Ultra-fast processing of gigapixel Tissue MicroArray images using high performance computing.

BACKGROUND:
tissue MicroArrays (TMAs) are a valuable platform for tissue based translational research and the discovery of tissue biomarkers. The digitised TMA slides or TMA Virtual Slides, are ultra-large digital images, and can contain several hundred samples. The processing of such slides is time-consuming, bottlenecking a potentially high throughput platform.
METHODS:
a High Performance Computing (HPC) platform for the rapid analysis of TMA virtual slides is presented in this study. Using an HP high performance cluster and a centralised dynamic load balancing approach, the simultaneous analysis of multiple tissue-cores were established. This was evaluated on Non-Small Cell Lung Cancer TMAs for complex analysis of tissue pattern and immunohistochemical positivity.
RESULTS:
the automated processing of a single TMA virtual slide containing 230 patient samples can be significantly speeded up by a factor of circa 22, bringing the analysis time to one minute. Over 90 TMAs could also be analysed simultaneously, speeding up multiplex biomarker experiments enormously.
CONCLUSIONS:
the methodologies developed in this paper provide for the first time a genuine high throughput analysis platform for TMA biomarker discovery that will significantly enhance the reliability and speed for biomarker research. This will have widespread implications in translational tissue based research.

Mitochondrial translation initiation factor 3 polymorphism and Parkinson's disease

Mitochondrial dysfunction has been proposed to play a role in the pathogenesis of Parkinson s disease (PD) Supportive of this hypothesis several genetic variants that regulate mitochondrial function and homeostasis have been described to alter PD susceptibility A recent report demonstrated association of a single nucleotide polymorphism in the mitochondrial translation initiation factor 3 (MTIF3) gene with PD risk The protein encoded by this nuclear gene is essential for initiation complex formation on the mitochondrial 55S ribosome and regulates translation of proteins within the mitochondria Changes in the function or expression of the MTIF3 protein may result in altered mitochondrial function ATP production or formation of reactive oxygen species thereby affecting susceptibility to PD We examined the association of rs7669 with sporadic PD in three Caucasian case control series (n = 2434) A significant association was observed in the largest series (Norwegian n = 1650) when comparing CC vs CT/TT genotypes with the Irish and US series having a similar but non-significant trend The combined series also revealed an association with risk of PD (P = 0 01) supporting the possible involvement of this gene in PD etiology Published by Elsevier Ireland Ltd

Massive stars exploding in a He-rich circumstellar medium - III. SN 2006jc: infrared echoes from new and old dust in the progenitor CSM

We present near- (NIR) and mid-infrared (MIR) photometric data of the Type Ibn supernova (SN) 2006jc obtained with the United Kingdom Infrared Telescope (UKIRT), the Gemini North Telescope and the Spitzer Space Telescope between days 86 and 493 post-explosion. We find that the IR behaviour of SN 2006jc can be explained as a combination of IR echoes from two manifestations of circumstellar material. The bulk of the NIR emission arises from an IR echo from newly condensed dust in a cool dense shell (CDs) produced by the interaction of the ejecta Outward shock with a dense shell of circumstellar material ejected by the progenitor in a luminous blue variable (LBV)-like outburst about two years prior to the SN explosion. The CDs dust mass reaches a modest 3.0 x 10(-4) M-circle dot by day 230. While dust condensation within a CDs formed behind the ejecta inward shock has been proposed before for one event (SN 1998S), SN 2006jc is the first one showing evidence for dust condensation in a CDs formed behind the ejecta outward shock in the circumstellar material. At later epochs, a substantial and growing contribution to the IR fluxes arises from an IR echo from pre-existing dust in the progenitor wind. The mass of the pre-existing circumstellar medium (CSM) dust is at least similar to 8 x 10(-3) M-circle dot. This paper therefore adds to the evidence that mass-loss from the progenitors of core-collapse SNe could be a major source of dust in the Universe. However, yet again, we see no direct evidence that the explosion of an SN produces anything other than a very modest amount of dust.

Redispersion Microreactor System for Phase Transfer Catalyzed Esterification

An interdigital mixer - redispersion capillary assembly was applied to prevent the liquid-liquid bubbly flow coalescence in microreactors. The redispersion capillary consisted of 1 mm long and 0.25 mm inner-diameter constrictions placed every 0.50 m along the channel length. The system was tested on the phase transfer catalyzed esterification to produce benzyl benzoate. The application of constrictions to prevent coalescence resulted in a better reproducibility compared to a capillary without the constrictions. By controlling the total flow rate and the aqueous-to-organic ratio the bubbly flow surface-volume ratio could be increased up to 230 700 m(2)m(-3). Compared to the conventional phase transfer catalyzed esterification, the continuous operation in the interdigital-redispersion capillary assembly eliminated the use of solvents and bases, removing an energy intensive step of distillation, while increasing process safety.

Determination of the molar extinction coefficient for the ferric reducing/antioxidant power assay

The FRAP reagent contains 2,4,6-tris(2-pyridyl)-s-triazine, which forms a blue-violet complex ion in the presence of ferrous ions. Although the FRAP (ferric reducing/antioxidant power) assay is popular and has been in use for many years, the correct molar extinction coefficient of this complex ion under FRAP assay conditions has never been published, casting doubt on the validity of previous calibrations. A previously reported value of 19.800 is an underestimate. We determined that the molar extinction coefficient was 21,140. The value of the molar extinction coefficient was also shown to depend on the type of assay and was found to be 22,230 under iron assay conditions, in good agreement with published data. Redox titration indicated that the ferrous sulfate heptahydrate calibrator recommended by Benzie and Strain, the FRAP assay inventors, is prone to efflorescence and, therefore, is unreliable. Ferrous ammonium sulfate hexahydrate in dilute sulfuric acid was a more stable alternative. Few authors publish their calibration data, and this makes comparative analyses impossible. A critical examination of the limited number of examples of calibration data in the published literature reveals only that Benzie and Strain obtained a satisfactory calibration using their method. (C) 2011 Elsevier Inc. All rights reserved.

Contesting public accountability: A dialogical exploration of accountability and social housing

This paper analyses the interaction between neoliberal inspired reforms of public services and the mechanisms for achieving public accountability. Where once accountability was exercised through the ballot box, now in the neoliberal age managerial and market based forms of accountability predominate. The analysis identifies resistance from civil society campaigns to the neoliberal restructuring of public services which leads to public accountability (PA) becoming a contested arena. To develop this analysis a re-theorisation of PA, as a relationship where civil society seeks to control the state, is explored in the context of social housing in England over the past thirty years. Central to this analysis is a dialogical analysis of key documents from a social housing regulator and civil society campaign. The analysis shows that the current PA practices are an outcome of both reforms from the government and resistance from civil society (in the shape of tenants’ campaigns). The outcome of which is to tell the story of the changes in PA (and accountability) centring on an analysis of discourse. Thus, the paper moves towards answering the question – what has happened to PA during the neoliberal age?

Transport properties of protic ionic liquids, pure and in aqueous solutions: Effects of the anion and cation structure

Ionic conductivities of twelve protic ionic liquids (PILs) and their mixtures with water over the whole composition range are reported at 298.15 K and atmospheric pressure. The selected PILs are the pyrrolidinium-based PILs containing nitrate, acetate or formate anions; the formate-based PILs containing diisopropylethylammonium, amilaminium, quinolinium, lutidinium or collidinium cations; and the pyrrolidinium alkylcarboxylates, [Pyrr][CnH2n+1COO] with n = 5–8. This study was performed in order to investigate the influence of molecular structures of the ions on the ionic conductivities in aqueous solutions. The ionic conductivities of the aqueous solutions are 2–30 times higher than the conductivities of pure PILs. The maximum in conductivity varies from ww=0.41???to???0.74 and is related to the nature of cations and anions. The molar conductance and the molar conductance at infinite dilution for (PIL + water) solutions are then determined. Self-diffusion coefficients of the twelve protic ionic liquids in water at infinite dilution and at 298.15 K are calculated by using the Nernst–Haskell, the original and the modified Wilke–Chang equations. These calculations show that similar values are obtained using the modified Wilke–Chang and the Nernst–Haskell equations. Finally, the effective hydrodynamic (or Stokes) radius of the PILs was determined by using the Stokes–Einstein equation. A linear relationship was established in order to predict this radius as a function of the anion alkyl chain length in the case of the pyrrolidinium alkylcarboxylates PILs.

Genetic susceptibility to invasive meningococcal disease: MBL2 structural polymorphisms revisited in a large case–control study and a systematic review

Invasive infection caused by Neisseria meningitidis is a worldwide public health problem. Previous reports have indicated that carriage of common ‘defective’ structural polymorphisms of the host mannose-binding lectin gene (MBL2) greatly increases an individual’s risk of developing the disease. We report the largest case–control study so far to investigate the effect of these polymorphisms in meningococcal disease (296 PCR-positive cases and 5196 population controls, all of European ancestry) and demonstrate that no change in risk is associated with the polymorphisms overall or in any age-defined subgroup. This finding contrasts with two smaller studies that reported an increase in risk. A systematic review of all studies of MBL2 polymorphisms in people of European ancestry published since 1999, including 24 693 individuals, revealed a population frequency of the combined ‘defective’MBL2 allele of 0.230 (95% confidence limits: 0.226–0.234). The past reported associations of increased risk of meningococcal disease were because of low ‘defective’ allele frequencies in their study control populations (0.13 and 0.04) that indicate systematic problems with the studies. The data from our study and all other available evidence indicate that MBL2 structural polymorphisms do not predispose children or adults to invasive meningococcal disease.