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.

Review of governance and accountability mechanisms in the General Medical Services schemes

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Governance von Universitätsbibliotheken : Optimierungsmöglichkeiten aus institutioneller Sicht

Ausgangspunkt der Arbeit bildet die Beobachtung, dass Universitäts­biblio­theken unterschiedliche Aufgaben zu Händen verschiedener Akteure erfüllen - so nehmen Universitätsbibliotheken in der Schweiz häufig Aufgaben einer Kantonsbibliothek wahr. Universitätsbibliotheken zeichnen sich durch unterschiedliche Rechts- und Organisationsformen aus, unterhalten Beziehungen zu Dritten und sind deshalb verschiedenen Instanzen zur Rechenschaft verpflichtet. Sie sind, schliesslich, in Zusammenschlüsse unterschiedlicher Natur eingebunden. Vor diesem Hintergrund wirft die vorliegende Arbeit die Frage nach der Steuerung des Unternehmens Universitätsbibliothek auf. Anhand ausgewählter Fallbeispiele wird aufgezeigt, wie sich unterschiedliche Governance-Modelle gestalten. Dabei wird insbesondere auf die Rechts- und Organisationsform, auf institutionelle Strukturen, auf Steuerungsinstrumente (Auftrag und finanzielle Rahmenbedingungen), auf institutionelle Beziehungen sowie auf die Autonomie der Bibliothek eingegangen. Darauf auf­bau­end werden Vor- und Nachteile der Modelle hinsichtlich der Erfüllung des Doppelauftrags (Universitäts- und Kantonsbibliothek) diskutiert. Es zeigt sich, dass Universitäts- und Kantonsauftrag komplementäre Funktionen darstellen, wobei allerdings vereinzelt Schwierigkeiten auftreten können. Die Rechts- und Organisationsform sowie, insbesondere, die Trägerschaft bilden ein zentrales Element im Hinblick auf die Auftragserfüllung. Gleichzeitig sind auch weitere Elemente zentral, beispielsweise Instrumente, welche nicht nur die Aufgaben, sondern die Zuständigkeiten der beteiligten Akteure festhalten. Parmi les nombreuses fonctions remplies par les bibliothèques universitaires en Suisse, celle de bibliothèque cantonale est la plus fréquente. Les formes juridiques et/ou d'organisation des bibliothèques universitaires suisses sont multiples ; les bibliothèques entretiennent des liens avec des tiers et elles sont, par conséquent, tenues de rendre des comptes à diverses instances. Comme toutes les bibliothèques, elles s'intègrent, finalement, à des réseaux de nature différente. Dans ce contexte, le présent travail soulève la question de la gouvernance de la bibliothèque universitaire. Il décrit, à partir d'exemples choisis, différents modèles de gouvernance en s'intéressant surtout à la forme juridique et/ou d'organisation, aux structures institutionnelles, aux instruments de gouvernance concernant la mission et les conditions cadres financières de la bibliothèque, aux relations institutionnelles et à l'autonomie de la bibliothèque. L'analyse permet ainsi une réflexion sur les avantages et les inconvénients des différents modèles de gouvernance au vu de la double mission universitaire et cantonale des bibliothèques. Le présent travail montre que les fonctions universitaires et cantonales sont à priori complémentaires et ne donnent lieu qu'à des difficultés mineures. La forme juridique et/ou d'organisation ainsi que l'autorité de tutelle constituent des éléments déterminants pour l'accomplissement de la (double) mission de la bibliothèque. Parallèlement, d'autres éléments jouent également un rôle important - par exemple, les instruments permettant non seulement de régler les tâches de la bibliothèque, mais aussi de déterminer les compétences de tous les acteurs intéressés.

Framework for Corporate and Financial Governance for Agencies funded by the Department of Health and Children

Corporate governance is the system by which organisations direct and control their functions and relate to their stakeholders in order to manage their business, achieve their mission and objectives and meet the necessary standards of accountability, integrity and propriety. It is a key element in improving efficiency and accountability as well as enhancing openness and transparency. A significant element of the Governmentâ?Ts programme for health service reform is the strengthening of governance and accountability arrangements across the health system. Read the Report (PDF, 1mb)

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.

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.

Health Care Quality Indicators in the Irish Health System

  Public reporting of quality indicators promotes the principle of a transparent and accountable health care system that encourages a continuing focus on improving the quality of care it provides. This work brings us a step further in enhancing the quality and safety of our system. It is important that this report is not relied upon to draw conclusions on quality of care. That was not the purpose of the exercise. The data is mostly over five years old and was collected from the system before the improvements to collection and reporting of information that the hospitals were asked to put in place as part of the work to prepare this report. The Department of Health will produce a report of quality indicators based on data from 2011 to 2013 inclusive later in 2014 which will identify regions and hospitals. A governance process will shortly be established to oversee the selection and reporting of these indicators. This system will report at national and regional level and will be aligned with international systems so that international comparisons can be reported. The publication of this report is an important step in the development of this national reporting system. It shows that we can use a major IT system called HIPE which captures information on all hospital stays in all public hospitals to examine quality and safety of care. Health Care Quality Indicators in the Irish Health System

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.

Inca expansion and parasitism in the Lluta Valley: preliminary data

Assessing the impact of cultural change on parasitism has been a central goal in archaeoparasitology. The influence of civilization and the development of empires on parasitism has not been evaluated. Presented here is a preliminary analysis of the change in human parasitism associated with the Inca conquest of the Lluta Valley in Northern Chile. Changes in parasite prevalence are described. It can be seen that the change in life imposed on the inhabitants of the Lluta Valley by the Incas caused an increase in parasitism.