Data mining of gene arrays for biomarkers of survival in ovarian cancer

The expected five-year survival rate from a stage III ovarian cancer diagnosis is a mere 22%; this applies to the 7000 new cases diagnosed yearly in the UK. Stratification of patients with this heterogeneous disease, based on active molecular pathways, would aid a targeted treatment improving the prognosis for many cases. While hundreds of genes have been associated with ovarian cancer, few have yet been verified by peer research for clinical significance. Here, a meta-analysis approach was applied to two care fully selected gene expression microarray datasets. Artificial neural networks, Cox univariate survival analyses and T-tests identified genes whose expression was consistently and significantly associated with patient survival. The rigor of this experimental design increases confidence in the genes found to be of interest. A list of 56 genes were distilled from a potential 37,000 to be significantly related to survival in both datasets with a FDR of 1.39859 × 10−11, the identities of which both verify genes already implicated with this disease and provide novel genes and pathways to pursue. Further investigation and validation of these may lead to clinical insights and have potential to predict a patient’s response to treatment or be used as a novel target for therapy

SCREENING FOR HEPATITIS C Response from Hepatitis C Trust, BASL, BIA, BVHG, BSG, and BHIVA to article asking whether widespread screening for hepatitis C is justified

This is the peer reviewed published version of the following article: Response from Hepatitis C Trust, BASL, BIA, BVHG, BSG, and BHIVA to article asking whether widespread screening for hepatitis C is justified, which has been published in final form at 10.1136/bmj.h998. This article may be used for non-commercial purposes in accordance with BMJ's Terms and Conditions for Self-Archiving.This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/ by/4.0

Diffeomorphic Demons using Normalised Mutual Information, Evaluation on Multi-Modal Brain MR Images

The demons algorithm is a fast non-parametric non-rigid registration method. In recent years great efforts have been made to improve the approach; the state of the art version yields symmetric inverse-consistent large-deformation diffeomorphisms. However, only limited work has explored inter-modal similarity metrics, with no practical evaluation on multi-modality data. We present a diffeomorphic demons implementation using the analytical gradient of Normalised Mutual Information (NMI) in a conjugate gradient optimiser. We report the first qualitative and quantitative assessment of the demons for inter-modal registration. Experiments to spatially normalise real MR images, and to recover simulated deformation fields, demonstrate (i) similar accuracy from NMI-demons and classical demons when the latter may be used, and (ii) similar accuracy for NMI-demons on T1w-T1w and T1w-T2w registration, demonstrating its potential in multi-modal scenarios

Risk assessment in mental health: introducing a traffic light system in a community mental health team.

AIMS: To reports a study in which action research approach was utilised to introduce a new system of risk assessment, based on traffic lights, into a community mental health team. BACKGROUND: Risk management is a serious concern in community mental healthcare where there is less direct, real-time supervision of clients than in other settings, and because inadequate management of risk can have fatal consequences when service users are a risk to themselves and/or others. DESIGN: An action research design was undertaken, using three phases of Look, Think and Act. METHODS: Data were collected between January and March of 2012. In the action research phases, qualitative data were collected in focus groups with the team's multi-disciplinary mental health professionals. Data were transcribed verbatim and analysed thematically, which involved agreement of themes and interpretations by two researchers. The Look, Think and Act phases guided the development of the project; team members worked collaboratively on the traffic light system, implemented and evaluated it. FINDINGS: Themes were constructed that were discussed across the focus groups. These themes were: Ease of use; Risk identification and management; Legal status; Different teams' views of risk; Post-implementation evaluation. CONCLUSION: Action research has been used to implement change in mental health risk management. Others internationally would benefit from considering a Traffic Light System, and in using action research to implement it

Do Institutional Structures Matter? A Comparative Analysis of Urban Carbon Management Policies in the UK and Germany

The paper addresses the important question of how institutional structures matter to the delivery of climate change policy for urban transport. It examines the strategic goals, policy tools in operation and initial progress towards carbon emission reduction in seven cities across the UK and Germany where different institutional structures exist. The UK has the presence of a strong national carbon target and strong hierarchical national-local government relationships whilst Germany has a more integrated system of local transport provision in a context where local and regional government is stronger. Our findings show that the carbon agenda has made very little difference to what is happening on the ground in the cities. Across all sites, progress is being made but largely through technological improvements which are being almost completely offset by population growth. Even in the more integrated city environments there has not be an additional stimulus to manage the demand for travel. Contrary to previous research therefore, we cannot conclude that institutional structures are paramount in delivering effective carbon reduction policies. The institutional structures in the UK and in Germany are not perfectly aligned to carbon management but, given the cross policy impacts of most transport interventions, this is perhaps inevitable. We can clearly conclude however that “better” structures are not sufficient to achieve the implementation of more effective carbon policies. Whilst institutional structures must matter, it is the broader governance environment and the resources and politics involved in transport policy that seem to dominate the importance of the carbon agenda and implementation paths that emerge

Quantitative X-ray microradiography for high-throughput phenotyping of osteoarthritis in mice

Objective To investigate and validate digital X-ray microradiography as a novel, high-throughput and cost-effective screening approach to identify abnormal joint phenotypes in mice. Method Digital X-ray microradiography was used to quantify the subchondral bone mineral content (BMC) in the medial tibial plateau. Accuracy and reproducibility of the method were determined in 22 samples from C57BL/6(B6Brd;B6Dnk;B6N-Tyrc-Brd) wild-type mice. The method was then validated in wild-type mice that had undergone surgical destabilisation of medial meniscus (DMM) and in a genetically modified mouse strain with an established increase in trabecular bone mass. Results The measurement of subchondral BMC by digital X-ray microradiography had a coefficient of variation of 3.6%. Digital X-ray microradiography was able to demonstrate significantly increased subchondral BMC in the medial tibial plateau of male mice 4 and 8 weeks after DMM surgery and in female mice 8 weeks after surgery. Furthermore, digital X-ray microradiography also detected the increase in subchondral BMC in a genetically modified mouse strain with high trabecular bone mass. Conclusion Quantitation of subchondral BMC by digital X-ray microradiography is a rapid, sensitive and cost-effective method to identify abnormal joint phenotypes in mice of both genders at several ages

Regenerative-Relational Tritangtu: Sundanese Triadic Transformation Model

 Tritangtu atau pola pikir tritunggal merupakan kosmologi masyarakat Sunda dan Minang yang terdiri dari tiga entitas (pola tiga). Tritangtu sebagai kearifan lokal juga melatarbelakangi struktur mental pelaku kreatif dalam membuat karya baik berupa pertunjukan, nilai filosofi artefak mau- pun produk budaya lainnya di masyarakat Indonesia. Penelitian ini menggunakan metode etnografi dengan teknik pengumpulan data observasi partisipasi, wawancara mendalam dan dokumentasi. Obyek penelitian ini adalah praktik pelaku kreatif di bidang desain di Bandung. Hasil penelitian ini menunjukkan adanya transformasi tritangtu Sunda dari struktur yang tetap menjadi struktur dinamis. Perubahan struktur ini ditentukan oleh relasi antar struktur pembentuk unsur desain de- ngan segmentasi pasar global. Peminjaman penanda identitas Sunda khususnya budaya rakyat atau tradisi masa lalu merupakan upaya regeneratif dalam usahanya untuk harmonisasi pola tiga dalam menghadapi dan memenangkan persaingan pasar bebas di Indonesia.

Leaf energy balance modelling as a tool to infer habitat preference in the early angiosperms

Despite more than a century of research, some key aspects of habitat preference and ecology of the earliest angiosperms remain poorly constrained. Proposed growth ecology has varied from opportunistic weedy species growing in full sun to slow-growing species limited to the shaded understorey of gymnosperm forests. Evidence suggests that the earliest angiosperms possessed low transpiration rates: gas exchange rates for extant basal angiosperms are low, as are the reconstructed gas exchange rates for the oldest known angiosperm leaf fossils. Leaves with low transpirational capacity are vulnerable to overheating in full sun, favouring the hypothesis that early angiosperms were limited to the shaded understorey. Here, modelled leaf temperatures are used to examine the thermal tolerance of some of the earliest angiosperms. Our results indicate that small leaf size could have mitigated the low transpirational cooling capacity of many early angiosperms, enabling many species to survive in full sun. We propose that during the earliest phases of the angiosperm leaf record, angiosperms may not have been limited to the understorey, and that some species were able to compete with ferns and gymnosperms in both shaded and sunny habitats, especially in the absence of competition from more rapidly growing and transpiring advanced lineages of angiosperms