Automated identification of Fos expression

The concentration of Fos, a protein encoded by the immediate-early gene c-fos, provides a measure of synaptic activity that may not parallel the electrical activity of neurons. Such a measure is important for the difficult problem of identifying dynamic properties of neuronal circuitries activated by a variety of stimuli and behaviours. We employ two-stage statistical pattern recognition to identify cellular nuclei that express Fos in two-dimensional sections of rat forebrain after administration of antipsychotic drugs. In stage one, we distinguish dark-stained candidate nuclei from image background by a thresholding algorithm and record size and shape measurements of these objects. In stage two, we compare performance of linear and quadratic discriminants, nearest-neighbour and artificial neural network classifiers that employ functions of these measurements to label candidate objects as either Fos nuclei, two touching Fos nuclei or irrelevant background material. New images of neighbouring brain tissue serve as test sets to assess generalizability of the best derived classification rule, as determined by lowest cross-validation misclassification rate. Three experts, two internal and one external, compare manual and automated results for accuracy assessment. Analyses of a subset of images on two separate occasions provide quantitative measures of inter- and intra-expert consistency. We conclude that our automated procedure yields results that compare favourably with those of the experts and thus has potential to remove much of the tedium, subjectivity and irreproducibility of current Fos identification methods in digital microscopy

The exploration of Sr isotopic analysis applied to Chinese glazes: part one

Ash glaze and limestone glaze are two major glaze types in southern Chinese ceramic technology. In this study strontium isotope compositions were determined in ash glaze samples from the Yue kiln dated to between the 10th and 12th centuries AD, limestone glaze samples from Jingdezhen dated to between the 15th and 18th centuries AD and ceramic raw materials from Jingdezhen. The Sr isotopic characteristics of limestone glaze and ash glaze are completely different. The Sr isotope characteristics of limestone glaze is characterised by low Sr concentrations, large 87Sr/86Sr variation, and a two component mixing line. On the other hand the strontium isotope characteristic of ash glaze samples is characterised by a consistent 87Sr/86Sr signature and high Sr concentrations with a large variation. The different Sr isotope compositions for the two types of glazes are a reflection of the various raw materials involved in making them. The Sr isotopic composition has been altered by the refinement process that the raw material was subjected to. It was found that the mineralogical changes caused by the alteration are reflected in the Sr isotope results. The potential of Sr isotopic analysis of Chinese glazes is evaluated according to the results produced by this, the first such stud

Novel Characteristics of Valveless Pumping

This study investigates the occurrence of valveless pumping in a fluidfilled system consisting of two open tanks connected by an elastic tube. We show that directional flow can be achieved by introducing a periodic pinching applied at an asymmetrical location along the tube, and that the flow direction depends on the pumping frequency. We propose a relation between wave propagation velocity, tube length, and resonance frequencies associated with shifts in the pumping direction using numerical simulations. The eigenfrequencies of the system are estimated from the linearized system, and we show that these eigenfrequencies constitute the resonance frequencies and the horizontal slope frequencies of the system; 'horizontal slope frequency' being a new concept. A simple model is suggested, explaining the effect of the gravity driven part of the oscillation observed in response to the tank and tube diameter changes. Results are partly compared with experimental findings.Art. no. 22450

Inactivation of viable Ascaris eggs during faecal sludge co-composting with chicken feathers and market waste

Faecal Sludge (FS) contains high concentrations of pathogenic microorganisms that are 10–100 times higher than those in domestic wastewater. Proper and sustainable treatment is required to inactivate these pathogens if FS is to be recycled in agriculture, so as to minimise public health and environmental risks. Composting is one of the common low-cost technologies of sanitising FS in Urban Africa; however, it is associated with longer pathogen inactivation periods that make it commercially uneconomical. This study investigated the effect of different organic wastes types and their mixing ratios with FS on the inactivation efficiency of viable Ascaris eggs (suum and lumbricoides) during composting. Dewatered FS was mixed with market waste (MW), chicken feathers (CF) and sawdust (SD) in different ratios. Compost piles of FS:MW:SD and FS:CF:SD both in volumetric ratios of 1:2:1 and 1:3:1 were set-up in duplicate (3m3 each), composted and monitored weekly for viable Ascaris eggs presence for a period of 15 weeks. The results suggest that the organic waste types have a significant effect on the temperature evolution and pathogen inactivation efficiency while their mixing ratios do not. Piles containing CF achieved the shortest pathogen survival period of 4 weeks compared with 6–8 weeks for those with MW. The temperature–time factor was found to be the most important variable responsible for viable Ascaris eggs inactivation. However, other mechanisms such as microbial antagonism or antibiotic action induced by indigenous microorganisms and toxic by-products such as free ammonia were found to have also played an important role in Ascaris eggs inactivation. All piles attained 100% Ascaris eggs inactivation from FS, and therefore, the compost was safe for use in agriculture. The study findings suggest that composting of FS with CF can reduce Ascaris eggs inactivation periods by 42%, which may thus reduce the operational costs of FS treatment facilities

Clone Detection via Structural Abstraction

This paper describes the design, implementation, and application of a new algorithm to detect cloned code. It operates on the abstract syntax trees formed by many compilers as an intermediate representation. It extends prior work by identifying clones even when arbitrary subtrees have been changed. On a 440,000-line code corpus, 20- 50%of the clones it detected were missed by previous methods. The method also identifies cloning in declarations, so it is somewhat more general than conventional procedural abstraction

Microflow of fluorescently labelled red blood cells in tumours expressing single isoforms of VEGF and their response to VEGF-R tyrosine kinase inhibition

This paper was presented at the 2nd Micro and Nano Flows Conference (MNF2009), which was held at Brunel University, West London, UK. The conference was organised by Brunel University and supported by the Institution of Mechanical Engineers, IPEM, the Italian Union of Thermofluid dynamics, the Process Intensification Network, HEXAG - the Heat Exchange Action Group and the Institute of Mathematics and its Applications.In this work we studied the functional differences between the microcirculation of murine tumours that only express single isoforms of vascular endothelial growth factor-A (VEGF), VEGF120 and VEGF188, and the effect of VEGF receptor tyrosine kinase (VEGF-R TK) inhibition on their functional response to the vascular disrupting agent, combretastatin A-4 phosphate (CA-4-P). We used measurement of fluorescentlylabelled red blood cell (RBC) velocities in tumour microvessels to study this functional response. RBC velocity for control VEGF120-expressing tumours was over 50% slower than for control VEGF188-expressing tumours, which may be due to the immature and haemorrhagic vasculature of the VEGF120 tumour. After chronic treatment with a VEGF-R tyrosine kinase inhibitor, SU5416, RBC velocities in VEGF120 tumours were significantly increased compared to control VEGF120 tumours, and similar to velocities in both VEGF188 treatment groups. Control and SU5416 treated VEGF188 tumours were not different from each other. Treatment of VEGF120 tumours with SU5416 reduced their vascular response to CA-4-P to a similar level to the VEGF188 tumours. Differential expression of VEGF isoforms not only affected vascular function in untreated tumours but also impacted on response to a vascular disrupting drug, CA-4-P, alone and in combination with an anti-angiogenic approach involving VEGF-R TK inhibition. Analysis of RBC velocities is a useful tool in measuring functional responses to vascular targeted treatments.This study is funded by the Cancer Research UK

Improving tuberculosis diagnosis: Better tests or better healthcare?

In a Perspective accompanying Sylvia and colleagues, Carlton Evans and colleagues discuss the challenge of squaring policies around tuberculosis diagnosis with the realities of clinical practice in small villages and low-resource settings

Border carbon adjustments and industrial competitiveness in a European Green Deal

As part of the European Green Deal, the EU is considering the introduction of a Border Carbon Adjustment (BCA) on imports as an alternative to free allocation of emission allowances to reduce the risk of carbon leakage under the EU’s Emissions Trading System (EU ETS). While a BCA for exports is not categorically excluded, it is less likely to be consistent with World Trade Organisation rules and therefore less likely to be proposed than an import-only BCA. In this paper, we show that replacing free allocation by an import-only BCA would weaken the competitiveness of EU producers in foreign markets. Free allocation also helps support the cost competitiveness of domestic products that are exported to non-EU markets. Therefore, a move to import-only BCAs does not necessarily make redundant the continued use of free allocation to help safeguard overall industrial competitiveness. While combining an import BCA with free allocation for exports can increase the risk of legal challenges, such risks may be reduced with an appropriate design. More broadly, policymakers need to navigate a complex trade-off between competitiveness support, a stronger carbon price signal, and extra fiscal revenue