Affordable High Powered Clustered Computing for Aerospace Simulation. G.U. Aero Report 9911

Motivated by a lack of sufficient local and national computing facilities for computational fluid dynamics simulations, the Affordable Systems Computing Unit (ASCU) was established to investigate low cost alternatives. The options considered have all involved cluster computing, a term which refers to the grouping of a number of components into a managed system capable of running both serial and parallel applications. Past work by the Unit has demonstrated the significant improvement in the efficiency of a Network of Workstations when management software is employed to scavenge spare cycles and schedule tasks, and has also investigated the use of a managed network for parallel CFD. The present work aims to extend this effort to a higher performance cluster based on commodity processors used for dedicated batch processing. The performance of the cluster has proved to be extremely cost effective, producing a 3 Gigaflops plus peak performance for less than 25K U.K. pounds sterling at current market prices. The experience gained on this system in terms of single node performance, message passing and parallel performance will be discussed. In particular, comparisons with the performance of other systems will be made. A large scale CFD simulation achieved using the new cluster will be presented to demonstrate the potential of commodity processor based parallel computers for aerodynamic simulation

Retromer controls planar polarity protein levels and asymmetric localization at intercellular junctions

The coordinated polarization of cells in the plane of a tissue, termed planar polarity, is a characteristic feature of epithelial tissues [1]. In the fly wing, trichome positioning is dependent on the core planar polarity proteins adopting asymmetric subcellular localizations at apical junctions, where they form intercellular complexes that link neighboring cells [1-3]. Specifically, the seven-pass transmembrane protein Frizzled and the cytoplasmic proteins Dishevelled and Diego localize to distal cell ends, the four-pass transmembrane protein Strabismus and the cytoplasmic protein Prickle localize proximally, and the seven-pass transmembrane spanning atypical cadherin Flamingo localizes both proximally and distally. To establish asymmetry, these core proteins are sorted from an initially uniform distribution; however, the mechanisms underlying this polarized trafficking remain poorly understood. Here, we describe the identification of retromer, a master controller of endosomal recycling [4-6], as a key component regulating core planar polarity protein localization in Drosophila. Through generation of mutants, we verify that loss of the retromer-associated Snx27 cargo adaptor, but notably not components of the Wash complex, reduces junctional levels of the core proteins Flamingo and Strabismus in the developing wing. We establish that Snx27 directly associates with Flamingo via its C-terminal PDZ binding motif, and we show that Snx27 is essential for normal Flamingo trafficking. We conclude that Wash-independent retromer function and the Snx27 cargo adaptor are important components in the endosomal recycling of Flamingo and Strabismus back to the plasma membrane and thus contribute to the establishment and maintenance of planar polarization

Adjuvant selection for influenza and RSV prefusion subunit vaccines

Subunit vaccines exhibit favorable safety and immunogenicity profiles and can be designed to mimic native antigen structures. However, pairing with an appropriate adjuvant is imperative in order to elicit effective humoral and cellular immune responses. In this study, we aimed to determine an optimal adjuvant pairing with the prefusion form of influenza haemagglutinin (HA) or respiratory syncytial virus (RSV) fusion (F) subunit vaccines in BALB/c mice in order to inform future subunit vaccine adjuvant selection. We tested a panel of adjuvants, including aluminum hydroxide (alhydrogel), QS21, Addavax, Addavax with QS21 (AdQS21), and Army Liposome Formulation 55 with monophosphoryl lipid A and QS21 (ALF55). We found that all adjuvants elicited robust humoral responses in comparison to placebo, with the induction of potent neutralizing antibodies observed in all adjuvanted groups against influenza and in AdQS21, alhydrogel, and ALF55 against RSV. Upon HA vaccination, we observed that none of the adjuvants were able to significantly increase the frequency of CD4+ and CD8+ IFN-γ+ cells when compared to unadjuvanted antigen. The varying responses to antigens with each adjuvant highlights that those adjuvants most suited for pairing purposes can vary depending on the antigen used and/or the desired immune response. We therefore suggest that an adjuvant trial for different subunit vaccines in development would likely be necessary in preclinical studies.Ariel Isaacs, Zheyi Li, Stacey T. M. Cheung, Danushka K. Wijesundara, Christopher L. D. McMillan, Naphak Modhiran ...et al

Diving into the vertical dimension of elasmobranch movement ecology

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements

A MODEST review

We present an account of the state of the art in the fields explored by the research community invested in 'Modeling and Observing DEnse STellar systems'. For this purpose, we take as a basis the activities of the MODEST-17 conference, which was held at Charles University, Prague, in September 2017. Reviewed topics include recent advances in fundamental stellar dynamics, numerical methods for the solution of the gravitational N-body problem, formation and evolution of young and old star clusters and galactic nuclei, their elusive stellar populations, planetary systems, and exotic compact objects, with timely attention to black holes of different classes of mass and their role as sources of gravitational waves. Such a breadth of topics reflects the growing role played by collisional stellar dynamics in numerous areas of modern astrophysics. Indeed, in the next decade, many revolutionary instruments will enable the derivation of positions and velocities of individual stars in the Milky Way and its satellites and will detect signals from a range of astrophysical sources in different portions of the electromagnetic and gravitational spectrum, with an unprecedented sensitivity. On the one hand, this wealth of data will allow us to address a number of long-standing open questions in star cluster studies; on the other hand, many unexpected properties of these systems will come to light, stimulating further progress of our understanding of their formation and evolution.Comment: 42 pages; accepted for publication in 'Computational Astrophysics and Cosmology'. We are much grateful to the organisers of the MODEST-17 conference (Charles University, Prague, September 2017). We acknowledge the input provided by all MODEST-17 participants, and, more generally, by the members of the MODEST communit

Improving the characterization of Quaternary deposits for groundwater vulnerability assessments using maps of recharge and attenuation potential

Assessing aquifer vulnerability is difficult for bedrock aquifers concealed by highly variable superficial deposits such as glacial till. Many current groundwater vulnerability maps, and the geological maps on which they are based, do not adequately account for regional and vertical variations in the characteristics of superficial deposits. A new method for characterizing recharge potential and contaminant retardation potential of superficial deposits is presented here, which captures primary geological and hydrogeological expert knowledge in a systematic manner. The method modifies existing superficial geology maps using Quaternary domains and their descriptions, bedrock lithology and thickness of superficial deposits, and applies additional information on superficial geology and bedrock lithology. Central to the method is a matrix that allows local geological and hydrogeological knowledge to be incorporated in a systematic and traceable manner. The scale-independent method has been piloted at 1:625 000 scale to produce maps of recharge and attenuation potential for Great Britain. Preliminary verification against several indicators (HOST data, the Scottish vulnerability screening tool, and nitrate data) has been encouraging. The method is being used by the Environment Agency as part of its vulnerability assessments for the characterization of groundwater bodies as required by the Water Framework Directive

Classification of artificial (man-made) ground

The legacy inherited from anthropogenic processes needs to be addressed in order to provide reliable and up-to-date ground information relevant to development and regeneration in the urban environment. The legacy includes voids as well as anthropogenic deposits (artificial ground). Their characteristics derive from former quarrying and mining activities, industrial processes creating derelict ground, variably consolidated made ground, and contaminated groundwater and soils. All need to be systematically assessed to inform the planning process and provide the basis for engineering solutions. Site-specific investigation needs to be conducted on the back of good quality geoscientific data. This comes from ‘field’ survey, remotely sensed data interpretation, historical maps, soil geochemical sampling, and geotechnical investigation. Three-dimensional and, in the future, four dimensional, characterization of superficial deposits is required to reach an understanding of the potential spatial lithological variability of artificial ground and the geometry of important surfaces, i.e. the boundary conditions. The classification scheme for artificial ground outlined in this paper and adopted by the British Geological Survey, will help in achieving this understanding