Meta-analysis of genome-wide association data identifies a risk locus for major mood disorders on 3p21.1.

The major mood disorders, which include bipolar disorder and major depressive disorder (MDD), are considered heritable traits, although previous genetic association studies have had limited success in robustly identifying risk loci. We performed a meta-analysis of five case-control cohorts for major mood disorder, including over 13,600 individuals genotyped on high-density SNP arrays. We identified SNPs at 3p21.1 associated with major mood disorders (rs2251219, P = 3.63 x 10(-8); odds ratio = 0.87; 95% confidence interval, 0.83-0.92), with supportive evidence for association observed in two out of three independent replication cohorts. These results provide an example of a shared genetic susceptibility locus for bipolar disorder and MDD.

Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data.

Despite the central role of quantitative PCR (qPCR) in the quantification of mRNA transcripts, most analyses of qPCR data are still delegated to the software that comes with the qPCR apparatus. This is especially true for the handling of the fluorescence baseline. This article shows that baseline estimation errors are directly reflected in the observed PCR efficiency values and are thus propagated exponentially in the estimated starting concentrations as well as 'fold-difference' results. Because of the unknown origin and kinetics of the baseline fluorescence, the fluorescence values monitored in the initial cycles of the PCR reaction cannot be used to estimate a useful baseline value. An algorithm that estimates the baseline by reconstructing the log-linear phase downward from the early plateau phase of the PCR reaction was developed and shown to lead to very reproducible PCR efficiency values. PCR efficiency values were determined per sample by fitting a regression line to a subset of data points in the log-linear phase. The variability, as well as the bias, in qPCR results was significantly reduced when the mean of these PCR efficiencies per amplicon was used in the calculation of an estimate of the starting concentration per sample.

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.

Epidemilogia de la Influença porcina

La influenza es una enfermedad de gran importancia debido a su impacto sanitario y social. La especie porcina tiene importancia epidemiológica debido a su capacidad de actuar como eslabón adaptando los virus aviares a los mamíferos. Un mejor conocimiento de la enfermedad en la especie porcina permitirá definir mejor los métodos de lucha frente la enfermedad tanto en la especie humana como en la porcina. En el presente proyecto se pretende determinar los subtipos de virus influenza actualmente presentes en la cabaña porcina de España y estimar su seroprevalencia, así como estudiar los factores de riesgo que predisponen a la presencia de los virus influenza en las granjas de porcino. Para ello, se realizará una encuesta seroepidemiológica en la que se recogerán muestras de suero de animales de distintas edades (cerdas y cerdos de engorde) y se reunirán datos correspondientes a las características de las distintas explotaciones mediante una encuesta epidemiológica. Por otro lado, y con el fin de determinar la dinámica de infección de la enfermedad, se llevará a cabo un estudio longitudinal en dos explotaciones de ciclo cerrado seropositivas frente a Influenza porcina. En éstas explotaciones se recogerán muestras de suero y de hisopos nasales de un lote entero de producción, en intervalos que oscilarán de semanalmente a mensualmente. Los animales se muestrearan desde las tres semanas de vida hasta que sean enviados al matadero (aproximadamente a los 6 meses de vida). A partir de las muestras obtenidas se realizaran pruebas diagnósticas de carácter virológico y serológico. Este estudio aportará información acerca de la diseminación de los virus influenza en las explotaciones de cerdos, por lo que refiere a su comportamiento endémico/epidémico, clinico/subclínico, etc.

Coronary MR angiography: comparison of quantitative and qualitative data from four techniques.

OBJECTIVE: The optimal coronary MR angiography sequence has yet to be determined. We sought to quantitatively and qualitatively compare four coronary MR angiography sequences. SUBJECTS AND METHODS. Free-breathing coronary MR angiography was performed in 12 patients using four imaging sequences (turbo field-echo, fast spin-echo, balanced fast field-echo, and spiral turbo field-echo). Quantitative comparisons, including signal-to-noise ratio, contrast-to-noise ratio, vessel diameter, and vessel sharpness, were performed using a semiautomated analysis tool. Accuracy for detection of hemodynamically significant disease (> 50%) was assessed in comparison with radiographic coronary angiography. RESULTS: Signal-to-noise and contrast-to-noise ratios were markedly increased using the spiral (25.7 +/- 5.7 and 15.2 +/- 3.9) and balanced fast field-echo (23.5 +/- 11.7 and 14.4 +/- 8.1) sequences compared with the turbo field-echo (12.5 +/- 2.7 and 8.3 +/- 2.6) sequence (p < 0.05). Vessel diameter was smaller with the spiral sequence (2.6 +/- 0.5 mm) than with the other techniques (turbo field-echo, 3.0 +/- 0.5 mm, p = 0.6; balanced fast field-echo, 3.1 +/- 0.5 mm, p < 0.01; fast spin-echo, 3.1 +/- 0.5 mm, p < 0.01). Vessel sharpness was highest with the balanced fast field-echo sequence (61.6% +/- 8.5% compared with turbo field-echo, 44.0% +/- 6.6%; spiral, 44.7% +/- 6.5%; fast spin-echo, 18.4% +/- 6.7%; p < 0.001). The overall accuracies of the sequences were similar (range, 74% for turbo field-echo, 79% for spiral). Scanning time for the fast spin-echo sequences was longest (10.5 +/- 0.6 min), and for the spiral acquisitions was shortest (5.2 +/- 0.3 min). CONCLUSION: Advantages in signal-to-noise and contrast-to-noise ratios, vessel sharpness, and the qualitative results appear to favor spiral and balanced fast field-echo coronary MR angiography sequences, although subjective accuracy for the detection of coronary artery disease was similar to that of other sequences.

Missed appointments in an adolescent outpatient clinic : descriptive analyses of consultations over eight years ; et, Missed appointments in an outpatient clinic for adolescents, an approache to predict the risk of missing

Rapport de synthèse: Les rendez-vous manqués représentent un problème important, tant du point de vue de la santé des patients que du point de vue économique. Pourtant peu d'études se sont penchées sur le sujet, particulièrement dans une population d'adolescents. Les buts de cette étude étaient de caractériser les adolescents qui sont à risque de manquer ou d'annuler leurs rendez-vous dans une clinique ambulatoire de santé pour adolescents, de comparer les taux des rendez-vous manqués et annulés entre les différents intervenants et d'estimer l'efficacité d'une politique de taxation des rendez-vous manqués non excusés. Finalement, un modèle multi-niveau markovien a été utilisé afin de prédire le risque de manquer un rendez-vous. Ce modèle tient compte du passé de l'adolescent en matière de rendez-vous manqués et d'autres covariables et permet de grouper les individus ayant un comportement semblable. On peut ensuite prédire pour chaque groupe le risque de manquer ou annuler et les covariables influençant significativement ce risque. Entre 1999 et 2006, 32816 rendez-vous fixés pour 3577 patients âgés de 12 à 20 ans ont été analysés. Le taux de rendez-vous manqués était de 11.8%, alors que 10.9% avaient été annulés. Soixante pour cent des patients n'ont pas manqué un seul de leur rendezvous et 14% en ont manqué plus de 25%. Nous avons pu mettre en évidence plusieurs variables associées de manière statistiquement significative avec les taux de rendez-vous manqués et d'annulations (genre, âge, heure, jour de la semaine, intervenant thérapeutique). Le comportement des filles peut être catégorisé en 2 groupes. Le premier groupe inclut les diagnostiques psychiatriques et de trouble du comportement alimentaire, le risque de manquer dans ce groupe étant faible et associé au fait d'avoir précédemment manqué un rendez-vous et au délai du rendez-vous. Les autres diagnostiques chez les filles sont associés à un second groupe qui montre un risque plus élevé de manquer un rendez-vous et qui est associé à l'intervenant, au fait d'avoir précédemment manqué ou annulé le dernier rendez-vous et au délai du rendez-vous. Les garçons ont tous globalement un comportement similaire concernant les rendez-vous manqués. Le diagnostic au sein de ce groupe influence le risque de manquer, tout comme le fait d'avoir précédemment manqué ou annulé un rendez-vous, le délai du rendez-vous et l'âge du patient. L'introduction de la politique de taxation des rendez-vous non excusés n'a pas montré de différence significative des tàux de rendez-vous manqués, cependant cette mesure a permis une augmentation du taux d'annulations. En conclusion, les taux de présence des adolescents à leurs rendez-vous sont dépendants de facteurs divers. Et, même si les adolescents sont une population à risque concernant les rendez-vous manqués, la majorité d'entre eux ne manquent aucun de leurs rendez-vous, ceci étant vrai pour les deux sexes. Etudier les rendez-vous manqués et les adolescents qui sont à risque de rater leur rendez-vous est un pas nécessaire vers le contrôle de ce phénomène. Par ailleurs, les moyens de contrôle concernant les rendez-vous manqués devraient cibler les patients ayant déjà manqué un rendez-vous. La taxation des rendez-vous manqués permet d'augmenter les rendez-vous annulés, ce qui a l'avantage de permettre de fixer un nouveau rendez-vous et, de ce fait, d'améliorer la continuité des soins.

Machine learning algorithms for spatial data. Case studies: Environmental pollution, natural hazards, renewable resources

This paper presents general problems and approaches for the spatial data analysis using machine learning algorithms. Machine learning is a very powerful approach to adaptive data analysis, modelling and visualisation. The key feature of the machine learning algorithms is that they learn from empirical data and can be used in cases when the modelled environmental phenomena are hidden, nonlinear, noisy and highly variable in space and in time. Most of the machines learning algorithms are universal and adaptive modelling tools developed to solve basic problems of learning from data: classification/pattern recognition, regression/mapping and probability density modelling. In the present report some of the widely used machine learning algorithms, namely artificial neural networks (ANN) of different architectures and Support Vector Machines (SVM), are adapted to the problems of the analysis and modelling of geo-spatial data. Machine learning algorithms have an important advantage over traditional models of spatial statistics when problems are considered in a high dimensional geo-feature spaces, when the dimension of space exceeds 5. Such features are usually generated, for example, from digital elevation models, remote sensing images, etc. An important extension of models concerns considering of real space constrains like geomorphology, networks, and other natural structures. Recent developments in semi-supervised learning can improve modelling of environmental phenomena taking into account on geo-manifolds. An important part of the study deals with the analysis of relevant variables and models' inputs. This problem is approached by using different feature selection/feature extraction nonlinear tools. To demonstrate the application of machine learning algorithms several interesting case studies are considered: digital soil mapping using SVM, automatic mapping of soil and water system pollution using ANN; natural hazards risk analysis (avalanches, landslides), assessments of renewable resources (wind fields) with SVM and ANN models, etc. The dimensionality of spaces considered varies from 2 to more than 30. Figures 1, 2, 3 demonstrate some results of the studies and their outputs. Finally, the results of environmental mapping are discussed and compared with traditional models of geostatistics.

Missed appointments in an adolescent outpatient clinic: descriptive analyses of consultations over 8 years.

Missed appointments represent an important medical and economical issue. Few studies on the subject are reported in the literature, particularly regarding adolescents. Our aim was to characterize missed and cancelled appointments in a multidisciplinary outpatient clinic for adolescents, to assess the effectiveness of a policy aimed at reducing missed appointments by introducing payment for those missed appointments not cancelled in advance, and to compare the rates between staff and resident physicians. A total of 32,816 consultations (representing 35 patients aged 12-20 years, 82.4% females) between 1999 and 200 were analysed. The missed appointment rate was 11.8% whilst another 10.9% were cancellations. Females cancelled more than males (11.3% vs. 8.4%, AOR 1.31, 99% CI 1.08-1.59), but there was no difference for missed appointments (11.6% vs. 12.3%, AOR 0.88, 99% CI 0.61-1.08). April and June to October (vacation months) were associated with more missed appointments. Globally mornings had higher rates of missed appointments than afternoons (13.6% vs. 11.2%, AOR 1.25, 99% CI 1.11-1.40). There was a slight difference in missed appointment rates between staff physicians and residents (10.4%; 11.8%, AOR 1.20, 99% CI 1.08-1.33). Missed appointment rates before and after the new policy on missed appointments were similar (1999-2003: 11.9%; 2004-2006: 11.6%, AOR 0.96, 99% CI 0.83-1.10). Conversely, cancellation rates increased from 8.4% (1999-2003) to 14.5% (2004-2006) (AOR 1.83, 99% CI 1.63-2.05). Attendance rates among adolescents show variations depending on vacation and school hours. Being attentive to these factors could help prevent missed appointments. Although having to pay for missed appointments does not increase attendance, it increases cancellations with the advantage that the appointment can be rescheduled.

Selecting control genes for RT-QPCR using public microarray data.

Background: Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely used techniques for expression profiling of selected genes. In order to obtain results that are comparable across assays, a stable normalization strategy is required. In general, the normalization of PCR measurements between different samples uses one to several control genes (e. g. housekeeping genes), from which a baseline reference level is constructed. Thus, the choice of the control genes is of utmost importance, yet there is not a generally accepted standard technique for screening a large number of candidates and identifying the best ones. Results: We propose a novel approach for scoring and ranking candidate genes for their suitability as control genes. Our approach relies on publicly available microarray data and allows the combination of multiple data sets originating from different platforms and/or representing different pathologies. The use of microarray data allows the screening of tens of thousands of genes, producing very comprehensive lists of candidates. We also provide two lists of candidate control genes: one which is breast cancer-specific and one with more general applicability. Two genes from the breast cancer list which had not been previously used as control genes are identified and validated by RT-QPCR. Open source R functions are available at http://www.isrec.isb-sib.ch/similar to vpopovic/research/ Conclusion: We proposed a new method for identifying candidate control genes for RT-QPCR which was able to rank thousands of genes according to some predefined suitability criteria and we applied it to the case of breast cancer. We also empirically showed that translating the results from microarray to PCR platform was achievable.

HIV and STI surveillance in Northern Ireland 2010: An analysis of data for the calendar year 2009

This annual analysis of data provides an overview of HIV and STI epidemiology in Northern Ireland for the calendar year 2009. Information from a variety of sources is collated and analysed in detail, while any evident trends over time are highlightedwithgraphs and tables. As well as a general summary of STI diagnoses and a number of overall conclusions, the report looks specifically at each of the following STIs: chlamydia, gonorrhoea, genital herpes, genital warts, syphilis, lymphogranuloma venereum (LGV) and HIV.