Data quality in European primary care research databases. Report of a workshop held in London September 2013

Primary care research databases provide a significant resource for health services and epidemiological research. However since data are recorded primarily for clinical care their suitability for research may vary widely according to the research application or recording practices of individual general practitioners. A methodological approach for characterising data quality is required. We describe a one-day workshop entitled “Towards a common protocol for measuring and monitoring data quality in European primary care research databases”. Researchers, database experts and clinicians were invited to give their perspectives on data quality and to exchange ideas on what data quality metrics should be made available to researchers. We report the main outcomes of this workshop, including a summary of the presentations and discussions and suggested way forward

A pragmatic approach for measuring data quality in primary care databases

There is currently no widely recognised methodology for undertaking data quality assessment in electronic health records used for research. In an attempt to address this, we have developed a protocol for measuring and monitoring data quality in primary care research databases, whereby practice-based data quality measures are tailored to the intended use of the data. Our approach was informed by an in-depth investigation of aspects of data quality in the Clinical Practice Research Datalink Gold database and presentations of the results to data users. Although based on a primary care database, much of our proposed approach would be equally applicable to other health care databases

Il Palazzo delle Liberta

Boggon was invited to participate in the exhibition ‘Il Palazzo delle Liberata’ Palazzo delle Papesse, Centro Arte Contemporanea, Siena, Italy by the curator Lorenzo Fusi. Artists were initially invited to visit the museum, a former Renaissance Palace, and to submit a proposal. Of particular interest to Boggon was the discovery that the astronomer Galileo had held secret meetings there. Research included visits to the Galileo Museum in Florence and information gathering about many other Scientists and Astronomers who had faced adversity and persecution in their quest for knowledge and truth. In the development of ‘Advesus Solemn ne Loquitor’ (made of books, mirror, model figure, marble) Boggon collected relevant second-hand books and created a ‘book periscope’ by hollowing out the interior of each book and stacking them on top of each other. The books were positioned against a blocked out window on a new marble shelf. When looking through the base of the periscope the interior scene is that of a corridor through the cut pages to a figure at the end and the Sienna sky, with a small hole bored through the artificial wall at the top rear of the periscope

Enclosure

As the first female artists-in-residence at Eton College, Liane Lang and Güler Ates decided to mark the historic occasion by inviting Flora Fairbairn to co-curate an exhibition of women artists in the Drawing Schools Gallery. The exhibition takes its title, FROWARD, from the 13th century word for ‘disposed to disobedience and opposition’, a school report criticism, but also a vital quality in people who wish to move society in a new direction. Anna Boggon's sculpture 'Enclosure' was included in this group exhibition, along with work by Alice Anderson, Güler Ates, Aideen Barry, Eileen Cooper, Liane Lang, Kate MccGwire, Veronica Smirnoff & Kate Terry. The artists were selected for their diverse range of artistic practices, which, brought together, created a thought-provoking insight into the contemporary art scene in Britain

Single-cell patterning and characterisation of antibiotic persistent bacteria using bio-sCAPA

In microbiology, accessing single-cell information within large populations is pivotal. Here we introduce bio-sCAPA, a technique for patterning bacterial cells in defined geometric arrangements and monitoring their growth in various nutrient environments. We demonstrate bio-sCAPA with a study of subpopulations of antibiotic-tolerant bacteria, known as persister cells, which can survive exposure to high doses of antibiotics despite lacking any genetic resistance to the drug. Persister cells are associated with chronic and relapsing infections, yet are difficult to study due in part to a lack of scalable, single-cell characterisation methods. As >10$^{5}$ cells can be patterned on each template, and multiple templates can be patterned in parallel, bio-sCAPA allows for very rare population phenotypes to be monitored with single-cell precision across various environmental conditions. Using bio-sCAPA, we analysed the phenotypic characteristics of single Staphylococcus aureus cells tolerant to flucloxacillin and rifampicin killing. We find that antibiotic-tolerant S. aureus cells do not display significant heterogeneity in growth rate and are instead characterised by prolonged lag-time phenotypes alone

Structural studies of cerebral cavernous malformations 2 (CCM2) reveal a folded helical domain at its C-terminus

AbstractCerebral cavernous malformations (CCM) are neurovascular dysplasias affecting up to 0.5% of the population. Mutations in the CCM2 gene are associated with acquisition of CCM. We identify a previously uncharacterized domain at the C-terminus of CCM2 and determine its 1.9Å resolution crystal structure. Because this domain is structurally homologous to the N-terminal domain of harmonin, we name it the CCM2 harmonin-homology domain or HHD. CCM2 HHD is observed in two conformations, and we employ analytical ultracentrifugation to test its oligomerization. Additionally, CCM2 HHD contains an unusually long 13-residue 310 helix. This study provides the first structural characterization of CCM2.Structured summary of protein interactionsCCM2 binds to CCM3 by pull down (View interaction)CCM2 and CCM2 bind by X-ray crystallography (View interaction)CCM2 and CCM2 bind by molecular sieving (View interaction

Molecular Basis for Integrin Adhesion Receptor Binding to p21-activated kinase 4 (PAK4)

Integrin adhesion receptors provide links between extracellular ligands and cytoplasmic signaling. Multiple kinases have been found to directly engage with integrin β tails, but the molecular basis for these interactions remain unknown. Here, we assess the interaction between the kinase domain of p21-activated kinase 4 (PAK4) and the cytoplasmic tail of integrin β5. We determine three crystal structures of PAK4-β5 integrin complexes and identify the PAK-binding site. This is a region in the membrane-proximal half of the β5 tail and confirmed by site-directed mutagenesis. The β5 tail engages the kinase substrate-binding groove and positions the non-phosphorylatable integrin residue Glu767 at the phosphoacceptor site. Consistent with this, integrin β5 is poorly phosphorylated by PAK4, and in keeping with its ability to occlude the substrate-binding site, weakly inhibits kinase activity. These findings demonstrate the molecular basis for β5 integrin-PAK4 interactions but suggest modifications in understanding the potential cellular role of this interaction

BIM Mediates EGFR Tyrosine Kinase Inhibitor-Induced Apoptosis in Lung Cancers with Oncogenic EGFR Mutations

Background: Epidermal growth factor receptor (EGFR) mutations are present in the majority of patients with non-small cell lung cancer (NSCLC) responsive to the EGFR tyrosine kinase inhibitors (TKIs) gefitinib or erlotinib. These EGFR-dependent tumors eventually become TKI resistant, and the common secondary T790M mutation accounts for half the tumors with acquired resistance to gefitinib. However, the key proapoptotic proteins involved in TKI-induced cell death and other secondary mutations involved in resistance remain unclear. The objective of this study was to identify the mechanism of EGFR TKI-induced apoptosis and secondary resistant mutations that affect this process. Methods and Findings: To study TKI-induced cell death and mechanisms of resistance, we used lung cancer cell lines (with or without EGFR mutations), Ba/F3 cells stably transfected with EGFR mutation constructs, and tumor samples from a gefitinib-resistant patient. Here we show that up-regulation of the BH3-only polypeptide BIM (also known as BCL2-like 11) correlated with gefitinib-induced apoptosis in gefitinib-sensitive EGFR-mutant lung cancer cells. The T790M mutation blocked gefitinib-induced up-regulation of BIM and apoptosis. This blockade was overcome by the irreversible TKI CL-387,785. Knockdown of BIM by small interfering RNA was able to attenuate apoptosis induced by EGFR TKIs. Furthermore, from a gefitinib-resistant patient carrying the activating L858R mutation, we identified a novel secondary resistant mutation, L747S in cis to the activating mutation, which attenuated the up-regulation of BIM and reduced apoptosis. Conclusions: Our results provide evidence that BIM is involved in TKI-induced apoptosis in sensitive EGFRmutant cells and that both attenuation of the up-regulation of BIM and resistance to gefitinibinduced apoptosis are seen in models that contain the common EGFR T790M and the novel L747S secondary resistance mutations. These findings also suggest that induction of BIM may have a role in the treatment of TKI-resistant tumors

Methods and measures for investigating microscale motility

Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile organisms and answer the intertwining biological and physical questions of how these diverse lifeforms navigate their surroundings. Herein, we give an overview of different experimental, analytical, and mathematical methods used to study a suite of microscale motility mechanisms across different scales encompassing molecular-, individual- to population-level. We identify transferable techniques, pressing challenges, and future directions in the field. This review can serve as a starting point for researchers who are interested in exploring and quantifying the movements of organisms in the microscale world.Comment: 24 pages, 2 figure