Tree models for difference and change detection in a complex environment

A new family of tree models is proposed, which we call "differential trees." A differential tree model is constructed from multiple data sets and aims to detect distributional differences between them. The new methodology differs from the existing difference and change detection techniques in its nonparametric nature, model construction from multiple data sets, and applicability to high-dimensional data. Through a detailed study of an arson case in New Zealand, where an individual is known to have been laying vegetation fires within a certain time period, we illustrate how these models can help detect changes in the frequencies of event occurrences and uncover unusual clusters of events in a complex environment.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS548 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

The streptomyces cytoskeletal protein (Scy) is a key component of the tip organising centre for polarized growth in streptomyces coelicolor

The Gram-positive bacterium Streptomyces coelicolor, is one of the main genetic model organisms in the phylum of the Actinobacteria. Streptomyces bacteria are soil dwelling filamentous bacteria with a complex life cycle consisting of multigenomic hyphae that then form unicellular spores. Bacterial cell shape determination has been influenced heavily by the discovery that bacteria have a number of eukaryotic cytoskeletal homologues as well as a number of accessory proteins unique to prokaryotes. As cell shape determination is dependent on the sites of insertion of new cell wall material, this is characteristically organised and driven by cytoskeletal proteins. Streptomyces coelicolor hyphal growth occurs through apical extension where new cell wall material is placed at the tips. This growth is driven in part by the cytoskeletal protein DivIVA. Here we characterise a novel Streptomyces cytoskeletal protein, Scy, encoded by the locus sco5397. Scy is a large protein with a novel coiled-coil 51-mer repeat structure. To study Scy, a scy knockout mutation was generated. The phenotype of the scy mutant suggests that it plays a significant role in cell shape, growth and chromosome positioning. Translational fluorescent protein fusions to scy were made and the subcellular localisation of Scy was determined to be strongly at growing hyphal tips. Further clarified here, Scy overexpression can recruit DivIVA protein and the cell wall synthesis machinery to new apical sites. The reciprocal is also shown whereby DivIVA overexpression can recruit Scy to new apical sites. Further to this in vivo and in vitro experiments were performed to determine that Scy and DivIVA interact, as well as the protein FilP encoded downstream of scy. The work here along with work in the field suggests that Scy forms part of a Tip Organising Centre (TIPOC) that alongside DivIVA, FilP, and numerous other proteins controls apical growth in the filamentous Streptomyces

Developing High Performance Computing Resources for Teaching Cluster and Grid Computing courses

High-Performance Computing (HPC) and the ability to process large amounts of data are of paramount importance for UK business and economy as outlined by Rt Hon David Willetts MP at the HPC and Big Data conference in February 2014. However there is a shortage of skills and available training in HPC to prepare and expand the workforce for the HPC and Big Data research and development. Currently, HPC skills are acquired mainly by students and staff taking part in HPC-related research projects, MSc courses, and at the dedicated training centres such as Edinburgh University’s EPCC. There are few UK universities teaching the HPC, Clusters and Grid Computing courses at the undergraduate level. To address the issue of skills shortages in the HPC it is essential to provide teaching and training as part of both postgraduate and undergraduate courses. The design and development of such courses is challenging since the technologies and software in the fields of large scale distributed systems such as Cluster, Cloud and Grid computing are undergoing continuous change. The students completing the HPC courses should be proficient in these evolving technologies and equipped with practical and theoretical skills for future jobs in this fast developing area. In this paper we present our experience in developing the HPC, Cluster and Grid modules including a review of existing HPC courses offered at the UK universities. The topics covered in the modules are described, as well as the coursework projects based on practical laboratory work. We conclude with an evaluation based on our experience over the last ten years in developing and delivering the HPC modules on the undergraduate courses, with suggestions for future work

Growing intimate privatepublics: Everyday utopia in the naturecultures of a young lesbian and bisexual women’s allotment

The Young Women’s Group in Manchester is a ‘young women’s peer health project, run by and for young lesbian and bisexual women’, which runs an allotment as one of its activities. At a time when interest in allotments and gardening appears to be on the increase, the existence of yet another community allotment may seem unremarkable. Yet we suggest that this queer allotment poses challenges for conventional theorisations of allotments, as well as for understandings of public and private. In this article we explore how the allotment project might be understood to be intensely engaged in ‘growing intimate publics’, or what we term ‘privatepublics’. These are paradoxical intimacies, privatepublic spaces which are not necessarily made possible in the usual private sphere of domestic homes. Here we focus on the work involved in materialising the allotment, which we understand as a queer privatepublic ‘natureculture’ (Haraway, 2008) which appears as an ‘everyday utopia’ (Cooper, 2014)

Propagation of highly nonlinear signals in a two dimensional network of granular chains

We report the first experimental observation of highly nonlinear signals propagating in a two dimensional system composed of granular chains. In this system one of the chains contacts two others to allow splitting and redirecting the solitary-like signal formed in the first chain. The system consists of a double Y-shaped guide in which high- and low-modulus chains of spheres are arranged in various geometries. We observed fast splitting of the initial pulse, rapid chaotization of the signal and sharp bending of the propagating acoustic information. Pulse and energy trapping was also observed in composite systems assembled from hard- and soft-particles in the branches

Implications of Shock Wave Experiments with Precompressed Materials for Giant Planet Interiors

This work uses density functional molecular dynamics simulations of fluid helium at high pressure to examine how shock wave experiments with precompressed samples can help characterizing the interior of giant planets. In particular, we analyze how large of a precompression is needed to probe a certain depth in a planet's gas envelope. We find that precompressions of up to 0.1, 1.0, 10, or 100 GPa are needed to characterized 2.5, 5.9, 18, to 63% of Jupiter's envelope by mass.Comment: Submitted As Proceedings Article For The American Physical Society Meeting On Shock Compression Of Condensed Matter, Hawaii, June, 200

Predicting C-H/π\pi interactions with nonlocal density functional theory

We examine the performance of a recently developed nonlocal density functional in predicting a model noncovalent interaction, the weak bond between an aromatic $\pi$ system and an aliphatic C-H group. The new functional is a significant improvement over traditional density functionals, providing results which compare favorably to high-level quantum-chemistry techniques but at considerably lower computational cost. Interaction energies in several model C-H/$\pi$ systems are in generally good agreement with coupled-cluster calculations, though equilibrium distances are consistently overpredicted when using the revPBE functional for exchange. The new functional correctly predicts changes in energy upon addition of halogen substituents.Comment: 5 pages, 4 figure

Climate and atmospheric circulation during the Early and Mid-Holocene inferred from lake-carbonate oxygen-isotope records from western Ireland

The Early to Mid-Holocene experienced marked climate change over the northern hemisphere mid-latitudes in response to changing insolation and declining ice volume. Oxygen isotopes from lake sediments provide a valuable climate proxy, encoding information regarding temperature, hydroclimate and moisture source. We present oxygen-isotope records from two lakes in western Ireland that are strongly influenced by the North Atlantic. Excellent replication between the records suggests they reflect regional, not local, influences. Carbonate oxygen-isotope values peaked at the start of the Holocene, between 11.2 and 11.1 cal ka bp, and then decreased markedly until 6 cal ka bp at both sites. Palaeoecological evidence supports only modest change in temperature or hydroclimate during this interval and we therefore explain the decrease primarily by a reduction in the oxygen-isotope composition of precipitation (δ18Oppt). We show a similar decrease in δ18O values in a forward model of carbonate isotopes between 12–11 and 6–5 cal ka bp. However, the inferred reduction in δ18Oppt between the Early and Mid-Holocene in the model is mainly linked to a decrease in the δ18O of the ocean source water from ice sheet melting whereas the lake carbonate isotope records are more consistent with changes in the transport pathway of moisture associated with atmospheric circulation change as the dominant cause