Regional environments and sector developments: the biotech sector in Oxfordshire

This paper explores the interdependence between national policy, the local characteristics of the UK’s biotechnology sectoral system of innovation and the growth of Oxfordshire’s biotech sector. It considers on the one hand the county’s research capacity and on the other its innovation performance. The latter is captured by a series of indicators from a recently completed study of the sector, recording the sector’s evolution both in the number of firms and their employment size, their status (independent, merged/acquired), product group and contribution to local employment and wealth creation. It considers the implications of the relative weaknesses in the system of innovation in this sector which relate to an underperformance of its firms in relation to the strength of the science base

Cluster Performance reconsidered: Structure, Linkages and Paths in the German Biotechnology Industry, 1996-2003

This paper addresses the evolution of biotechnology clusters in Germany between 1996 and 2003, paying particular attention to their respective composition in terms of venture capital, basic science institutions and biotechnology firms. Drawing upon the significance of co-location of "money and ideas", the literature stressing the importance of a cluster's openness and external linkages, and the path dependency debate, the paper aims to analyse how certain cluster characteristics correspond with its overall performance. After identifying different cluster types, we investigate their internal and external interconnectivity in comparative manner and draw on changes in cluster composition. Our results indicate that the structure, i.e. to which group the cluster belongs, and the openness towards external knowledge flows deliver merely unsystematic indications with regard to a cluster's overall success. Its ability to change composition towards a more balanced ratio of science and capital over time, on the other hand, turns out as a key explanatory factor. Hence, the dynamic perspective proves effective illuminating cluster growth and performance, where our explorative findings provide a promising avenue for further evolutionary research

Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis

Background: Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood. Methodology/Principal Findings: The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, ,40% of the ,2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three ,90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors. Conclusions/Significance: The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance

The Generation of Successive Unmarked Mutations and Chromosomal Insertion of Heterologous Genes in Actinobacillus pleuropneumoniae Using Natural Transformation

We have developed a simple method of generating scarless, unmarked mutations in Actinobacillus pleuropneumoniae by exploiting the ability of this bacterium to undergo natural transformation, and with no need to introduce plasmids encoding recombinases or resolvases. This method involves two successive rounds of natural transformation using linear DNA: the first introduces a cassette carrying cat (which allows selection by chloramphenicol) and sacB (which allows counter-selection using sucrose) flanked by sequences to either side of the target gene; the second transformation utilises the flanking sequences ligated directly to each other in order to remove the cat-sacB cassette. In order to ensure efficient uptake of the target DNA during transformation, A. pleuropneumoniae uptake sequences are added into the constructs used in both rounds of transformation. This method can be used to generate multiple successive deletions and can also be used to introduce targeted point mutations or insertions of heterologous genes into the A. pleuropneumoniae chromosome for development of live attenuated vaccine strains. So far, we have applied this method to highly transformable isolates of serovars 8 (MIDG2331), which is the most prevalent in the UK, and 15 (HS143). By screening clinical isolates of other serovars, it should be possible to identify other amenable strains

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

<p>Abstract</p> <p>Background</p> <p>Next-generation sequencing technologies have led to the high-throughput production of sequence data (reads) at low cost. However, these reads are significantly shorter and more error-prone than conventional Sanger shotgun reads. This poses a challenge for the <it>de novo </it>assembly in terms of assembly quality and scalability for large-scale short read datasets.</p> <p>Results</p> <p>We present DecGPU, the first parallel and distributed error correction algorithm for high-throughput short reads (HTSRs) using a hybrid combination of CUDA and MPI parallel programming models. DecGPU provides CPU-based and GPU-based versions, where the CPU-based version employs coarse-grained and fine-grained parallelism using the MPI and OpenMP parallel programming models, and the GPU-based version takes advantage of the CUDA and MPI parallel programming models and employs a hybrid CPU+GPU computing model to maximize the performance by overlapping the CPU and GPU computation. The distributed feature of our algorithm makes it feasible and flexible for the error correction of large-scale HTSR datasets. Using simulated and real datasets, our algorithm demonstrates superior performance, in terms of error correction quality and execution speed, to the existing error correction algorithms. Furthermore, when combined with Velvet and ABySS, the resulting DecGPU-Velvet and DecGPU-ABySS assemblers demonstrate the potential of our algorithm to improve <it>de novo </it>assembly quality for <it>de</it>-<it>Bruijn</it>-graph-based assemblers.</p> <p>Conclusions</p> <p>DecGPU is publicly available open-source software, written in CUDA C++ and MPI. The experimental results suggest that DecGPU is an effective and feasible error correction algorithm to tackle the flood of short reads produced by next-generation sequencing technologies.</p

Districts, multinationals and global/digital networks

This paper reflects on what remains of Becattini’s utopia in the new context of a globalized and digital economy. Can one still foresee a global world populated with local societies able to produce value by following their own inspirations and chorally participating in a world-wide division of cognitive labor? It is suggested that the interpretive value of Becattini’s theorizing remains, to the extent that one moves away from the consideration of the classical district model, and adopts his more general way of thinking about the economy, which is only exemplified by the historical circumstance of industrial districts. His view may well apply to a variety of circumstances, not only to industrial districts and it is flexible enough to encompass economic change under different environmental conditions

A framework for the integration of green and lean six sigma for superior sustainability performance

Evidence suggests that Lean, Six Sigma and Green approaches make a positive contribution to the economic, social and environmental (i.e. sustainability) performance of organizations. However, evidence also suggests that organizations have found their integration and implementation challenging. The purpose of this research is therefore to present a framework that methodically guides companies through a five stages and sixteen steps process to effectively integrate and implement the Green, Lean and Six Sigma approaches to improve their sustainability performance. To achieve this, a critical review of the existing literature in the subject area was conducted to build a research gap, and subsequently develop the methodological framework proposed. The paper presents the results from the application of the proposed framework in four organizations with different sizes and operating in a diverse range of industries. The results showed that the integration of Lean Six Sigma and Green helped the organizations to averagely reduce their resources consumption from 20% to 40% and minimize the cost of energy and mass streams by 7-12%. The application of the framework should be gradual, the companies should assess their weaknesses and strengths, set priorities, and identify goals for successful implementation. This paper is one of the very first researches that presents a framework to integrate Green and Lean Six Sigma at a factory level, and hence offers the potential to be expanded to multiple factories or even supply chains

Research ethics committees: agents of research policy?

The purpose of this commentary is to describe the unintended effects ethics committees may have on research and to analyse the regulatory and administrative problems of clinical trials. DISCUSSION: The Finnish law makes an arbitrary distinction between medical research and other health research, and the European Union's directive for good clinical trials further differentiates drug trials. The starting point of current rules is that clinical trials are lesser in the interest of patients and society than routine health care. However, commercial interests are not considered unethical. The contrasting procedures in research and normal health care may tempt physicians to continue introducing innovations into practice by relying on unsystematic and uncontrolled observations. Tedious and bureaucratic rules may lead to the disappearance of trials initiated by researchers. Trying to accommodate the special legislative requirements for new drug trials into more complex interventions may result in poor designs with unreliable results and increased costs. Meanwhile, current legal requirements may undermine the morale of ethics committee members. CONCLUSION: The aims and the quality of the work of ethics committees should be evaluated, and a reformulation of the EU directive on good clinical trials is needed. Ethical judgement should consider the specific circumstance of each trial, and ethics committees should not foster poor research for legal reasons

The Role of Regional Knowledge Production in University Technology Transfer: Isolating Coevolutionary Effects

The rate and magnitude of university-to-industry-technology-transfer (UITT) is a function not only of university characteristics but also of regional factors. A university's embeddedness in an innovative regional milieu moderates UITT. This necessary balance of the supply side (technology push) and demand side (market pull) of technology transfer has so far neither been systematically addressed in the technology transfer literature nor has it been acknowledged by policy makers.We investigate UITT as a function of the interrelation of the industrial innovative milieu of a region and the characteristics of regional universities to identify the impact of the industry on UITT. Thereby we do not only aim to reduce the existing empirical gap in the academic entrepreneurship literature but also to inform policy in its attempt to foster UITT in European regions