Towards convection-resolving, global atmospheric simulations with the Model for Prediction Across Scales (MPAS) v3.1: an extreme scaling experiment, links to sourcecode of model and grides

The Model for Prediction Across Scales (MPAS) is a novel set of Earth system simulation components and consists of an atmospheric model, an ocean model and a land-ice model. Its distinct features are the use of unstructured Voronoi meshes and C-grid discretisation to address shortcomings of global models on regular grids and the use of limited area models nested in a forcing data set, with respect to parallel scalability, numerical accuracy and physical consistency. This concept allows one to include the feedback of regional land use information on weather and climate at local and global scales in a consistent way, which is impossible to achieve with traditional limited area modelling approaches. Here, we present an in-depth evaluation of MPAS with regards to technical aspects of performing model runs and scalability for three medium-size meshes on four different high-performance computing (HPC) sites with different architectures and compilers. We uncover model limitations and identify new aspects for the model optimisation that are introduced by the use of unstructured Voronoi meshes. We further demonstrate the model performance of MPAS in terms of its capability to reproduce the dynamics of the West African monsoon (WAM) and its associated precipitation in a pilot study. Constrained by available computational resources, we compare 11-month runs for two meshes with observations and a reference simulation from the Weather Research and Forecasting (WRF) model. We show that MPAS can reproduce the atmospheric dynamics on global and local scales in this experiment, but identify a precipitation excess for the West African region. Finally, we conduct extreme scaling tests on a global 3?km mesh with more than 65 million horizontal grid cells on up to half a million cores. We discuss necessary modifications of the model code to improve its parallel performance in general and specific to the HPC environment. We confirm good scaling (70?% parallel efficiency or better) of the MPAS model and provide numbers on the computational requirements for experiments with the 3?km mesh. In doing so, we show that global, convection-resolving atmospheric simulations with MPAS are within reach of current and next generations of high-end computing facilities.

Future fish distributions constrained by depth in warming seas

European continental shelf seas have experienced intense warming over the past 30 years1. In the North Sea, fish have been comprehensively monitored throughout this period and resulting data provide a unique record of changes in distribution and abundance in response to climate change2, 3. We use these data to demonstrate the remarkable power of generalized additive models (GAMs), trained on data earlier in the time series, to reliably predict trends in distribution and abundance in later years. Then, challenging process-based models that predict substantial and ongoing poleward shifts of cold-water species4, 5, we find that GAMs coupled with climate projections predict future distributions of demersal (bottom-dwelling) fish species over the next 50 years will be strongly constrained by availability of habitat of suitable depth. This will lead to pronounced changes in community structure, species interactions and commercial fisheries, unless individual acclimation or population-level evolutionary adaptations enable fish to tolerate warmer conditions or move to previously uninhabitable locations.

Future fish distributions constrained by depth in warming seas

European continental shelf seas have experienced intense warming over the past 30 years1. In the North Sea, fish have been comprehensively monitored throughout this period and resulting data provide a unique record of changes in distribution and abundance in response to climate change2, 3. We use these data to demonstrate the remarkable power of generalized additive models (GAMs), trained on data earlier in the time series, to reliably predict trends in distribution and abundance in later years. Then, challenging process-based models that predict substantial and ongoing poleward shifts of cold-water species4, 5, we find that GAMs coupled with climate projections predict future distributions of demersal (bottom-dwelling) fish species over the next 50 years will be strongly constrained by availability of habitat of suitable depth. This will lead to pronounced changes in community structure, species interactions and commercial fisheries, unless individual acclimation or population-level evolutionary adaptations enable fish to tolerate warmer conditions or move to previously uninhabitable locations.

Optimisation of a droplet digital PCR assay for the diagnosis of Schistosoma japonicum infection: A duplex approach with DNA binding dye chemistry

Schistosomiasis is a chronically debilitating helminth infection with a significant socio-economic and public health impact. Accurate diagnostics play a pivotal role in achieving current schistosomiasis control and elimination goals. However, many of the current diagnostic procedures, which rely on detection of schistosome eggs, have major limitations including lack of accuracy and the inability to detect pre-patent infections. DNA-based detection methods provide a viable alternative to the current tests commonly used for schistosomiasis diagnosis. Here we describe the optimisation of a novel droplet digital PCR (ddPCR) duplex assay for the diagnosis of Schistosoma japonicum infection which provides improved detection sensitivity and specificity. The assay involves the amplification of two specific and abundant target gene sequences in S. japonicum; a retrotransposon (SjR2) and a portion of a mitochondrial gene (nad1). The assay detected target sequences in different sources of schistosome DNA isolated from adult worms, schistosomules and eggs, and exhibits a high level of specificity, thereby representing an ideal tool for the detection of low levels of parasite DNA in different clinical samples including parasite cell free DNA in the host circulation and other bodily fluids. Moreover, being quantitative, the assay can be used to determine parasite infection intensity and, could provide an important tool for the detection of low intensity infections in low prevalence schistosomiasis-endemic areas.

Energy efficiency optimization in hardware-constrained large-scale MIMO systems

Large-scale multiple-input multiple-output (MIMO) communication systems can bring substantial improvement in spectral efficiency and/or energy efficiency, due to the excessive degrees-of-freedom and huge array gain. However, large-scale MIMO is expected to deploy lower-cost radio frequency (RF) components, which are particularly prone to hardware impairments. Unfortunately, compensation schemes are not able to remove the impact of hardware impairments completely, such that a certain amount of residual impairments always exists. In this paper, we investigate the impact of residual transmit RF impairments (RTRI) on the spectral and energy efficiency of training-based point-to-point large-scale MIMO systems, and seek to determine the optimal training length and number of antennas which maximize the energy efficiency. We derive deterministic equivalents of the signal-to-noise-and-interference ratio (SINR) with zero-forcing (ZF) receivers, as well as the corresponding spectral and energy efficiency, which are shown to be accurate even for small number of antennas. Through an iterative sequential optimization, we find that the optimal training length of systems with RTRI can be smaller compared to ideal hardware systems in the moderate SNR regime, while larger in the high SNR regime. Moreover, it is observed that RTRI can significantly decrease the optimal number of transmit and receive antennas.

No second chance: junior neonatal nurses' experiences of caring for babies at the end-of-life and their families

Death of an infant is acutely stressful for parents and professionals. Little is known about junior nurses' experiences providing end-of-life care in Neonatal units (NNU). This study aimed to better understand junior nurses' experiences providing end-of-life care in NNU. Neonatal nurses (n = 12) with less than 3 years experience participated in a focus group. Nominal Group Technique (NGT) was used to build consensus around the challenges faced, alongside suggested developments in improving future care provision. Primary analysis involved successive rounds of ranking and decision-making whilst secondary analysis involved thematic analysis. All issues, whether environmental, professional or social appeared driven by an awareness on the part of nurses, that there was no ‘second chance’ which created a huge pressure to ‘get if right’ for the infants and families. Regarding future care 2 areas of improvement identified were ‘Education and Training’ and Support. This paper unpacks these findings making recommendations for practice.

Physical model parameter optimisation for calibrated emulation of the Dallas Rangemaster Treble Booster guitar pedal

In this work we explore optimising parameters of a physical circuit model relative to input/output measurements, using the Dallas Rangemaster Treble Booster as a case study. A hybrid metaheuristic/gradient descent algorithm is implemented, where the initial parameter sets for the optimisation are informed by nominal values from schematics and datasheets. Sensitivity analysis is used to screen parameters, which informs a study of the optimisation algorithm against model complexity by fixing parameters. The results of the optimisation show a significant increase in the accuracy of model behaviour, but also highlight several key issues regarding the recovery of parameters.

No second chance: the experiences of junior neonatal nurses in providing end-of-life care for babies and families in the NNU

Background

An infant’s death is acutely stressful for parents and professionals. Little is known about junior nurses’ experiences providing end-of-life care in Neonatal Units (NNU).

Objectives

To better understand junior nurses’ experiences providing end-of-life care in NNU, the study explored the challenges and opportunities inherent in their practice relating to providing such care to babies and their families.

Methods

Neonatal nurses (n=12) with less than 3 years’ experience who were undergoing a neonatal education programme participated. Two focus groups were convened each with 6 nurses. The Ethics Committee at the relevant University approved the study. Nominal Group Technique (NGT) was used in the focus groups to build consensus around the challenges faced by junior nurses, alongside suggested developments in improving future care provision. Primary analysis involved successive rounds of ranking and decision making whilst secondary analysis involved thematic analysis.

Results

The study identified the pressures these nurses felt in having only one chance to ‘get it right’ for the infants and their families. They perceived the need for further ‘education and training’ highlighting that improved education provision would include both additional courses and internal training sessions. Greater ‘support’ from mentors themselves more experienced in this aspect of care within the NNU was identified as important in addressing issues around confidence building and skill development.

Conclusions

The results highlight junior nurses’ need for specific education and mentorship around end-of-life care for babies. This presentation will outline the implications for practice, education and further research.

Fast iterative solvers for time-dependent PDE-constrained optimization problems

Otto-von-Guericke-Universität Magdeburg, Fakultät für Mathematik, Kumulative Habilitation, 2016

Caractérisation et optimisation d'un détecteur à scintillation à 2 points

Ce projet de recherche s’inscrit dans le domaine de la dosimétrie à scintillation en radiothérapie, plus précisément en curiethérapie à haut débit de dose (HDR). Lors de ce type de traitement, la dose est délivrée localement, ce qui implique de hauts gradients de dose autour de la source. Le but de ce travail est d’obtenir un détecteur mesurant la dose en 2 points distincts et optimisé pour la mesure de dose en curiethérapie HDR. Pour ce faire, le projet de recherche est séparé en deux études : la caractérisation spectrale du détecteur à 2-points et la caractérisation du système de photodétecteur menant à la mesure de la dose. D’abord, la chaine optique d’un détecteur à scintillation à 2-points est caractérisée à l’aide d’un spectromètre afin de déterminer les composantes scintillantes optimales. Cette étude permet de construire quelques détecteurs à partir des composantes choisies pour ensuite les tester avec le système de photodétecteur multi-point. Le système de photodétecteur est aussi caractérisé de façon à évaluer les limites de sensibilité pour le détecteur 2-points choisi précédemment. L’objectif final est de pouvoir mesurer le débit de dose avec précision et justesse aux deux points de mesure du détecteur multi-point lors d’un traitement de curiethérapie HDR.

Optimisation de l’élevage intensif des larves de doré jaune (sander vitreus) dans les systèmes aquacoles en recirculation

Les percidés, dont le doré jaune (Sander vitreus), représentent une opportunité considérable de diversification de l’offre pour l’industrie aquacole au Canada, mais aussi ailleurs dans le monde. Malgré son fort potentiel, les producteurs de dorés sont marginaux, car l’élevage larvaire s’avère difficile et complexe, résultant en des succès de survie variables. Pour un développement durable de l’aquaculture, mais aussi pour assurer un meilleur contrôle des paramètres environnementaux, et conséquemment une meilleure rentabilité, les nouvelles méthodes d’élevage s’orientent vers l’utilisation de systèmes en recirculation où l’eau est majoritairement filtrée et recyclée. Un premier volet de nos travaux réalisés en 2014 a confirmé que (i) les méthodes intensives d’élevage larvaire peuvent être adaptés dans les systèmes en recirculation, que (ii) la moulée commerciale enrichie de farine de krills offre une meilleure croissance qu’une moulée commerciale enrichie aux microalgues, (iii) que des artémies vivantes ne favorise pas l’ingestion alimentaire lorsqu’ils sont ajoutés à des rations d’une moulée commerciale enrichie de farine de krills et (iv) que le développement de la vessie natatoire est le défi principal afin de produire du doré en circuit recyclé de façon rentable. Une étude menée en 2015 visait à favoriser le développement de la vessie natatoire du doré dans les systèmes en recirculation. Quatre traitements ont été comparés soit, un jet d’eau de surface faible, un jet d’eau de surface fort, un microbulleur et un rondin commercial d’absorption d’huile. Nous avons démontré que (i) l’utilisation d’un jet d’eau de surface faible n’était pas suffisant pour favoriser le développement de la vessie natatoire du doré dans les systèmes où l’eau est fortement recirculée et (ii) qu’un rondin d’absorption d’huile est le dispositif le plus efficace pour favoriser le développement de la vessie natatoire du doré. Les prochains travaux devraient se pencher sur (i) l’élaboration de bassins adaptés aux réalités de l’élevage intensif des percidés, (ii) sur des efforts de domestication du doré par sélection génétique afin d’augmenter la survie dans les systèmes en recirculation et sur (iii) des études bioéconomiques afin de réduire les risques associés aux démarrages de nouvelles piscicultures.