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Local authorities, the UK government and the European Commission have benefitted from the widespread application of new molecular methodologies, developed in 2005 and applied by the University of Reading's Vertebrate Pests Unit (VPU) to identify and quantify anticoagulant rodenticide resistance in rodent populations. Rodents are a major global pest that consumes our food, causes contamination with urine and faeces, damages structures through gnawing, transmits diseases, and impacts on species of conservation concern. Due to historical success and recent regulatory restrictions, anticoagulant rodenticides are the most common control method for these pests. However, physiological resistance to anticoagulants is now widespread and the VPU has been involved in mapping this resistance and identifying the genetic basis for the resistance. Their research has led to new methodologies to identify anticoagulant resistance that have been adopted by the global plant science industry and to new guidance in treating resistant populations that has been adopted by the European biocides industry.
This case study describes the development, application and commercialisation of an open source tool, BSMBench that enables supercomputer vendors and computing centres to benchmark their system's performance. It comprehensively informs the design and testing of new computing architectures well beyond other benchmarking tools on the market, such as Linpack.
The significance of our code is that, unlike other benchmarking tools, it interpolates from a communication- to a computation-dominated regime simply by varying the (physics) parameters in the code, thus providing a perfect benchmark suite to test the response of modern multi-CPU systems along this axis. The impact of this work has great reach: a start-up company, BSMbench Ltd, has been founded to develop and commercialise the software; adopters have included IBM - one of the giants of the supercomputer world (where it uncovered errors in their compilers); it has been deployed by Fujitsu to validate its systems, by HPC Wales, a multi-site, commercially focussed national computer centre and by Transtec, an HPC company employing over 150 staff; and tutorial articles about BSMBench have appeared in magazines such as Linux Format.
This software tool spawned from our research into "Beyond the Standard Model" (BSM) physics which aims to understand the Higgs mechanism in particle physics at a fundamental level. This involved simulating quantum field theories using bespoke code on some of the fastest supercomputers on the planet.
The Abraham solvation parameter approach developed at UCL has become integral to the work carried out by drug discovery teams at [text removed for publication] and other major pharmaceutical companies, as well as research and development groups at international chemical companies including Syngenta and [text removed for publication]. It enables chemists to predict physicochemical and biochemical properties of chemicals, including drugs and agrochemicals, rapidly and efficiently, without the need to conduct time-consuming experiments. The method helps drug discovery teams to identify and optimise the most promising compounds, and often results in fewer compounds being made before a candidate is selected, saving time and resources. The approach has been integrated into software used for drug discovery [text removed for publication].
In partnership with the US company Nalco, the University's Surfactant & Colloid Group developed a new multifunctional technology (Clean n Cor) for the oil industry that both removes accumulated deposits at a metal surface (enabling "break-through" of corrosion inhibitor to the metal surface) and inhibits corrosion. Clean n Cor technology not only protects assets such as oil pipelines against corrosion but also maximises oil production through enhancing water injectivity (water flow per unit pressure drop). Since its launch in 2007, it is currently one of Nalco's fastest growing new technologies and is used at over 100 production locations worldwide.
The performance of absolute distance measuring systems has been improved in terms of accuracy, traceability, reliability and cost through the introduction of new methodology arising from research at the University of Oxford. This has brought commercial benefit to a German company making measurement systems, through the creation of a new product line. New capabilities for measurement have been delivered to a first customer in Germany. The research has also resulted in the establishment of new activity at the National Physical Laboratory, and influenced UK and European technology roadmaps for future manufacturing.
Knowledge of the three-dimensional structures of macromolecules is a prerequisite for understanding their function at the atomic level, an essential component of modern drug development. Most structures are determined by X-ray crystallography: the majority using molecular replacement (MR, which exploits known structures of related proteins), and about half of the remainder using single-wavelength anomalous diffraction (SAD). The Phaser crystallographic software, developed by Read and colleagues, implements powerful new likelihood-based methods for MR and SAD phasing and has made a large impact, accelerating over the period 2008-2013. At the pharma giant, AstraZeneca, Phaser is considered the "tool of choice" for solving structures by MR.
Novel bioluminescent bacterial biosensors developed at UWE, Bristol, and commercialised by Randox, have been used by a range of companies to demonstrate effectiveness of drugs and decontamination procedures. This has improved development processes at companies including Clavis Pharma, Purest Solutions and Dycem, leading to new manufacturing processes and quality control test methods. The biosensors are used in novel applications to give pharmacodynamic data on effectiveness of drugs and real time in-situ demonstration of effectiveness of decontamination processes. These biosensors, pioneered and developed by Vyv Salisbury's group, have been commercially adopted and used for evaluation by at least six collaborating companies.
Pre-eclampsia is a major contributor to death and disability in pregnancy. Diagnosis, based on accurate blood pressure (BP)/proteinuria determination, is limited by measurement errors and being late features of the disease. In collaboration with industry, King's College London (KCL) researchers have developed an inexpensive, accurate, simple BP device suitable for rural clinics. This device allows intervention to reduce mortality/morbidity and is currently being rolled out in a Gates Foundation project in Africa and Asia. KCL researchers have also helped the company Alere Inc. with the development of a diagnostically accurate test of placental growth factor (PlGF) in women with suspected pre-eclampsia: Alere Triage®PlGF. This demonstrates high sensitivity, superior to current tests, and following commercialisation is being adopted internationally. Their work is additionally reflected in guidelines of international standards for BP device accuracy.
Development of the human cell GADD45a assay enabled accurate identification of carcinogens in vitro, with a low rate of misleading positives. Through the spin-out company Gentronix, this research is reducing costs to industry and decreasing the use of animals in research. Industrial collaboration has enabled commercial adoption of the technology in many sectors. With a 10-fold increase in orders in 2012 versus 2008, Gentronix is a profitable business employing 17 people and with an annual turnover of £1.88m. During 2008-12, Gentronix released a series of new products, established testing services, and signed a product license agreement with GlaxoSmithKline. More than 100 companies worldwide are using Gentronix kits, including pharmaceutical, agricultural and health and beauty companies, along with manufacturers of food flavourings and household goods. The Gentronix assay is currently being reviewed by the European Centre for the Validation of Alternative Methods.
OxCal is the most popular software package world-wide for calibrating and analysing dates within the carbon dating process, enabling the accurate dating of objects from the past. The brainchild of Prof. Christopher Bronk Ramsey, Director of the Oxford Radiocarbon Accelerator Unit (ORAU), OxCal is based on chronologies refined by the use of Bayesian statistical methods, and provides users with access to high-quality calibration of chronological data, now the basis for global chronologies. It is available online and free to download, and has played a highly significant role in establishing the ORAU as one of the pre-eminent international radiocarbon dating facilities. Funded by the NERC, and used widely within professional archaeology as well as other disciplines, OxCal has also played a key role in research projects (within Oxford and beyond) brought to the attention of the general public by the media.