Consensus clustering and functional interpretation of gene-expression data

Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus clustering, which provides such an advantage. When coupled with a statistically based gene functional analysis, our method allowed the identification of novel genes regulated by NFκB and the unfolded protein response in certain B-cell lymphomas

Effect of Q-switched laser surface texturing of titanium on osteoblast cell response

Titanium and its alloys are important biomedical materials. It is known that the surface texture of implanted medical devices affects cell response. Control of cell response has the potential to enhance fixation of implants into bone and, in other applications, to prevent undesired cell adhesion. The potential use of a 100W Q-switched YAG laser miller (DMG Lasertec 60 HSC) for texturing titanium is investigated. A series of regular features with dimensions of the order of tens of micrometers are generated in the surface of titanium samples and the cell response to these features is determined. Characterisation of the laser milled features reveals features with a lengthscale of a few microns superposed on the larger scale structures, this is attributed to resolidification of molten droplets generated and propelled over the surface by individual laser pulses. The laser textured samples are exposed to osteoblast cells and it is seen that cells do respond to the features in the laser textured surfaces

Interacting dark matter contribution to the Galactic 511 keV gamma ray emission: constraining the morphology with INTEGRAL/SPI observations

We compare the full-sky morphology of the 511 keV gamma ray excess measured by the INTEGRAL/SPI experiment to predictions of models based on dark matter (DM) scatterings that produce low-energy positrons: either MeV-scale DM that annihilates directly into e+e- pairs, or heavy DM that inelastically scatters into an excited state (XDM) followed by decay into e+e- and the ground state.By direct comparison to the data, we find that such explanations are consistent with dark matter halo profiles predicted by numerical many-body simulations for a Milky Way-like galaxy. Our results favor an Einasto profile over the cuspier NFW distribution and exclude decaying dark matter scenarios whose predicted spatial distribution is too broad. We obtain a good fit to the shape of the signal using six fewer degrees of freedom than previous empirical fits to the 511 keV data. We find that the ratio of flux at Earth from the galactic bulge to that of the disk is between 1.9 and 2.4, taking into account that 73% of the disk contribution may be attributed to the beta decay of radioactive 26Al.Comment: 7 pages, 4 figures. Includes minor corrections, and a discussion of threshold energies in XDM models. Published in JCA

Dorset Adult Integrated Care Service (DAIRS): Service Evalaution

EXECUTIVE SUMMARY This early process evaluation of the newly established Dorset Adult Integrated Respiratory Service (DAIRS) in three localities in Dorset was conducted by Bournemouth University using a mixed-methods approach. Our evaluation showed staff commitment and enthusiasm for a pan-Dorset approach to respiratory care and a very positive acclaim from service users. Mindful of the fact that DAIRS had been in operation for four months only, the evaluation flags up strengths and issues of concern at the initial stages of service implementation. Discussion of the findings has been linked with current thinking to emerge in the White Paper from NHS Improving Quality around service improvement and change management (Bevan & Fairman, 2014). Given that DAIRS has been commissioned in the first instance for a period of two years, this early evaluation will be valuable for stakeholders to address the issues raised in a timely manner. Recommendations 1. Build upon the high levels of satisfaction to engage service user users more widely in the on-going development of DAIRS. 2. Shared documentation needs to be agreed and implemented as soon as possible, including the DAIRS card. 3. DAIRS should be officially launched with appropriate information for different stakeholders: service users, community staff and non-DAIRS hospital staff. 4. The change process should be actively managed; concerns and challenges expressed by participants should be acknowledged and a supportive environment provided for collaborative problem-solving. 5. Consider selection and use of grass roots ‘change champions’ across the sites and disciplines to facilitate a more inclusive model of organisational change. 6. Further integration between localities should be explored particularly around staff education, as well as to facilitate on-going peer support. 7. New staff would benefit from being supernumerary for their first month and visiting neighbouring DAIRS localities. 8. Inclusion and exclusion criteria need to be revisited to ensure a shared understanding amongst DAIRS staff, particularly around co-morbidities. 9. Information and service provision concerning emotional support for service users and carers needs to be reviewed. 10. The current Single Point of Access System (SPOA) should be reviewed to improve compliance. 11. Information Technology (IT) systems and possibilities for joint DAIRS systems should be explored. 12. Perceived financial inequities need to be addressed in service planning. 13. Our evaluation provides a base-line for future work, a further more comprehensive evaluation after two years of DAIRS operation is needed to inform future funding and service development. Suggested factors to include: • Outcome data • Cross-locality service user involvement (avoiding winter peak time), using systematic PREM questionnaire distribution processes. • Community staff perspectives. • Input from related respiratory services, currently not part of DAIRS. • Investigation of impact of a differing skill mix across localities. • More detailed service user feedback. • Evaluation of staff education (DAIRS and non-DAIRS)

Voltage dip generator for testing wind turbines connected to electrical networks

This paper describes a new voltage dip generator that allows the shape of the time profile of the voltage generated to be configured. The use of this device as a tool to test the fault ride-through capability of wind turbines connected to the electricity grid can provide some remarkable benefits: First, this system offers the possibility of adapting the main features of the time–voltage profile generated (dip depth, dip duration, the ramp slope during the recovery process after clearing fault, etc.) to the specific requirements set forth by the grid operation codes, in accordance with different network electrical systems standards. Second, another remarkable ability of this system is to provide sinusoidal voltage and current wave forms during the overall testing process without the presence of harmonic components. This is made possible by the absence of electronic converters. Finally, the paper includes results and a discussion on the experimental data obtained with the use of a reduced size laboratory prototype that was constructed to validate the operating features of this new device

Partial wave analysiss of pbar-p -> piminus-piplus, pizero-pizero, eta-eta and eta-etaprime

A partial wave analysis is presented of Crystal Barrel data on pbar-p -> pizero-pizero, eta-eta and eta-etaprime from 600 to 1940 MeV/c, combined with earlier data on d\sigma /d\Omega and P for pbar-p->piminus-piplus. The following s-channel I=0 resonances are identified: (i) J^{PC} = 5^{--} with mass and width (M,\Gamma) at (2295+-30,235^{+65}_{-40}) MeV, (ii) J^{PC} = 4^{++} at (2020+-12, 170+-15) MeV and (2300+-25, 270+-50) MeV, (iii) 3D3 JPC = 3^{--} at (1960+-15, 150+-25) MeV and (2210+-4$, 360+-55) MeV, and a 3G3 state at (2300 ^{+50}_{-80}, 340+-150) MeV, (iv) JPC = 2^{++} at (1910+-30, 260+-40) MeV, (2020+-30, 275+-35) MeV, (2230+-30, 245+-45) MeV, and (2300+-35, 290+-50) MeV, (v) JPC = 1^{--} at (2005+-40, 275+-75) MeV, and (2165+-40, 160 ^{+140}_{-70}) MeV, and (vi) JPC = 0^{++} at (2005+-30, 305+-50) MeV, (2105+-15, 200+-25) MeV, and (2320+-30, 175+-45) MeV. In addition, there is a less well defined 6^{++} resonance at 2485+-40 MeV, with Gamma = 410+-90 MeV. For every JP, almost all these resonances lie on well defined linear trajectories of mass squared v. excitation number. The slope is 1.10+-0.03 Gev^2 per excitation. The f_0(2105) has strong coupling to eta-\eta, but much weaker coupling to pizero-pizero. Its flavour mixing angle between q-qbar and s-sbar is (59-71.6)deg, i.e. dominant decays to s-sbar. Such decays and its strong production in pbar-p interactions strongly suggest exotic character.Comment: Makes available the combined fit to Crystal Barrel data on pbar-p -> 2-body final states. 29 pages, 11 figures. Typo corrected in version

Corrections to the Central Limit Theorem for Heavy-Tailed Probability Densities

Classical Edgeworth expansions provide asymptotic correction terms to the Central Limit Theorem (CLT) up to an order that depends on the number of moments available. In this paper, we provide subsequent correction terms beyond those given by a standard Edgeworth expansion in the general case of regularly varying distributions with diverging moments (beyond the second). The subsequent terms can be expressed in a simple closed form in terms of certain special functions (Dawson's integral and parabolic cylinder functions), and there are qualitative differences depending on whether the number of moments available is even, odd or not an integer, and whether the distributions are symmetric or not. If the increments have an even number of moments, then additional logarithmic corrections must also be incorporated in the expansion parameter. An interesting feature of our correction terms for the CLT is that they become dominant outside the central region and blend naturally with known large-deviation asymptotics when these are applied formally to the spatial scales of the CLT

ISPIDER Central: an integrated database web-server for proteomics

Despite the growing volumes of proteomic data, integration of the underlying results remains problematic owing to differences in formats, data captured, protein accessions and services available from the individual repositories. To address this, we present the ISPIDER Central Proteomic Database search (http://www.ispider.manchester.ac.uk/cgi-bin/ProteomicSearch.pl), an integration service offering novel search capabilities over leading, mature, proteomic repositories including PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas and the Global Proteome Machine. It enables users to search for proteins and peptides that have been characterised in mass spectrometry-based proteomics experiments from different groups, stored in different databases, and view the collated results with specialist viewers/clients. In order to overcome limitations imposed by the great variability in protein accessions used by individual laboratories, the European Bioinformatics Institute's Protein Identifier Cross-Reference (PICR) service is used to resolve accessions from different sequence repositories. Custom-built clients allow users to view peptide/protein identifications in different contexts from multiple experiments and repositories, as well as integration with the Dasty2 client supporting any annotations available from Distributed Annotation System servers. Further information on the protein hits may also be added via external web services able to take a protein as input. This web server offers the first truly integrated access to proteomics repositories and provides a unique service to biologists interested in mass spectrometry-based proteomics