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.

Advances in biosensor-based analysis for antimicrobial residues in foods

Biosensors are used for a large number of applications within biotechnology, including the pharmaceutical industry and life sciences. Since the production of Biacore surface-plasmon resonance instruments in the early 1990s, there has been steadily growing use of this technology for the detection of food contaminants (e.g., veterinary drugs, mycotoxins, marine toxins, food dyes and processing contaminants). Other biosensing technologies (e.g., electrochemical and piezoelectric) have also been employed for the analysis of small-molecule contaminants. This review concentrates on recent advances made in detection and quantification of antimicrobial compounds with different types of biosensors and on the emergence of multiplexing, which is highly desirable as it increases sample analysis at lower cost and in less time. (C) 2010 Elsevier Ltd. All rights reserved.

Synthesis of nucleoside analogues in a ball mill: fast, chemoselective and high yielding acylation without undesirable solvents

The chemoselective acylation of primary aliphatic amines has been achieved in under ten minutes (and for aromatic amines under 120 min) using vibration ball-milling, avoiding undesirable solvents which are typically employed for such reactions (e.g. DMF). Under optimised conditions, the synthesis of amides in the presence of both primary and secondary alcohol functions was achieved in high to excellent yields (65-94%). Overall, the methods described have significant practical advantages over conventional approaches based upon bulk solvents including greater yields, higher chemoselectivity and easier product separation.

Fast automatic two-stage nonlinear model identification based on the extreme learning machine

It is convenient and effective to solve nonlinear problems with a model that has a linear-in-the-parameters (LITP) structure. However, the nonlinear parameters (e.g. the width of Gaussian function) of each model term needs to be pre-determined either from expert experience or through exhaustive search. An alternative approach is to optimize them by a gradient-based technique (e.g. Newton’s method). Unfortunately, all of these methods still need a lot of computations. Recently, the extreme learning machine (ELM) has shown its advantages in terms of fast learning from data, but the sparsity of the constructed model cannot be guaranteed. This paper proposes a novel algorithm for automatic construction of a nonlinear system model based on the extreme learning machine. This is achieved by effectively integrating the ELM and leave-one-out (LOO) cross validation with our two-stage stepwise construction procedure [1]. The main objective is to improve the compactness and generalization capability of the model constructed by the ELM method. Numerical analysis shows that the proposed algorithm only involves about half of the computation of orthogonal least squares (OLS) based method. Simulation examples are included to confirm the efficacy and superiority of the proposed technique.

Development and validation of a fast monoclonal based disequilibrium enzyme-linked immunosorbent assay for the detection of triphenylmethane dyes and their metabolites in fish

Malachite Green (MG), Crystal Violet (CV) and Brilliant Green (BC) are antibacterial, antifungal and antiparasitic agents that have been used for treatment and prevention of diseases in fish. These dyes are metabolized into reduced leuco forms (LMG, LCV, LBG) that can be present in fish muscles for a long period. Due to the carcinogenic properties they are banned for use in fish for human consumption in many countries including the European Union and the United States. HPLC and LC-MS techniques are generally used for the detection of these compounds and their metabolites in fish. This study presents the development of a fast enzyme-linked immunosorbent assay (ELISA) method as an alternative for screening purposes. A first monoclonal cell line producing antibodies to MG was generated using a hybridoma technique. The antibody had good cross-reactivates with related chromatic forms of triphenylmethane dyes such as CV, BC, Methyl Green, Methyl Violet and Victoria Blue R. The monoclonal antibody (mAb) was used to develop a fast (20 min) disequilibrium ELISA screening method for the detection of triphenylmethanes in fish. By introducing an oxidation step with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) during sample extraction the assay was also used to detect the presence of the reduced metabolites of triphenylmethanes. The detection capability of the assay was 1 ng g(-1) for MG, LMG, CV, LCV and BC which was below the minimum required performance limit (MRPL) for the detection method of total MG (sum of MG and LMG) set by the Commission Decision 2004/25/EC (2 ng g(-1)). The mean recoveries for fish samples spiked at 0.5 MRPL and MRPL levels with MG and LMG were between 74.9 and 117.0% and inter- and intra-assay coefficients of variation between 4.7 and 25.7%. The validated method allows the analysis of a batch of 20 samples in two to three hours. Additionally, this procedure is substantially faster than other ELISA methods developed for MG/LMG thus far. The stable and efficient monoclonal cell line obtained is an unlimited source of sensitive and specific antibody to MG and other triphenylmethanes. (C) 2011 Elsevier B.V. All rights reserved.

Investigating the mechanism of the H 2-assisted selective catalytic reduction (SCR) of NOx with octane using fast cycling transient in situ DRIFTS-MS analysis

A mechanistic study of the H-2-assisted Selective Catalytic Reduction (SCR) of NOx with octane as reductant over a Ag/Al2O3 catalyst was carried out using a modified DRIFTS cell coupled to a mass spectrometer Using fast transient cycling switching of H-2 with a time resolution of a few seconds It was possible to differentiate potential reaction intermediates from other moieties that are clearly spectator species Using such a periodic operation mode effects were uncovered that are normally hidden in conventional transient studies which typically consist of a single transient In experiments based on a single transient addition of H-2 to or removal of H-2 from the SCR feed it was found that the changes in the concentrations of gaseous species (products and reactants) were not matched by changes at comparable timescales of the concentration of surface species observed by IR This observation indicates that the majority of sur face species observed by DRIFTS under steady-state reaction conditions are spectators In contrast under fast cycling experimental conditions It was found that a surface isocyanate species had a temporal response that matched that of N-15(2) This suggests that some of the isocyanate species observed by infrared spectroscopy could be important intermediates in the hydrogen-assisted SCR reaction although it is emphasised that this may be dependent on the way in which the infrared spectra are obtained It is concluded that the use of fast transient cycling switching techniques may provide useful mechanistic information under certain circumstances.

Optical and infrared observations of SN 2002dj: some possible common properties of fast-expanding Type Ia supernovae

As part of the European Supernova Collaboration, we obtained extensive photometry and spectroscopy of the Type Ia supernova (SN Ia) SN 2002dj covering epochs from 11 d before to nearly two years after maximum. Detailed optical and near-infrared observations show that this object belongs to the class of the high-velocity gradient events as indicated by Si, S and Ca lines. The light curve shape and velocity evolution of SN 2002dj appear to be nearly identical to SN 2002bo. The only significant difference is observed in the optical to near-infrared colours and a reduced spectral ernission beyond 6500 A. For high-velocity gradient SNe Ia, we tentatively identify a faster rise to maximum, a more pronounced inflection in the V and R light curves after maximum and a brighter, slower declining late-time B light curve as common photometric properties of this class of object. They also seem to be characterized by a different colour and colour evolution with respect to 'normal' SNe Ia. The usual light Curve shape parameters do not distinguish these events. Stronger, more blueshifted absorption features of intermediate-mass elements and lower temperatures are the most prominent spectroscopic features of SNe Ia displaying high-velocity gradients. It appears that these events burn more intermediate-mass elements in the outer layers. Possible connections to the metallicity of the progenitor star are explored.