Evolution in controls methods for the SPS power converters

In common with much accelerator specific material, there is a constant need to improve both hardware and software for power converter control. Maintenance and performance improvements of older systems have become extremely tedious and in some areas impossible. By using modern real-time software and the latest high-performance processors, such problems should be substantially reduced. This paper describes the software concepts and the hardware chosen for the upgrade of the existing facilities. Using the UNIX compatible LynxOS real time kernel, running on a PowerPC 603 in a VME environment, this new approach provides excellent performance while retaining the desired flexibility for future enhancements. The 64 channel system is implemented as a set of cooperating processes, several of which are multi-threaded. Processes include analogue function generation, analogue measurement and digital I/O, all of which are accurately scheduled by the accelerator timing system. This generalised structure, which performs complex sequences of operations is described in detail, as well as how it can be adapted to a wide variety of accelerator tasks

Depletion of polycistronic transcripts using short interfering RNAs: cDNA synthesis method affects levels of non-targeted genes determined by quantitative PCR.

BACKGROUND: Short interfering RNAs (siRNAs) are often used to deplete viral polycistronic transcripts, such as those encoded by human papillomavirus (HPV). There are conflicting data in the literature concerning how siRNAs targeting one HPV gene can affect levels of other genes in the polycistronic transcripts. We hypothesised that the conflict might be partly explained by the method of cDNA synthesis used prior to transcript quantification. FINDINGS: We treated HPV16-positive cervical keratinocytes with siRNAs targeting the HPV16 E7 gene and used quantitative PCR to compare transcript levels of E7 with those of E6 and E2, viral genes located upstream and downstream of the target site respectively. We compared our findings from cDNA generated using oligo-dT primers alone with those from cDNA generated using a combination of random hexamer and oligo-dT primers. Our data show that when polycistronic transcripts are targeted by siRNAs, there is a period when untranslatable cleaved mRNA upstream of the siRNA binding site remains detectable by PCR, if cDNA is generated using random hexamer primers. Such false indications of mRNA abundance are avoided using oligo-dT primers. The period corresponds to the time taken for siRNA activity and degradation of the cleaved transcripts. Genes downstream of the siRNA binding site are detectable during this interval, regardless of how the cDNA is generated. CONCLUSIONS: These data emphasise the importance of the cDNA synthesis method used when measuring transcript abundance following siRNA depletion of polycistronic transcripts. They provide a partial explanation for erroneous reports suggesting that siRNAs targeting HPV E7 can have gene-specific effects.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Feedback Loops of the Mammalian Circadian Clock Constitute Repressilator

Mammals evolved an endogenous timing system to coordinate their physiology and behaviour to the 24h period of the solar day. While it is well accepted that circadian rhythms are generated by intracellular transcriptional feedback loops, it is still debated which network motifs are necessary and sufficient for generating self-sustained oscillations. Here, we systematically explore a data-based circadian oscillator model with multiple negative and positive feedback loops and identify a series of three subsequent inhibitions known as “repressilator” as a core element of the mammalian circadian oscillator. The central role of the repressilator motif is consistent with time-resolved ChIP- seq experiments of circadian clock transcription factors and loss of rhythmicity in core clock gene knockouts

Radiocarbon Isotopic Classification of Deep Tropical Forest Soils

Tropical forest soils have an important role in global carbon (C) stocks. Small changes in the cycling of C could drastically affect atmospheric carbon dioxide (CO2) concentrations and active cycling of carbon in a forest community. Currently, little is understood of how tropical forest soils will respond to the increasing global temperatures. To examine the effects of warming/ drought on losses of older versus younger soil C pools, we implemented radiocarbon (14C) isotopic characterization of various soil plot samples and depths from the Luquillo Experimental Forest, Puerto Rico. 14C was measured using Accelerated Mass Spectrometry (AMS) from catalytically condensed carbon in order to examine the initial carbon stocks of the test plots. This examination was done in order to determine the age of the carbon in the soil plots before implementation of a long term warming experiment. In addition to determining the age of the soil C, the samples were submitted to a Density Fractionation Process to obtain varying aggregate fractions. These were also submitted to AMS for mean residence time of the C stocks. The soil 14C was significantly different in the Heavy and Free Light density fractions. This implies that the soil C turnover increases as you near the top depth of the soil pit samples. The results will be used to establish the initial composition of the sample soils for a warming experiment that will model future changes in climate

The All-digital Approach to LHC Power Converter Current Control

The design of the LHC machine imposes severe demands upon the control of current in the 1700 magnet circuits. This has required the use of novel methods for the control of individual power converters and of the magnet current control system as a whole. This paper will review the chosen hardware and software methods and architectures. The digital regulation techniques used to achieve the overall targets for short-term stability (<3ppm) and reproducibility (<10ppm) of the 24 principal LHC circuits will be discussed. While the proposed system architecture will follow the canonical three-layer design, so successfully exploited in LEP, the software will be far from traditional. This software must be more reliable and maintainable than ever before, and will need to integrate with advanced object-oriented applications via commercial middleware. These challenges will be faced by applying object-oriented techniques throughout the system and by harnessing the power of XML for system definition

A Strategy for Controlling the LHC Magnet Currents

The LHC will require an unprecedented precision of a few ppm in the control of the current in the major magnetic circuits. As a result of the optimisation of the machine design, the machine will be powered in eight sectors with separate power converters. This scheme, along with other operational constraints, has led to a re-evaluation of the methods needed to ensure adequate performance. An overview of the strategy envisaged to meet this new challenge is presented, along with details of digital control and correction methods, new techniques for analogue to digital conversion and improvements in DC current transducers above 10 kA

High-current performance evaluation of DCCTs

The evaluation of high performance DCCT's to the ppm level has never been an easy task. With the LHC demanding currents up to 13 kA, a whole series of problems has arisen in the accurate measurement of these devices. In order to tackle these problems, new facilities have been designed for laboratory measurements under full power operating conditions. These include a high performance low voltage 20 kA power converter, quasi-coaxial bus-bar structures, Kusters Bridge range extenders and a novel bipolar 0 - 10 A current calibrator with resolution and linearity better than ± 0.5 ppm. This paper will present an overview of the complete facility and give more detail on the new current calibrator. Initial results will be presented, along with application areas which advance the state of the art in this field of measurements

Deep-C storage: Biological, chemical and physical strategies to enhance carbon stocks in agricultural subsoils

Due to their substantial volume, subsoils contain more of the total soil carbon (C) pool than topsoils. Much of this C is thousands of years old, suggesting that subsoils offer considerable potential for long-term C sequestration. However, knowledge of subsoil C behaviour and manageability remains incomplete, and subsoil C storage potential has yet to be realised at a large scale, particularly in agricultural systems. A range of biological (e.g. deep-rooting), chemical (e.g. biochar burial) and physical (e.g. deep ploughing) C sequestration strategies have been proposed, but are yet to be assessed. In this review, we identify the main factors that regulate subsoil C cycling and critically evaluate the evidence and mechanistic basis of subsoil strategies designed to promote greater C storage, with particular emphasis on agroecosystems. We assess the barriers and opportunities for the implementation of strategies to enhance subsoil C sequestration and identify 5 key current gaps in scientific understanding. We conclude that subsoils, while highly heterogeneous, are in many cases more suited to long-term C sequestration than topsoils. The proposed strategies may also bring other tangible benefits to cropping systems (e.g. enhanced water holding capacity and nutrient use efficiency). Furthermore, while the subsoil C sequestration strategies we reviewed have large potential, more long-term studies are needed across a diverse range of soils and climates, in conjunction with chronosequence and space-for-time substitutions. Also, it is vital that subsoils are more consistently included in modelled estimations of soil C stocks and C sequestration potential, and that subsoil-explicit C models are developed to specifically reflect subsoil processes. Finally, further mapping of subsoil C is needed in specific regions (e.g. in the Middle East, Eastern Europe, South and Central America, South Asia and Africa). Conducting both immediate and long-term subsoil C studies will fill the knowledge gaps to devise appropriate soil C sequestration strategies and policies to help in the global fight against climate change and decline in soil quality. In conclusion, our evidence-based analysis reveals that subsoils offer an untapped potential to enhance global C storage in terrestrial ecosystems