UncertWeb processing service:making models easer to access on the web

Models are central tools for modern scientists and decision makers, and there are many existing frameworks to support their creation, execution and composition. Many frameworks are based on proprietary interfaces, and do not lend themselves to the integration of models from diverse disciplines. Web based systems, or systems based on web services, such as Taverna and Kepler, allow composition of models based on standard web service technologies. At the same time the Open Geospatial Consortium has been developing their own service stack, which includes the Web Processing Service, designed to facilitate the executing of geospatial processing - including complex environmental models. The current Open Geospatial Consortium service stack employs Extensible Markup Language as a default data exchange standard, and widely-used encodings such as JavaScript Object Notation can often only be used when incorporated with Extensible Markup Language. Similarly, no successful engagement of the Web Processing Service standard with the well-supported technologies of Simple Object Access Protocol and Web Services Description Language has been seen. In this paper we propose a pure Simple Object Access Protocol/Web Services Description Language processing service which addresses some of the issues with the Web Processing Service specication and brings us closer to achieving a degree of interoperability between geospatial models, and thus realising the vision of a useful 'model web'.

Solar thermal collectors for use in hybrid solar-biomass power plants in India

This thesis examined solar thermal collectors for use in alternative hybrid solar-biomass power plant applications in Gujarat, India. Following a preliminary review, the cost-effective selection and design of the solar thermal field were identified as critical factors underlying the success of hybrid plants. Consequently, the existing solar thermal technologies were reviewed and ranked for use in India by means of a multi-criteria decision-making method, the Analytical Hierarchy Process (AHP). Informed by the outcome of the AHP, the thesis went on to pursue the Linear Fresnel Reflector (LFR), the design of which was optimised with the help of ray-tracing. To further enhance collector performance, LFR concepts incorporating novel mirror spacing and drive mechanisms were evaluated. Subsequently, a new variant, termed the Elevation Linear Fresnel Reflector (ELFR) was designed, constructed and tested at Aston University, UK, therefore allowing theoretical models for the performance of a solar thermal field to be verified. Based on the resulting characteristics of the LFR, and data gathered for the other hybrid system components, models of hybrid LFR- and ELFR-biomass power plants were developed and analysed in TRNSYS®. The techno-economic and environmental consequences of varying the size of the solar field in relation to the total plant capacity were modelled for a series of case studies to evaluate different applications: tri-generation (electricity, ice and heat), electricity-only generation, and process heat. The case studies also encompassed varying site locations, capacities, operational conditions and financial situations. In the case of a hybrid tri-generation plant in Gujarat, it was recommended to use an LFR solar thermal field of 14,000 m2 aperture with a 3 tonne biomass boiler, generating 815 MWh per annum of electricity for nearby villages and 12,450 tonnes of ice per annum for local fisheries and food industries. However, at the expense of a 0.3 ¢/kWh increase in levelised energy costs, the ELFR increased saving of biomass (100 t/a) and land (9 ha/a). For solar thermal applications in areas with high land cost, the ELFR reduced levelised energy costs. It was determined that off-grid hybrid plants for tri-generation were the most feasible application in India. Whereas biomass-only plants were found to be more economically viable, it was concluded that hybrid systems will soon become cost competitive and can considerably improve current energy security and biomass supply chain issues in India.

The development and investigation of a novel pulsatile heart assist device

Cardiovascular diseases (CVD) contributed to almost 30% of worldwide mortality; with heart failure being one class of CVD. One popular and widely available treatment for heart failure is the intra-aortic balloon pump (IABP). This heart assist device is used in counterpulsation to improve myocardial function by increasing coronary perfusion, and decreasing aortic end-diastolic pressure (i.e. the resistance to blood ejection from the heart). However, this device can only be used acutely, and patients are bedridden. The subject of this research is a novel heart assist treatment called the Chronic Intermittent Mechanical Support (CIMS) which was conceived to offer advantages of the IABP device chronically, whilst overcoming its disadvantages. The CIMS device comprises an implantable balloon pump, a percutaneous drive line, and a wearable driver console. The research here aims to determine the haemodynamic effect of balloon pump activation under in vitro conditions. A human mock circulatory loop (MCL) with systemic and coronary perfusion was constructed, capable of simulating various degrees of heart failure. Two prototypes of the CIMS balloon pump were made with varying stiffness. Several experimental factors (balloon inflation/deflation timing, Helium gas volume, arterial compliance, balloon pump stiffness and heart valve type) form the factorial design experiments. A simple modification to the MCL allowed flow visualisation experiments using video recording. Suitable statistical tests were used to analyse the data obtained from all experiments. Balloon inflation and deflation in the ascending aorta of the MCL yielded favourable results. The sudden balloon deflation caused the heart valve to open earlier, thus causing longer valve opening duration in a cardiac cycle. It was also found that pressure augmentation in diastole was significantly correlated with increased cardiac output and coronary flowrate. With an optimum combination (low arterial compliance and low balloon pump stiffness), systemic and coronary perfusions were increased by 18% and 21% respectively, while the aortic end-diastolic pressure (forward flow resistance) decreased by 17%. Consequently, the ratio of oxygen supply and demand to myocardium (endocardial viability ratio, EVR) increased between 33% and 75%. The increase was mostly attributed to diastolic augmentation rather than systolic unloading.

Describing and communicating uncertainty within the semantic web

The Semantic Web relies on carefully structured, well defined, data to allow machines to communicate and understand one another. In many domains (e.g. geospatial) the data being described contains some uncertainty, often due to incomplete knowledge; meaningful processing of this data requires these uncertainties to be carefully analysed and integrated into the process chain. Currently, within the SemanticWeb there is no standard mechanism for interoperable description and exchange of uncertain information, which renders the automated processing of such information implausible, particularly where error must be considered and captured as it propagates through a processing sequence. In particular we adopt a Bayesian perspective and focus on the case where the inputs / outputs are naturally treated as random variables. This paper discusses a solution to the problem in the form of the Uncertainty Markup Language (UncertML). UncertML is a conceptual model, realised as an XML schema, that allows uncertainty to be quantified in a variety of ways i.e. realisations, statistics and probability distributions. UncertML is based upon a soft-typed XML schema design that provides a generic framework from which any statistic or distribution may be created. Making extensive use of Geography Markup Language (GML) dictionaries, UncertML provides a collection of definitions for common uncertainty types. Containing both written descriptions and mathematical functions, encoded as MathML, the definitions within these dictionaries provide a robust mechanism for defining any statistic or distribution and can be easily extended. Universal Resource Identifiers (URIs) are used to introduce semantics to the soft-typed elements by linking to these dictionary definitions. The INTAMAP (INTeroperability and Automated MAPping) project provides a use case for UncertML. This paper demonstrates how observation errors can be quantified using UncertML and wrapped within an Observations & Measurements (O&M) Observation. The interpolation service uses the information within these observations to influence the prediction outcome. The output uncertainties may be encoded in a variety of UncertML types, e.g. a series of marginal Gaussian distributions, a set of statistics, such as the first three marginal moments, or a set of realisations from a Monte Carlo treatment. Quantifying and propagating uncertainty in this way allows such interpolation results to be consumed by other services. This could form part of a risk management chain or a decision support system, and ultimately paves the way for complex data processing chains in the Semantic Web.

Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

Background: The methylotrophic, Crabtree-negative yeast Pichia pastoris is widely used as a heterologous protein production host. Strong inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters are typically used to drive gene expression. Notably, genes involved in methanol utilization are not only repressed by the presence of glucose, but also by glycerol. This unusual regulatory behavior prompted us to study the regulation of carbon substrate utilization in different bioprocess conditions on a genome wide scale. Results: We performed microarray analysis on the total mRNA population as well as mRNA that had been fractionated according to ribosome occupancy. Translationally quiescent mRNAs were defined as being associated with single ribosomes (monosomes) and highly-translated mRNAs with multiple ribosomes (polysomes). We found that despite their lower growth rates, global translation was most active in methanol-grown P. pastoris cells, followed by excess glycerol- or glucose-grown cells. Transcript-specific translational responses were found to be minimal, while extensive transcriptional regulation was observed for cells grown on different carbon sources. Due to their respiratory metabolism, cells grown in excess glucose or glycerol had very similar expression profiles. Genes subject to glucose repression were mainly involved in the metabolism of alternative carbon sources including the control of glycerol uptake and metabolism. Peroxisomal and methanol utilization genes were confirmed to be subject to carbon substrate repression in excess glucose or glycerol, but were found to be strongly de-repressed in limiting glucose-conditions (as are often applied in fed batch cultivations) in addition to induction by methanol. Conclusions: P. pastoris cells grown in excess glycerol or glucose have similar transcript profiles in contrast to S. cerevisiae cells, in which the transcriptional response to these carbon sources is very different. The main response to different growth conditions in P. pastoris is transcriptional; translational regulation was not transcript-specific. The high proportion of mRNAs associated with polysomes in methanol-grown cells is a major finding of this study; it reveals that high productivity during methanol induction is directly linked to the growth condition and not only to promoter strength.

Public scientific communication on Twitter:visual analytic approach

Purpose - The purpose of this paper is to assess high-dimensional visualisation, combined with pattern matching, as an approach to observing dynamic changes in the ways people tweet about science topics. Design/methodology/approach - The high-dimensional visualisation approach was applied to three scientific topics to test its effectiveness for longitudinal analysis of message framing on Twitter over two disjoint periods in time. The paper uses coding frames to drive categorisation and visual analytics of tweets discussing the science topics. Findings - The findings point to the potential of this mixed methods approach, as it allows sufficiently high sensitivity to recognise and support the analysis of non-trending as well as trending topics on Twitter. Research limitations/implications - Three topics are studied and these illustrate a range of frames, but results may not be representative of all scientific topics. Social implications - Funding bodies increasingly encourage scientists to participate in public engagement. As social media provides an avenue actively utilised for public communication, understanding the nature of the dialog on this medium is important for the scientific community and the public at large. Originality/value - This study differs from standard approaches to the analysis of microblog data, which tend to focus on machine driven analysis large-scale datasets. It provides evidence that this approach enables practical and effective analysis of the content of midsize to large collections of microposts.

Low-temperature isothermal Rankine cycle for desalination

In brackish groundwater desalination, high recovery ratio (of fresh water from saline feed) is desired to minimise concentrate reject. To this effect, previous studies have developed a batch reverse osmosis (RO) desalination system, DesaLink, which proposed to expand steam in a reciprocating piston cylinder and transmit the driving force through a linkage crank mechanism to pressurise batches of saline water (recirculating) in a water piston cylinder unto RO membranes. However, steam is largely disadvantaged at operation from low temperature (< 150oC) thermal sources; and organic working fluids are more viable, though, the obtainable thermal cycle efficiencies are generally low with low temperatures. Consequently, this thesis proposed to investigate the use of organic working fluid Rankine cycle (ORC) with isothermal expansion, to drive the DesaLink machine, at improved thermal efficiency from low temperature thermal sources. Following a review of the methods of achieving isothermal expansion, ‘liquid flooded expansion’ and ‘expansion chamber surface heating’ were identified as potential alternative methods. Preliminary experimental comparative analysis of variants of the heated expansion chamber technique of effecting isothermal expansion favoured a heated plain wall technique, and as such was adopted for further optimisation and development. Further, an optimised isothermal ORC engine was built and tested at < 95oC heat source temperature, with R245fa working fluid – which was selected from 16 working fluids that were analysed for isothermal operation. Upon satisfactory performance of the test engine, a larger (10 times) version was built and coupled to drive the DesaLink system. Operating the integrated ORC-RO DesaLink system, gave freshwater (approximately 500 ppm) production of about 12 litres per hour (from 4000 ppm feed water) at a recovery ratio of about 0.7 and specific energy consumption of 0.34 kWh/m3; and at a thermal efficiency of 7.7%. Theoretical models characterising the operation and performance of the integrated system was developed and utilised to access the potential field performance of the system, when powered by two different thermal energy sources – solar and industrial bakery waste heat – as case studies.

Design and application of nanoscale actuators using block-copolymers

Block copolymers are versatile designer macromolecules where a “bottom-up” approach can be used to create tailored materials with unique properties. These simple building blocks allow us to create actuators that convert energy from a variety of sources (such as chemical, electrical and heat) into mechanical energy. In this review we will discuss the advantages and potential pitfalls of using block copolymers to create actuators, putting emphasis on the ways in which these materials can be synthesised and processed. Particular attention will be given to the theoretical background of microphase separation and how the phase diagram can be used during the design process of actuators. Different types of actuation will be discussed throughout.

Fabrication and application of short and novel structure in-fibre Bragg gratings

This thesis presents details on progress made in the fabrication and application of short and novel structure fibre Bragg gratings. The basic theoretical concepts of in-fibre Bragg gratings and photosensitive mechanisms are introduced together with an overview of fabrication methods and applications presented to date. The fabrication of fibre Bragg gratings using a quadrupled Nd:YAG laser is presented and some of the issues of grating fabrication using a fabrication using a phasemask are investigated, including the variation of the separation of the fibre and phasemask, and other alignment issues. A new apodisation technique is presented, enabling the production of gratings with a wide range of spectral profiles. The technique is used to investigate the design and fabrication of length limited fibre Bragg gratings for use in telecommunication systems as filters. Application to devices designed for use in WDM systems is presented. The use of fibre Bragg gratings as high spatial resolution distributed sensors is investigated. Grating sensing arrays comprising very short apodised gratings are demonstrated and Chirped Moiré gratings are implemented as distributed sensors achieving high spatial resolution with miniature point sensing sub-elements. A novel grating sensing element designed to imitate an interferometer is also presented. Finally, the behaviour of gratings fabricated in Boron-Germania-co-doped fibre is investigated, revealing atypical behaviour of the Bragg wavelength during ageing.

The synthesis and application of room temperature ionic liquids

This research project is concerned with the development and use of eco-friendly reaction media for a variety of organic transformations in the preparation of organic chemicals with potential pharmaceutical applications. These chemicals will then be investigated for their anti-cancer, anti-bacterial and anti-inflammation properties. In this project, different methods were used to synthesize various kinds of ionic liquids. Some new ionic liquids were prepared. In addition, Knoevenagel condensation reactions were investigated in RTILs. For the first time, some neutral ionic liquids such as [BMIM]+[BF4]-, [MeOEtMIM]+[CF3COO]- acted as both catalysts and solvents to promote Knoevenagel reactions. All these experiments indicated that RTILs have a great potential as alternative solvents in synthetic chemistry. Furthermore, nucleoside chemistry is an important research area in drug discovery. Various chemical modified nucleosides have therapeutic activities. However, these compounds usually have poor solubility in common organic solvents. RTILs such as [MeOEtMIM]+[CH3SO3]- have good dissolving capability for these chemicals. A range of thio-substituted nucleobases and nucleosides with potential pharmaceutical applications have been synthesized in several RTILs. These chemicals will then be investigated for their anti-cancer properties.

PIP-DB:the protein isoelectric point database

A protein's isoelectric point or pI corresponds to the solution pH at which its net surface charge is zero. Since the early days of solution biochemistry, the pI has been recorded and reported, and thus literature reports of pI abound. The Protein Isoelectric Point database (PIP-DB) has collected and collated these data to provide an increasingly comprehensive database for comparison and benchmarking purposes. A web application has been developed to warehouse this database and provide public access to this unique resource. PIP-DB is a web-enabled SQL database with an HTML GUI front-end. PIP-DB is fully searchable across a range of properties.

Design of an information system for metrology contents

Dimensional and form inspections are key to the manufacturing and assembly of products. Product verification can involve a number of different measuring instruments operated using their dedicated software. Typically, each of these instruments with their associated software is more suitable for the verification of a pre-specified quality characteristic of the product than others. The number of different systems and software applications to perform a complete measurement of products and assemblies within a manufacturing organisation is therefore expected to be large. This number becomes even larger as advances in measurement technologies are made. The idea of a universal software application for any instrument still appears to be only a theoretical possibility. A need for information integration is apparent. In this paper, a design of an information system to consistently manage (store, search, retrieve, search, secure) measurement results from various instruments and software applications is introduced. Two of the main ideas underlying the proposed system include abstracting structures and formats of measurement files from the data so that complexity and compatibility between different approaches to measurement data modelling is avoided. Secondly, the information within a file is enriched with meta-information to facilitate its consistent storage and retrieval. To demonstrate the designed information system, a web application is implemented. © Springer-Verlag Berlin Heidelberg 2010.