Obituary: Arthur Cruickshank 1932 - 2011. A native Gondwanan, who studied the former continent's fossil tetrapods

Dr Arthur Richard Ivor Cruickshank died on 4th December 2011, aged 79, in the Borders General Hospital, Melrose, Scotland. Arthur Cruickshank was part of the post-war generation of palaeontologists who laid the foundations on which today’s researchers build. Appropriately for someone from an expatriate Scots family living in Kenya, much of his work was on the extinct reptiles of the great southern palaeocontinent of Gondwana

Improving research and policy interactions requires a better understanding of what works in different contexts.

There is keen interest in many jurisdictions in finding ways to improve the way that research evidence informs policy. One possible mechanism for this is to embed academics within government agencies either as advisers or full staff members. Our commentary argues that, in addition to considering the role of academics in government as proposed by Glied and colleagues, we need to understand better how research and policy interactions function across policy sectors. We believe more comparative research is needed to understand if and why academics from certain disciplines are more likely to be recruited to work in some policy sectors rather than others. We caution against treating government as monolithic by advocating the same model for collaborative interaction between academics and government. Lastly, we contend that contextualized research is needed to illuminate important drivers of research and policy interactions before we can recommend what is likely to be more and less effective in different policy sectors

FINN: A Framework for Fast, Scalable Binarized Neural Network Inference

Research has shown that convolutional neural networks contain significant redundancy, and high classification accuracy can be obtained even when weights and activations are reduced from floating point to binary values. In this paper, we present FINN, a framework for building fast and flexible FPGA accelerators using a flexible heterogeneous streaming architecture. By utilizing a novel set of optimizations that enable efficient mapping of binarized neural networks to hardware, we implement fully connected, convolutional and pooling layers, with per-layer compute resources being tailored to user-provided throughput requirements. On a ZC706 embedded FPGA platform drawing less than 25 W total system power, we demonstrate up to 12.3 million image classifications per second with 0.31 {\mu}s latency on the MNIST dataset with 95.8% accuracy, and 21906 image classifications per second with 283 {\mu}s latency on the CIFAR-10 and SVHN datasets with respectively 80.1% and 94.9% accuracy. To the best of our knowledge, ours are the fastest classification rates reported to date on these benchmarks.Comment: To appear in the 25th International Symposium on Field-Programmable Gate Arrays, February 201

On the Fourier dimension of (d,k)-sets and Kakeya sets with restricted directions

Funding: JMF was financially supported by an EPSRC Standard Grant (EP/R015104/1) and a Leverhulme Trust Research Project Grant (RPG-2019-034).A (d, k)-set is a subset of ℝd containing a k-dimensional unit ball of all possible orientations. Using an approach of D. Oberlin we prove various Fourier dimension estimates for compact (d, k)-sets. Our main interest is in restricted (d, k)-sets, where the set only contains unit balls with a restricted set of possible orientations Γ. In this setting our estimates depend on the Hausdorff dimension of Γ and can sometimes be improved if additional geometric properties of Γ are assumed. We are led to consider cones and prove that the cone in ℝd+1 has Fourier dimension d−1, which may be of interest in its own right.Publisher PDFPeer reviewe

Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes

Laboratory-directed evolution as a tool for anticipating insecticide resistance

The evolution of insecticide resistance provides a eukaryotic model system for studying enzyme evolution. Understanding the molecular basis of insecticide resistance can assist both the development of new methods to combat resistance and the anticipation of future resistance. Three insect species have independently evolved catalytic organophosphate (OP) insecticide resistance through a single active-site mutation (Gly\u3eAsp) in the αE7 enzyme1-3. To explore the evolutionary potential of αE7, we subjected αE7 from the blowfly Lucilia cuprina to nine rounds of mutation and selection, resulting in a \u3e1000-fold increase in OP-hydrolase activity and a kcat / KM \u3e 106 M-1 min-1. Kinetic and structural analysis of the evolutionary trajectory revealed the molecular basis for the increase in catalytic efficiency. Mutations occurring in the early stages of the trajectory enrich the productive side chain conformation of the key aspartic acid residue, while mutations in later stages remodel the binding pocket. Remarkably, mutations appearing in the later rounds yielded larger improvements in catalytic efficiency compared to initial mutations, indicating that the initial Gly\u3eAsp mutation represents only a fraction of the αE7 evolutionary potential. Worryingly, this suggests that the Gly\u3eAsp could be the first of many steps toward efficient OP-insecticide detoxification. Please click Additional Files below to see the full abstract