Development and application of a microarray meter tool to optimize microarray experiments

<p>Abstract</p> <p>Background</p> <p>Successful microarray experimentation requires a complex interplay between the slide chemistry, the printing pins, the nucleic acid probes and targets, and the hybridization milieu. Optimization of these parameters and a careful evaluation of emerging slide chemistries are a prerequisite to any large scale array fabrication effort. We have developed a 'microarray meter' tool which assesses the inherent variations associated with microarray measurement prior to embarking on large scale projects.</p> <p>Findings</p> <p>The microarray meter consists of nucleic acid targets (reference and dynamic range control) and probe components. Different plate designs containing identical probe material were formulated to accommodate different robotic and pin designs. We examined the variability in probe quality and quantity (as judged by the amount of DNA printed and remaining post-hybridization) using three robots equipped with capillary printing pins.</p> <p>Discussion</p> <p>The generation of microarray data with minimal variation requires consistent quality control of the (DNA microarray) manufacturing and experimental processes. Spot reproducibility is a measure primarily of the variations associated with printing. The microarray meter assesses array quality by measuring the DNA content for every feature. It provides a post-hybridization analysis of array quality by scoring probe performance using three metrics, a) a measure of variability in the signal intensities, b) a measure of the signal dynamic range and c) a measure of variability of the spot morphologies.</p

Symptom-based stratification of patients with primary Sjögren's syndrome: multi-dimensional characterisation of international observational cohorts and reanalyses of randomised clinical trials

Background Heterogeneity is a major obstacle to developing effective treatments for patients with primary Sjögren's syndrome. We aimed to develop a robust method for stratification, exploiting heterogeneity in patient-reported symptoms, and to relate these differences to pathobiology and therapeutic response. Methods We did hierarchical cluster analysis using five common symptoms associated with primary Sjögren's syndrome (pain, fatigue, dryness, anxiety, and depression), followed by multinomial logistic regression to identify subgroups in the UK Primary Sjögren's Syndrome Registry (UKPSSR). We assessed clinical and biological differences between these subgroups, including transcriptional differences in peripheral blood. Patients from two independent validation cohorts in Norway and France were used to confirm patient stratification. Data from two phase 3 clinical trials were similarly stratified to assess the differences between subgroups in treatment response to hydroxychloroquine and rituximab. Findings In the UKPSSR cohort (n=608), we identified four subgroups: Low symptom burden (LSB), high symptom burden (HSB), dryness dominant with fatigue (DDF), and pain dominant with fatigue (PDF). Significant differences in peripheral blood lymphocyte counts, anti-SSA and anti-SSB antibody positivity, as well as serum IgG, κ-free light chain, β2-microglobulin, and CXCL13 concentrations were observed between these subgroups, along with differentially expressed transcriptomic modules in peripheral blood. Similar findings were observed in the independent validation cohorts (n=396). Reanalysis of trial data stratifying patients into these subgroups suggested a treatment effect with hydroxychloroquine in the HSB subgroup and with rituximab in the DDF subgroup compared with placebo. Interpretation Stratification on the basis of patient-reported symptoms of patients with primary Sjögren's syndrome revealed distinct pathobiological endotypes with distinct responses to immunomodulatory treatments. Our data have important implications for clinical management, trial design, and therapeutic development. Similar stratification approaches might be useful for patients with other chronic immune-mediated diseases. Funding UK Medical Research Council, British Sjogren's Syndrome Association, French Ministry of Health, Arthritis Research UK, Foundation for Research in Rheumatology

How adolescents experience the rhythmic gymnastics community in the Oslo region: Identity and relative poverty

This master’s thesis aims to obtain an in-depth understanding of adolescents’ experience in the rhythmic gymnastics community in the Oslo region, with a specific focus on their identities and to what extent, if any, they experience relative poverty. To date, research on the rhythmic gymnastics community, within a hermeneutical paradigm, appears to be minimal and this project hopes to contribute to filling this gap. The project is based on previous research from various fields and uses insights from theorists such as Zygmunt Bauman and Anthony Giddens and also takes into account my own experience from within the community. Ten semi-structured interviews were conducted. The participants were all female adolescents, with varying levels of performance, time spent in the sport and most trained approximately 12 to 15 hours per week. Through the analysis and interpretation of the generated data I found that they all identified as a gymnast at some point in their career, and the sport seemed to be an important part of their lives. Relative poverty did not appear to be a direct issue, however, consumption, brand awareness and comparing items were seemingly a pronounced feature in the community

Organising, providing and evaluating technical training for early career researchers: a case study

This paper considers the importance of providing technical training opportunities for Early Career Researchers (ECRs) worldwide through the case study of a MATLAB training programme, which was proposed, organised, managed and evaluated by a team of five ECRs at the University of Southampton. The effectiveness of the programme in terms of the improvement in technical competency and the encouragement of interdisciplinary collaboration between the ECRs receiving this training was evaluated using measures relating to levels 1 (Reaction), 2 (Learning) and 3 (Behaviour) of the Rugby Team Impact Framework evaluation model. Overall reaction to the training course was extremely positive and data from pre- and post-course surveys suggest a positive change in the long-term behaviour of delegates. The ECRs who organised this project gained valuable experience in team working, grant writing, project management and the development of teaching materials. Details of the organisation and evaluation of the course are presented.<br/

An economic survey of the Pacific area.

"Designed to supplement and bring up to date the key sections of the Economic handbook of the Pacific area, published by the Institute of Pacific relations in 1934."--pt. I, p. V.Frederick V. Field, general editor, pt. I-II.Parts I and III are also included in the I. P. R. inquiry series.Maps on lining-papers, pt. I-II.pt. I. Population and land utilization, by K. J. Pelzer.--pt. II. Transportation, by Katrine R. C. Greene. Foreign trade, by J. D. Phillips.--pt. III. Industrialization of the western Pacific, by Kate L. Mitchell.Mode of access: Internet

Minimum Information about an Uncultivated Virus Genome (MIUViG)

International audienceWe present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere