Biomedical subjects

David Montaner

Publications and source records attributed to David Montaner.

7 recordsLinked to original sources

PubMed2006

Prophet, a web-based tool for class prediction using microarray data.

UNLABELLED: Sample classification and class prediction is the aim of many gene expression studies. We present a web-based application, Prophet, which builds prediction rules and allows using them for further sample classification. Prophet automatically chooses the best classifier, along with the optimal selection of genes, using a strategy that renders unbiased cross-validated errors. Prophet is linked to different microarray data analysis modules, and includes a unique feature: the possibility of performing the functional interpretation of the molecular signature found. AVAILABILITY: Prophet can be found at the URL http://prophet.bioinfo.cipf.es/ or within the GEPAS package at http://www.gepas.org/ SUPPLEMENTARY INFORMATION: http://gepas.bioinfo.cipf.es/tutorial/prophet.html.

Algorithms↗

PubMed2006

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.

We present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at http://www.babelomics.org.

Animals↗

PubMed2006

Next station in microarray data analysis: GEPAS.

The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it has evolved to keep pace with the new interests and trends in the still changing world of microarray data analysis. GEPAS has been designed to provide an intuitive although powerful web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-colour microarray experiments and other preprocessing options), to the final step of the functional annotation of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), and include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. GEPAS is extensively used by researchers of many countries and its records indicate an average usage rate of 400 experiments per day. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.

Cluster Analysis↗

PubMed2006

Self-reported smoking cessation interventions were not associated with quitting in older women.

OBJECTIVE: To determine the extent to which smoking cessation interventions are used in the community and their relative success in older women. STUDY DESIGN AND SETTING: Prospective cohort study located in 23 general practices in England, Scotland. and Wales and including 3,622 women aged 60 to 79 years at recruitment from the British Women's Heart and Health Study. RESULTS: Of the 370 smokers at baseline, 77 (21%) had stopped smoking at 3 years, reducing the prevalence of smoking from 10.2% to 8.8%. Women who were light smokers (<10 per day) at baseline were more likely to have quit than heavier smokers. The most common interventions reported by women who smoked at baseline were advice from a general practitioner (GP), family or friend's advice, and use of nicotine replacement, but 42% of the women reported having no intervention to help them to stop smoking. None of the individual interventions were associated with increased odds of quitting smoking over the follow-up period. Women reported finding a GP's advice, referral to a clinic, and nicotine replacement more useful than complementary treatments (acupuncture and hypnotherapy) or advice from family and friends. CONCLUSION: Smoking cessation rates in this study were in line with national targets and surveys. Self-reports of ever receiving interventions were not associated with quitting smoking among these older women. Different and innovative approaches to smoking cessation may need to be developed, and evaluated in future randomized clinical trials, for individuals who have smoked for a long period of time and for whom other smoking cessation interventions have not proved successful.

Age Distribution↗

PubMed2006

Selective pressures at a codon-level predict deleterious mutations in human disease genes.

Deleterious mutations affecting biological function of proteins are constantly being rejected by purifying selection from the gene pool. The non-synonymous/synonymous substitution rate ratio (omega) is a measure of selective pressure on amino acid replacement mutations for protein-coding genes. Different methods have been developed in order to predict non-synonymous changes affecting gene function. However, none has considered the estimation of selective constraints acting on protein residues. Here, we have used codon-based maximum likelihood models in order to estimate the selective pressures on the individual amino acid residues of a well-known model protein: p53. We demonstrate that the number of residues under strong purifying selection in p53 is much higher than those that are strictly conserved during the evolution of the species. In agreement with theoretical expectations, residues that have been noted to be of structural relevance, or in direct association with DNA, were among those showing the highest signals of purifying selection. Conversely, those changing according to a neutral, or nearly neutral mode of evolution, were observed to be irrelevant for protein function. Finally, using more than 40 human disease genes, we demonstrate that residues evolving under strong selective pressures (omega<0.1) are significantly associated (p<0.01) with human disease. We hypothesize that non-synonymous change on amino acids showing omega<0.1 will most likely affect protein function. The application of this evolutionary prediction at a genomic scale will provide an a priori hypothesis of the phenotypic effect of non-synonymous coding single nucleotide polymorphisms (SNPs) in the human genome.

Amino Acid Sequence↗

PubMed2004

How acceptable are innovative health-care technologies? A survey of public beliefs and attitudes in England and Wales.

There has been a continuing debate about the extent to which the public finds health-care technological innovation acceptable. The public's ambivalence about scientific medicine may have been exacerbated, more recently, by developments such as the introduction of the 'new genetics' with their associated ethical and social implications and the claims that public trust in health care and practitioners and, more widely, in society has been eroded. The aim of this paper is to examine public attitudes to a range of innovative health-care technologies to see whether (i) certain technologies are perceived as particularly problematic, and (ii) attitudes to new health-care technologies are associated more broadly with beliefs about science, trust in health care and social trust, and perceptions of the benefits and risks of complementary and alternative medicine versus orthodox (technological) medicine. These questions are examined through a statistical analysis of data collected in a national, postal survey of the adult population (n = 1187) in England and Wales. The results showed public ambivalence about new health-care technologies, although genetic technologies, as a whole, were not seen to be problematic and their acceptability depended on their ability to control serious diseases. However, there was a level of consistency in attitude across the different technologies. Those consistently against new health-care technologies were also more likely to be suspicious of science, and doubtful about the benefits of other established, orthodox technologies (screening; medications) and to have less trust in health and health-care practitioners.

Adolescent↗

PubMed2004

Clustering of risk factors and social class in childhood and adulthood in British women's heart and health study: cross sectional analysis.

OBJECTIVE: To examine co-occurrence and clustering of risk factors used in the Framingham equation by social class in childhood and adult life. DESIGN: Cross sectional study. SETTING: 23 towns across England, Wales, and Scotland. PARTICIPANTS: 2936 women aged 60-79 years. MAIN OUTCOME MEASURES: Prevalence of risk factors (hypertension, obesity, smoking, left ventricular hypertrophy on electrocardiography, diabetes, and low concentration of high density cholesterol); ratios of observed to expected frequencies of clusters of risk factors. RESULTS: Risk factors were more common in women from manual social classes in either childhood or adult life, and the co-occurrence of three or four of these risk factors was greater among more disadvantaged groups. Within the four socioeconomic groups, these risk factors occurred together more than would be expected from their individual frequency distributions, indicating that they were clustered. The extent of this clustering was similar in all four social class groups. CONCLUSIONS: Clustering of risk factors included in the Framingham risk function occurs in all social class groups, but the lack of social patterning makes it unlikely that clustering is an explanation of socioeconomic inequalities in cardiovascular disease. As the proportion of women with co-occurrence of risk factors is greatest in those from manual social class in childhood, this measure of socioeconomic position might prove useful in risk prediction.

Aged↗