Two new rapid SNP-typing methods for classifying Mycobacterium tuberculosis complex into the main phylogenetic lineages

There is increasing evidence that strain variation in Mycobacterium tuberculosis complex (MTBC) might influence the outcome of tuberculosis infection and disease. To assess genotype-phenotype associations, phylogenetically robust molecular markers and appropriate genotyping tools are required. Most current genotyping methods for MTBC are based on mobile or repetitive DNA elements. Because these elements are prone to convergent evolution, the corresponding genotyping techniques are suboptimal for phylogenetic studies and strain classification. By contrast, single nucleotide polymorphisms (SNP) are ideal markers for classifying MTBC into phylogenetic lineages, as they exhibit very low degrees of homoplasy. In this study, we developed two complementary SNP-based genotyping methods to classify strains into the six main human-associated lineages of MTBC, the "Beijing" sublineage, and the clade comprising Mycobacterium bovis and Mycobacterium caprae. Phylogenetically informative SNPs were obtained from 22 MTBC whole-genome sequences. The first assay, referred to as MOL-PCR, is a ligation-dependent PCR with signal detection by fluorescent microspheres and a Luminex flow cytometer, which simultaneously interrogates eight SNPs. The second assay is based on six individual TaqMan real-time PCR assays for singleplex SNP-typing. We compared MOL-PCR and TaqMan results in two panels of clinical MTBC isolates. Both methods agreed fully when assigning 36 well-characterized strains into the main phylogenetic lineages. The sensitivity in allele-calling was 98.6% and 98.8% for MOL-PCR and TaqMan, respectively. Typing of an additional panel of 78 unknown clinical isolates revealed 99.2% and 100% sensitivity in allele-calling, respectively, and 100% agreement in lineage assignment between both methods. While MOL-PCR and TaqMan are both highly sensitive and specific, MOL-PCR is ideal for classification of isolates with no previous information, whereas TaqMan is faster for confirmation. Furthermore, both methods are rapid, flexible and comparably inexpensive.

iTRAQ identification of candidate serum biomarkers associated with metastatic progression of human prostate cancer

A major challenge in the management of patients with prostate cancer is identifying those individuals at risk of developing metastatic disease, as in most cases the disease will remain indolent. We analyzed pooled serum samples from 4 groups of patients (n = 5 samples/group), collected prospectively and actively monitored for a minimum of 5 yrs. Patients groups were (i) histological diagnosis of benign prostatic hyperplasia with no evidence of cancer 'BPH', (ii) localised cancer with no evidence of progression, 'non-progressing' (iii) localised cancer with evidence of biochemical progression, 'progressing', and (iv) bone metastasis at presentation 'metastatic'. Pooled samples were immuno-depleted of the 14 most highly abundant proteins and analysed using a 4-plex iTRAQ approach. Overall 122 proteins were identified and relatively quantified. Comparisons of progressing versus non-progressing groups identified the significant differential expression of 25 proteins (p<0.001). Comparisons of metastatic versus progressing groups identified the significant differential expression of 23 proteins. Mapping the differentially expressed proteins onto the prostate cancer progression pathway revealed the dysregulated expression of individual proteins, pairs of proteins and 'panels' of proteins to be associated with particular stages of disease development and progression. The median immunostaining intensity of eukaryotic translation elongation factor 1 alpha 1 (eEF1A1), one of the candidates identified, was significantly higher in osteoblasts in close proximity to metastatic tumour cells compared with osteoblasts in control bone (p = 0.0353, Mann Whitney U). Our proteomic approach has identified leads for potentially useful serum biomarkers associated with the metastatic progression of prostate cancer. The panels identified, including eEF1A1 warrant further investigation and validation.

Guidance for the preparation of neurological management guidelines by EFNS scientific task forces - revised recommendations 2012

This paper is meant to provide guidance to anyone wishing to write a neurological guideline for diagnosis or treatment, and is directed at the Scientist Panels and task forces of the European Federation of Neurological Societies (EFNS). It substitutes the previous guidance paper from 2004. It contains several new aspects: the guidance is now based on a change of the grading system for evidence and for the resulting recommendations, and has adopted The Grading of Recommendations, Assessment, Development and Evaluation system (GRADE). The process of grading the quality of evidence and strength of recommendations can now be improved and made more transparent. The task forces embarking on the development of a guideline must now make clearer and more transparent choices about outcomes considered most relevant when searching the literature and evaluating their findings. Thus, the outcomes chosen will be more critical, more patient-oriented and easier to translate into simple recommendations. This paper also provides updated practical recommendations for planning a guideline task force within the framework of the EFNS. Finally, this paper hopes to find the approval also by the relevant bodies of our future organization, the European Academy of Neurology.

Pancreatic carcinoma, pancreatitis, and healthy controls: metabolite models in a three-class diagnostic dilemma

Metabolomics as one of the most rapidly growing technologies in the "-omics" field denotes the comprehensive analysis of low molecular-weight compounds and their pathways. Cancer-specific alterations of the metabolome can be detected by high-throughput mass-spectrometric metabolite profiling and serve as a considerable source of new markers for the early differentiation of malignant diseases as well as their distinction from benign states. However, a comprehensive framework for the statistical evaluation of marker panels in a multi-class setting has not yet been established. We collected serum samples of 40 pancreatic carcinoma patients, 40 controls, and 23 pancreatitis patients according to standard protocols and generated amino acid profiles by routine mass-spectrometry. In an intrinsic three-class bioinformatic approach we compared these profiles, evaluated their selectivity and computed multi-marker panels combined with the conventional tumor marker CA 19-9. Additionally, we tested for non-inferiority and superiority to determine the diagnostic surplus value of our multi-metabolite marker panels. Compared to CA 19-9 alone, the combined amino acid-based metabolite panel had a superior selectivity for the discrimination of healthy controls, pancreatitis, and pancreatic carcinoma patients [Formula: see text] We combined highly standardized samples, a three-class study design, a high-throughput mass-spectrometric technique, and a comprehensive bioinformatic framework to identify metabolite panels selective for all three groups in a single approach. Our results suggest that metabolomic profiling necessitates appropriate evaluation strategies and-despite all its current limitations-can deliver marker panels with high selectivity even in multi-class settings.

Exogenous gonadotropins have little impact on follicular but considerable effect on serum cytokine concentrations – a comparison between Natural Cycle and stimulated IVF using a multiplexed assay platform

Introduction: Throughout follicular growth and subsequent corpus luteum formation the leukocyte number increases and follicular vascularisation changes. These processes are enhanced under exogenous stimulation with gonadotropins. Cytokines released by leukocytes contribute to further recruitment and vascularisation of the follicle, and they play an important role in regulating ovarian steroidogenesis by influencing theca and granulosa–lutein cell function. Changes in cytokine and vascular endothelial growth factor (VEGF) concentrations in the ovary as a consequence of gonadotropin stimulation may negatively influence oocyte quality. In this project we have compared the intrafollicular production of inflammatory cytokines and growth factors between natural IVF cycles (NC) and classical, gonadotropin-stimulated IVF cycles (gsIVF). Material and Methods: Serum on the day of oocyte retrieval and follicular fluid (FF) were collected in 37 NC and 39 gsIVF cycles. Thirteen women within this population underwent one NC and one gsIVF cycle each. A total of 14 cytokines from Bio-Plex panels I and II were determined in matched serum and FF samples using Luminex xMAP technology on the Bio-Plex(R) platform, using the serum protocol. Results: Tumour necrosis factor-alpha, RANTES, eotaxin and interferon-gamma-induced protein-10 levels were lower in FF than in serum, and thus not further investigated. Interleukin (IL)-6, -8, -10, -15, -18, monocyte chemotactic protein-1 (MCP-1), VEGF and leukaemia inhibitory factor (LIF) showed higher median concentrations in FF than in serum, indicating possible ovarian production. Moreover, most of these showed higher evels in the gsIVF than in the NC groups in the serum, but not in the follicular fluid. IL-8 was reduced in gsIVF cycles. Conclusion: The fact that serum but not FF levels of the studied cytokines were higher in the stimulated than in the natural cycles can be attributed to the increased number of active follicles present after controlled ovarian stimulation.

Drug eluting and bare metal stents in people with and without diabetes: collaborative network meta-analysis

Objective To compare the effectiveness and safety of three types of stents (sirolimus eluting, paclitaxel eluting, and bare metal) in people with and without diabetes mellitus. Design Collaborative network meta-analysis. Data sources Electronic databases (Medline, Embase, the Cochrane Central Register of Controlled Trials), relevant websites, reference lists, conference abstracts, reviews, book chapters, and proceedings of advisory panels for the US Food and Drug Administration. Manufacturers and trialists provided additional data. Review methods Network meta-analysis with a mixed treatment comparison method to combine direct within trial comparisons between stents with indirect evidence from other trials while maintaining randomisation. Overall mortality was the primary safety end point, target lesion revascularisation the effectiveness end point. Results 35 trials in 3852 people with diabetes and 10 947 people without diabetes contributed to the analyses. Inconsistency of the network was substantial for overall mortality in people with diabetes and seemed to be related to the duration of dual antiplatelet therapy (P value for interaction 0.02). Restricting the analysis to trials with a duration of dual antiplatelet therapy of six months or more, inconsistency was reduced considerably and hazard ratios for overall mortality were near one for all comparisons in people with diabetes: sirolimus eluting stents compared with bare metal stents 0.88 (95% credibility interval 0.55 to 1.30), paclitaxel eluting stents compared with bare metal stents 0.91 (0.60 to 1.38), and sirolimus eluting stents compared with paclitaxel eluting stents 0.95 (0.63 to 1.43). In people without diabetes, hazard ratios were unaffected by the restriction. Both drug eluting stents were associated with a decrease in revascularisation rates compared with bare metal stents in people both with and without diabetes. Conclusion In trials that specified a duration of dual antiplatelet therapy of six months or more after stent implantation, drug eluting stents seemed safe and effective in people both with and without diabetes.

[Swiss Research Agenda for Nursing (SRAN): the development of an agenda for clinical nursing research in Switzerland]

In many Anglo-Saxon and North European countries nursing research agendas have been developed to address priorities in nursing research in accordance with a nationally defined health policy. In Switzerland, due to lack of a nationwide governmental health policy, co-ordination of nursing research so far was scarce. The "Swiss Research Agenda for Nursing (SRAN)" project developed an agenda for clinical nursing research between 2005 and 2007. Based on literature reviews, expert panels and a national survey a project team formulated an agenda which passed a consensus conference. The agenda recommends aspects that should lead research and defines seven research priorities for nursing in Switzerland for the time between 2007 and 2017. Nursing research should prioritize to investigate 1) the effectiveness of nursing interventions; 2) the influences of service adaptations in a changing health care system; 3) the phenomena in patients requiring nursing care; 4) the influence of the work environment on the quality of nursing care; 5) the functioning of family and social systems; 6) varieties of life circumstances and their integration; and 7) the implementation of ethical principles in nursing. Written in German and French, the Swiss Research Agenda for Nursing for the first time formulates priorities for nursing research in Switzerland and can be used for strategic discussions. As a next step, the development of an action plan to enhance nursing research will take place in Switzerland.

Analysis of independent microarray datasets of renal biopsies identifies a robust transcript signature of acute allograft rejection

Transcriptomics could contribute significantly to the early and specific diagnosis of rejection episodes by defining 'molecular Banff' signatures. Recently, the description of pathogenesis-based transcript sets offered a new opportunity for objective and quantitative diagnosis. Generating high-quality transcript panels is thus critical to define high-performance diagnostic classifier. In this study, a comparative analysis was performed across four different microarray datasets of heterogeneous sample collections from two published clinical datasets and two own datasets including biopsies for clinical indication, and samples from nonhuman primates. We characterized a common transcriptional profile of 70 genes, defined as acute rejection transcript set (ARTS). ARTS expression is significantly up-regulated in all AR samples as compared with stable allografts or healthy kidneys, and strongly correlates with the severity of Banff AR types. Similarly, ARTS were tested as a classifier in a large collection of 143 independent biopsies recently published by the University of Alberta. Results demonstrate that the 'in silico' approach applied in this study is able to identify a robust and reliable molecular signature for AR, supporting a specific and sensitive molecular diagnostic approach for renal transplant monitoring.

Strategies to advance translational research into brain barriers

There is a paucity of therapies for most neurological disorders--from rare lysosomal storage diseases to major public health concerns such as stroke and Alzheimer's disease. Advances in the targeting of drugs to the CNS are essential for the future success of neurotherapeutics; however, the delivery of many potentially therapeutic and diagnostic compounds to specific areas of the brain is restricted by the blood-brain barrier, the blood-CSF barrier, or other specialised CNS barriers. These brain barriers are now recognised as a major obstacle to the treatment of most brain disorders. The challenge to deliver therapies to the CNS is formidable, and the solution will require concerted international efforts among academia, government, and industry. At a recent meeting of expert panels, essential and high-priority recommendations to propel brain barrier research forward in six topical areas were developed and these recommendations are presented here.

La philanthropie: alliée ou concurrente des politiques sociales étatiques (I, 1880-1945)

La philanthropie joue actuellement un rôle très important en Suisse. On estime que la moitié des personnes domiciliées en Suisse est active dans le champ d’action du bénévolat. Toutefois, cet objet d’études a longtemps été délaissé par les historiens. Ces deux panels viseront à rendre compte des recherches récentes en s’intéressant à la dimension comparative et transnationale de la philanthropie en Suisse de 1880 à nos jours. Deux dimensions seront privilégiées. D’une part, l’accent sera mis sur les rapports entre les associations philanthropiques privées et l’Etat social. Les études tendent le plus souvent à mettre l’accent sur l’opposition, dans le domaine social, entre activités de bienfaisance ou de bénévolat et les politiques publiques. Or, les relations entre ces deux pôles ne se résument pas à cette opposition et oscillent, selon les lieux et les périodes, entre coopération étroite et concurrence acharnée, à moins que ne s’instaure, comme cela semble le cas de la Suisse, une division du travail plus ou moins institutionnalisée. D’autre part, une attention toute particulière sera mise sur les jeux d’échelle. Les activités des associations philanthropiques couvrent des espaces géographiques très différents : certaines se concentrent sur un quartier urbain, d’autres se focalisent sur l’ensemble de la planète. Toutefois, nous postulons que cette spatialisation ne se confine pas à un antagonisme local/global. Bien au contraire, les différentes échelles – locale, nationale, globale ou transnationale – interagissent étroitement. Des contributions d’historiens étrangers permettront d’inscrire le cas suisse dans une perspective comparative.

Kinder ohne Zukunft? Kinder in Armut und Bildungsungleichheit in Ostdeutschland seit 1990

Im vorliegenden Beitrag werden Auswirkungen von Armut auf Bildungschancen von Kindern in Ostdeutschland untersucht. Die Mechanismen rationaler Bildungsentscheidungen werden auf der Ebene des Haushaltes, der Partnerschaftsbeziehung, der Eltern- Kind-Beziehung und der persönlichen Entwicklung des Kindes betrachtet. Neben den klassenspezifischen Bildungspräferenzen und der Einkommenslage des Haushaltes wird das mit der Bildung der Eltern verbundene kulturelle und soziale Kapital des Elternhauses berücksichtigt. Diese Ressourcen sind sowohl für Bildungsinvestitionen als auch für die Verarbeitung sozio- ökonomischer Deprivation relevant. Die empirischen Analysen basieren auf Daten des Sozio-ökonomischen Panels. Es wurde festgestellt, daß prekäre Einkommenslagen und Armut die Bildungschancen von Kindern beeinträchtigen. Werden andere sozio-kulturelle Ressourcen im Haushalt mobilisiert, können diese Beeinträchtigungen jedoch kompensiert werden. Dagegen haben - erwartungsgemäß - Kinder aus Elternhäusern mit ausreichendem ökonomischen, kulturellen und sozialen Kapital günstige Bildungschancen und wechseln eher auf das Gymnasium als Kinder mit ungünstigen Startchancen.

Bildung und Lebenserwartung in Deutschland

Aus der Lebensverlaufsperspektive wird Bildung als eine der wichtigsten Ursachenletten für sozial bedingte Ungleichheit von Lebenszeiten untersucht. Zum einen ist die Einführung der Schulpflicht mitverantwortlich für die Abnahme der Mortalitätsrisiken im frühen Lebenslauf. Zum anderen haben Humankapital, das über Ausbildung und Erwerbstätigkeit angeeignet wird, und das im Sozialisationsprozess vermittelte kulturelle Kapital zur Verschiebung von Mortalitätsrisiken ins höhere Alter beigetragen. Für die empirische Analyse werden Längsschnittdaten des Sozio-ökonomischen Panels und der deutschen Lebensverlaufsstudie verwendet. Mit einem Kohortenansatz und Verfahren der Ereignisanalyse wird für den Zeitraum von 1871 bis 1989 bei Kontrolle anderer sozialer Determinanten, insbesondere von sozialer Schicht, der Zusammenhand von Bildungsungleichheit und sozial ungleicher Lebensdauer beigetragen. Andererseits ist die Persistenz von intergenerationaler Bildungsvererbung und Ungleichheit von Bildungschancen mitverantwortlich für die Streuung von Lebenserwartung nach sozialen Schichten und Klassen.

Dynamik rationaler Bildungsentscheidungen im Familien- und Haushaltskontext. Eine empirische Untersuchung zum Bildungserfolg von ostdeutschen Jugendlichen in Armut

In der vorliegenden Studie wird der Frage nachgegangen, welche Auswirkungen Einkommensverluste und Armut auf den Bildungserfolg von ostdeutschen Jugendlichen haben. Aus einer lebensverlaufs- und handlungstheoretischen Perspektive wird ein dynamisches Mehrebenen-Modell entwickelt, um die Bedingungen und Kontexteffekte für rationale Bildungsentscheidungen aufzuzeigen. Demnach führt sozio-ökonomische Deprivation zu suboptimalen, risikoaversen Entscheidungen zugunsten kürzerer Schullaufbahnen und frühen Schulabschlüssen. Eltern mit einer ausreichenden Ausstattung mit ökonomischen und nicht-ökonomischen Ressourcen können jedoch ungünstige Auswirkungen von Arbeitslosigkeit und Armut verarbeiten und ihre Präferenzen für maximale Humankapitalinvestitionen aufrechterhalten. Für die empirischen Analysen werden Daten des Sozio-ökonomischen Panels (SOEP) herangezogen. Es bestätigte sich, daß ökonomisch benachteiligte, insbesondere arme Schüler auch beim Bildungserfolg benachteiligt sind. Familien können ökonomisch bedingte Nachteile in der Bildungskarriere ihrer Kinder teilweise durch die Mobilisierung ihres kulturellen und sozialen Kapitals ausgleichen. In Ostdeutschland bestehen Tendenzen für eine intergenerationale Transmission von Arbeitslosigkeits- und Armutsrisiken infolge mißlungener Schulausbildung von deprivierten Kindern und Jugendlichen.

Wohlfahrtsstaatsentwicklung und Lebenserwartung in Ost- und Westdeutschland

Im vorliegenden Beitrag wird die soziale Ungleichheit von Lebenserwartung in Deutschland untersucht. Es wird die These vertreten, daß der Wohlfahrtsstaat mit seinen institutionellen Vorgaben nicht nur zur Strukturierung von Lebensverläufen, sondern auch zur Verbesserung der individuellen Lebenserwartung beigetragen hat. Insbesondere die Durchsetzung der Schulpflicht und die Ausdehnung der Bildungsbeteiligung waren für diese demographische Entwicklung bedeutsam. Mit Hilfe von Längsschnittdaten des Sozio-ökonomischen Panels und der Lebensverlaufsstudie wurde gezeigt, daß sich die Lebensdauer von Männern und Frauen in der Generationenfolge erhöht hat. Während in der Bundesrepublik die Lebenszeiten zunahmen, verringerte sich in der DDR seit den 70er Jahren die Lebenserwartung. In Ostdeutschland hatten verheiratete Frauen geringere Mortalitätsrisiken als ledige Frauen. Wurden ostdeutsche Männer oder Frauen geschieden, stiegen ihre Sterbewahrscheinlichkeiten sprunghaft an. In der westdeutschen Population hatten insbesondere verwitwete Personen eine hohe Sterblichkeit. Bildung begünstigt die Lebensdauer. Mit zunehmendem Bildungsniveau sinkt das Risiko, vorzeitig zu sterben. Dieser Befund unterstreicht die Bedeutung des Wohlfahrtsstaates für Lebensverläufe und der Bildung als soziales und kulturelles Kapital.

Resolving Cl and SO4 Profiles in a Clay-Rich Rock Sequence

The chloride and sulfate concentration profiles in a 260 m thick clay-rich Mesozoic sediment sequence have been analyzed by various methods. Chloride data generally indicate a good consistency between different methods if anion exclusion is accounted for in leaching tests. For sulfate, however, there is an apparent inconsistency between leaching data and those obtained from the other methods, which points to the dissolution of a sulfur-bearing mineral. Traces of diagenetic gypsum seem to be a likely source, but other sulfur minerals cannot be ruled out.