

Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated with BP at our p < 8.56 × 10(-7) study-specific significance threshold and six suggestively associated SNPs in a further 59,349 individuals. We identified and replicated a SNP at LSP1/TNNT3, a SNP at MTHFR-NPPB independent (r(2) = 0.33) of previous reports, and replicated SNPs at AGT and ATP2B1 reported previously. An analysis of combined discovery and follow-up data identified SNPs significantly associated with BP at p < 8.56 × 10(-7) at four further loci (NPR3, HFE, NOS3, and SOX6). The high number of discoveries made with modest genotyping effort can be attributed to using a large-scale yet targeted genotyping array and to the development of a weighting scheme that maximized power when meta-analyzing results from samples ascertained with extreme phenotypes, in combination with results from nonascertained or population samples. Chromatin immunoprecipitation and transcript expression data highlight potential gene regulatory mechanisms at the MTHFR and NOS3 loci. These results provide candidates for further study to help dissect mechanisms affecting BP and highlight the utility of studying SNPs and samples that are independent of those studied previously even when the sample size is smaller than that in previous studies.

Desencuentros comunicativos dentro y fuera del aula L2 para inmigrantes adultos

In the past few years, the studies on communicative troubles emerging in intercultural communication highlight cultural differences. Some disciplines have created training guides where those differences are made explicit so that in the case of international communication misunderstandings are avoided. Examples can be found in non-verbal communication protocols for health services and in the business world. In this regard the field of second-language teaching is beginning to include the socio-pragmatic features of language in the teaching materials. For this reason, this dissertation attempts to describe the communicative conflicts that arise in conversation between immigrants and natives in the city of Barcelona. Thanks to the theoretical and methodological tools provided by Conversation Analysis and Discourse Analysis, we can ethnographically analyze the interviews held with the informants, and the interactions they had with Barcelonan people, by taking into account the linguistic and paralinguistic features which are salient in the interaction (Gumperz y Roberts, 1991; Gumperz, 1992; Hérédia, 1996 y Trognon y Saint-Dizier, 1999). For this purpose, we first examine the causes that produce the conflict as well as the consequences that derive from it. Second, we describe the strategies that the speakers use in the negotiation of the meaning that generated the misunderstanding. Although it is obvious that the nature of the conversations, the personal characteristics of the participants and the context of the conversations have a noticeable influence on the participants’ communicative attitudes (Hinnenkamp, 1987; Codó, 2003; van Dijk, 2003 y Bertrán, 2009), there are somemisunderstandings that none of the interlocutors are able to detect or solve. The results show that not all of the misunderstandings that emerge in intercultural communication have a negative effect and, therefore, its usage in the L2 teaching classroom is essential for acquiring socio-cultural and intercultural competence (Miquel, 1997; Oliveras, 2000 y Miquel y Sans 2004).