Extensible Component Based Architecture for FLASH, A Massively Parallel, Multiphysics Simulation Code

FLASH is a publicly available high performance application code which has evolved into a modular, extensible software system from a collection of unconnected legacy codes. FLASH has been successful because its capabilities have been driven by the needs of scientific applications, without compromising maintainability, performance, and usability. In its newest incarnation, FLASH3 consists of inter-operable modules that can be combined to generate different applications. The FLASH architecture allows arbitrarily many alternative implementations of its components to co-exist and interchange with each other, resulting in greater flexibility. Further, a simple and elegant mechanism exists for customization of code functionality without the need to modify the core implementation of the source. A built-in unit test framework providing verifiability, combined with a rigorous software maintenance process, allow the code to operate simultaneously in the dual mode of production and development. In this paper we describe the FLASH3 architecture, with emphasis on solutions to the more challenging conflicts arising from solver complexity, portable performance requirements, and legacy codes. We also include results from user surveys conducted in 2005 and 2007, which highlight the success of the code.Comment: 33 pages, 7 figures; revised paper submitted to Parallel Computin

Randomised trial of cord clamping at very preterm birth: outcomes at 2 years

Objective: To report outcomes at 2 years corrected age for children of women recruited to a trial comparing alternative policies for timing of cord clamping and immediate neonatal care at very preterm birth. Design: Parallel group randomised (1:1) trial. Setting: Eight UK tertiary maternity units. Participants: Two hundred and seventy six babies born to 261 women expected to have a livebirth before 32+0 weeks gestation. Interventions: Deferred cord clamping (≥2 minutes) and immediate neonatal care with cord intact, or immediate (≤20 seconds) clamping and immediate neonatal care after clamping. Main outcome measure: Composite of death or adverse neurodevelopmental outcome at 2 years corrected age. Results: Six babies born after 35+6 weeks were excluded. At 2 years corrected age, outcome data were not available for a further 52 children, leaving 218 for analysis (115 deferred clamping, 103 immediate clamping). Overall, 24/115 (21%) children allocated deferred clamping died or had an adverse neurodevelopmental outcome compared with 35/103 (34%) allocated immediate clamping; relative risk (RR) 0.61 (95% confidence interval [CI] 0.39 to 0.96); risk difference (RD) -13% (95% CI -25% to -1%). Multiple imputation for missing data gave a RR 0.69 (95% CI 0.44 to 1.09) and RD -9% (95% CI -21% to 2%). Conclusions: Deferred clamping and immediate neonatal care with cord intact may reduce the risk of death or adverse neurodevelopmental outcome at 2 years of age for children born very premature. Confirmation in larger studies is needed to determine the real benefits and harms

How to Get Engagement Right in Mental Health Research:Lessons from the Higher Education Sector

This resource pack outlines the benefits of engagement with students and other key stakeholders in the Higher Education sector. It also discusses the challenges, how these might be navigated, and resources and practices that would support engagement. This is based on what we have learned as a network, and will complement and signpost to existing resources. There are lots of different ways to involve non-research stakeholders, and we have provided case examples to showcase all the different things we have done during SMaRteN as well as provide guidance for the sector. This guidance is also aimed at students and other key stakeholders who are interested in getting involved in research

Images of Research:An Art Gallery and Puzzle Book

Images of Research is an annual competition that challenges researchers to capture their work in a single image, alongside a short description. This competition has been run at the University of Dundee since 2020 and represents just a handful of the research projects being carried out by postgraduate researchers.The competition celebrates our research and the many original ways it can be expressed. This collection showcases the winning entries, mixed with fun sketches and puzzles to complete

Images of Research:An Art Gallery and Puzzle Book

Images of Research is an annual competition that challenges researchers to capture their work in a single image, alongside a short description. This competition has been run at the University of Dundee since 2020 and represents just a handful of the research projects being carried out by postgraduate researchers.The competition celebrates our research and the many original ways it can be expressed. This collection showcases the winning entries, mixed with fun sketches and puzzles to complete

Shaping electron wave functions in a carbon nanotube with a parallel magnetic field

A magnetic field, through its vector potential, usually causes measurable changes in the electron wave function only in the direction transverse to the field. Here we demonstrate experimentally and theoretically that in carbon nanotube quantum dots, combining cylindrical topology and bipartite hexagonal lattice, a magnetic field along the nanotube axis impacts also the longitudinal profile of the electronic states. With the high (up to 17T) magnetic fields in our experiment the wave functions can be tuned all the way from "half-wave resonator" shape, with nodes at both ends, to "quarter-wave resonator" shape, with an antinode at one end. This in turn causes a distinct dependence of the conductance on the magnetic field. Our results demonstrate a new strategy for the control of wave functions using magnetic fields in quantum systems with nontrivial lattice and topology.Comment: 5 figure

RLP/K enrichment sequencing; a novel method to identify receptor-like protein (RLP) and receptor-like kinase (RLK) genes

The identification of immune receptors in crop plants is time-consuming but important for disease control. Previously, resistance gene enrichment sequencing (RenSeq) was developed to accelerate mapping of nucleotide-binding domain and leucine-rich repeat containing (NLR) genes. However, resistances mediated by pattern recognition receptors (PRRs) remain less utilized. Here, our pipeline shows accelerated mapping of PRRs. Effectoromics leads to precise identification of plants with target PRRs, and subsequent RLP/K enrichment sequencing (RLP/KSeq) leads to detection of informative single nucleotide polymorphisms that are linked to the trait. Using Phytophthora infestans as a model, we identified Solanum microdontum plants that recognize the apoplastic effectors INF1 or SCR74. RLP/KSeq in a segregating Solanum population confirmed the localization of the INF1 receptor on chromosome 12, and led to the rapid mapping of the response to SCR74 to chromosome 9. By using markers obtained from RLP/KSeq in conjunction with additional markers, we fine-mapped the SCR74 receptor to a 43-kbp G-LecRK locus. Our findings show that RLP/KSeq enables rapid mapping of PRRs and is especially beneficial for crop plants with large and complex genomes. This work will enable the elucidation and characterization of the nonNLR plant immune receptors and ultimately facilitate informed resistance breeding.</p

Mapping the H2 resistance effective against Globodera pallida pathotype Pa1 in tetraploid potato

This work was supported by the Rural & Environment Science & Analytical Services Division of the Scottish Government, the BBSRC, through the joint projects CRF/2009/SCRI/SOP 0929, BB/L008025/1 and BB/K018299/1. Additional funding was obtained through the James Hutton Institute SEEDCORN initiative, AHDB Potato, the Perry Foundation and The Felix Cobbold Trust. Amanpreet Kaur was supported by the Commonwealth Scholarship Commission through a Commonwealth split-site Ph.D. grant.Key message: The nematode resistance gene H2 was mapped to the distal end of chromosome 5 in tetraploid potato. The H2 resistance gene, introduced into cultivated potatoes from the wild diploid species Solanum multidissectum, confers a high level of resistance to the Pa1 pathotype of the potato cyst nematode Globodera pallida. A cross between tetraploid H2-containing breeding clone P55/7 and susceptible potato variety Picasso yielded an F1 population that segregated approximately 1:1 for the resistance phenotype, which is consistent with a single dominant gene in a simplex configuration. Using genome reduction methodologies RenSeq and GenSeq, the segregating F1 population enabled the genetic characterisation of the resistance through a bulked segregant analysis. A diagnostic RenSeq analysis of the parents confirmed that the resistance in P55/7 cannot be explained by previously characterised resistance genes. Only the variety Picasso contained functionally characterised disease resistance genes Rpi-R1, Rpi-R3a, Rpi-R3b variant, Gpa2 and Rx, which was independently confirmed through effector vacuum infiltration assays. RenSeq and GenSeq independently identified sequence polymorphisms linked to the H2 resistance on the top end of potato chromosome 5. Allele-specific KASP markers further defined the locus containing the H2 gene to a 4.7 Mb interval on the distal short arm of potato chromosome 5 and to positions that correspond to 1.4 MB and 6.1 MB in the potato reference genome.Publisher PDFPeer reviewe