Coastal Modelling Environment version 1.0: a framework for integrating landform-specific component models in order to simulate decadal to centennial morphological changes on complex coasts

The ability to model morphological changes on complex, multi-landform coasts over decadal to centennial timescales is essential for sustainable coastal management worldwide. One approach involves coupling of landform-specific simulation models (e.g. cliffs, beaches, dunes and estuaries) that have been independently developed. An alternative, novel approach explored in this paper is to capture the essential characteristics of the landform-specific models using a common spatial representation within an appropriate software framework. This avoid the problems that result from the model-coupling approach due to between-model differences in the conceptualizations of geometries, volumes and locations of sediment. In the proposed framework, the Coastal Modelling Environment (CoastalME), change in coastal morphology is represented by means of dynamically linked raster and geometrical objects. A grid of raster cells provides the data structure for representing quasi-3-D spatial heterogeneity and sediment conservation. Other geometrical objects (lines, areas and volumes) that are consistent with, and derived from, the raster structure represent a library of coastal elements (e.g. shoreline, beach profiles and estuary volumes) as required by different landform-specific models. As a proof-of-concept, we illustrate the capabilities of an initial version of CoastalME by integrating a cliff–beach model and two wave propagation approaches. We verify that CoastalME can reproduce behaviours of the component landform-specific models. Additionally, the integration of these component models within the CoastalME framework reveals behaviours that emerge from the interaction of landforms, which have not previously been captured, such as the influence of the regional bathymetry on the local alongshore sediment-transport gradient and the effect on coastal change on an undefended coastal segment and on sediment bypassing of coastal structures

Growth and renal function dynamics of renal oncocytomas on active surveillance

OBJECTIVES: To study the natural history of renal oncocytomas and address indications for intervention by determining how growth is associated with renal function over time, the reasons for surgery and ablation, and disease-specific survival. PATIENTS AND METHODS: The study was conducted in a retrospective cohort of consecutive patients with renal oncocytoma on active surveillance reviewed at the Specialist Centre for Kidney Cancer at the Royal Free London NHS Foundation Trust (2012 to 2019). Comparison between groups was performed using Mann–Whitney U-tests and chi-squared tests. A mixed-effects model with a random intercept for patient was used to study the longitudinal association between tumour size and estimated glomerular filtration rate (eGFR). RESULTS: Longitudinal data from 98 patients with 101 lesions were analysed. Most patients were men (68.3%) and the median (interquartile range [IQR]) age was 69 (13) years. The median (IQR) follow-up was 29 (26) months. Most lesions were small renal masses, and 24% measured over 4 cm. Over half (64.4%) grew at a median (IQR) rate of 2 (4) mm per year. No association was observed between tumour size and eGFR over time (P = 0.871). Nine lesions (8.9%) were subsequently treated. Two deaths were reported, neither were related to the diagnosis of renal oncocytoma. CONCLUSION: Natural history data from the largest active surveillance cohort of renal oncocytomas to date show that renal function does not seem to be negatively impacted by growing oncocytomas, and confirms clinical outcomes are excellent after a median follow-up of over 2 years. Active surveillance should be considered the 'gold standard' management of renal oncocytomas up to 7cm

BOUT++ : Recent and current developments

BOUT++ is a 3D nonlinear finite-difference plasma simulation code, capable of solving quite general systems of PDEs, but targeted particularly on studies of the edge region of tokamak plasmas. BOUT++ is publicly available, and has been adopted by a growing number of researchers worldwide. Here we present improvements which have been made to the code since its original release, both in terms of structure and its capabilities. Some recent applications of these methods are reviewed, and areas of active development are discussed. We also present algorithms and tools which have been developed to enable creation of inputs from analytic expressions and experimental data, and for processing and visualisation of output results. This includes a new tool Hypnotoad for the creation of meshes from experimental equilibria. Algorithms have been implemented in BOUT++ to solve a range of linear algebraic problems encountered in the simulation of reduced MHD and gyro-fluid models: A preconditioning scheme is presented which enables the plasma potential to be calculated efficiently using iterative methods supplied by the PETSc library, without invoking the Boussinesq approximation. Scaling studies are also performed of a linear solver used as part of physics-based preconditioning to accelerate the convergence of implicit time-integration schemes

GEANT4 : a simulation toolkit

Abstract Geant4 is a toolkit for simulating the passage of particles through matter. It includes a complete range of functionality including tracking, geometry, physics models and hits. The physics processes offered cover a comprehensive range, including electromagnetic, hadronic and optical processes, a large set of long-lived particles, materials and elements, over a wide energy range starting, in some cases, from 250 eV and extending in others to the TeV energy range. It has been designed and constructed to expose the physics models utilised, to handle complex geometries, and to enable its easy adaptation for optimal use in different sets of applications. The toolkit is the result of a worldwide collaboration of physicists and software engineers. It has been created exploiting software engineering and object-oriented technology and implemented in the C++ programming language. It has been used in applications in particle physics, nuclear physics, accelerator design, space engineering and medical physics. PACS: 07.05.Tp; 13; 2

Hydraulic engineering in the 21st century: Where to?

For centuries, hydraulic engineers were at the forefront of science. The last forty years marked a change of perception in our society with a focus on environmental sustainability and management, particularly in developed countries. Herein, the writer illustrates his strong belief that the future of hydraulic engineering lies upon a combination of innovative engineering, research excellence and higher education of quality. This drive continues a long tradition established by eminent scholars like Arthur Thomas IPPEN, John Fisher KENNEDY and Hunter ROUSE

Modification of SOL profiles and fluctuations with line-average density and divertor flux expansion in TCV

A set of Ohmic density ramp experiments addressing the role of parallel connection length in modifying scrape off layer (SOL) properties has been performed on the TCV tokamak. The parallel connection length has been modified by varying the poloidal flux expansion f x . It will be shown that this modification does not influence neither the detachment density threshold, nor the development of a flat SOL density profile which instead depends strongly on the increase of the core line average density. The modification of the SOL upstream profile, with the appearance of what is generally called a density shoulder , has been related to the properties of filamentary blobs. Blob size increases with density, without any dependence on the parallel connection length both in the near and far SOL. The increase of the density decay length, corresponding to a profile flattening, has been related to the variation of the divertor normalized collisionality ##IMG## [http://ej.iop.org/images/0029-5515/57/11/116014/nfaa7db3ieqn001.gif] {$\Lambda_{\rm div}$} (Myra et al 2006 Phys. Plasmas 13 112502, Carralero et al , ASDEX Upgrade Team, JET Contributors and EUROfusion MST1 Team 2015 Phys. Rev. Let . 115 215002), showing that in TCV the increase of ##IMG## [http://ej.iop.org/images/0029-5515/57/11/116014/nfaa7db3ieqn002.gif] {$\Lambda_{\rm div}$} is not sufficient to guarantee the SOL upstream profile flattening

AVONET: Morphological, ecological and geographical data for all birds

Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.Fil: Tobias, Joseph A.. Imperial College London; Reino Unido. University of Oxford; Reino UnidoFil: Sheard, Catherine. University of Oxford; Reino Unido. University of Bristol; Reino UnidoFil: Pigot, Alex L.. University of Oxford; Reino Unido. University College London; Estados UnidosFil: Devenish, Adam J. M.. Imperial College London; Reino UnidoFil: Yang, Jingyi. Imperial College London; Reino UnidoFil: Sayol, Ferran. University College London; Estados UnidosFil: Neate Clegg, Montague H. C.. University of Oxford; Reino Unido. University of Utah; Estados UnidosFil: Alioravainen, Nico. University of Oxford; Reino Unido. Natural Resources Institute Finland; FinlandiaFil: Weeks, Thomas L.. Imperial College London; Reino Unido. Natural History Museum; Reino UnidoFil: Barber, Robert A.. Imperial College London; Reino UnidoFil: Walkden, Patrick A.. Imperial College London; Reino Unido. Natural History Museum; Reino UnidoFil: MacGregor, Hannah E. A.. University of Oxford; Reino Unido. University of Bristol; Reino UnidoFil: Jones, Samuel E. I.. University of Oxford; Reino Unido. University of London; Reino UnidoFil: Vincent, Claire. Organización de Las Naciones Unidas; ArgentinaFil: Phillips, Anna G.. Senckenberg Biodiversity And Climate Research Centre; AlemaniaFil: Marples, Nicola M.. Trinity College; Estados UnidosFil: Montaño Centellas, Flavia A.. Universidad Mayor de San Andrés; Bolivia. University of Florida; Estados UnidosFil: Leandro Silva, Victor. Universidade Federal de Pernambuco; BrasilFil: Claramunt, Santiago. University of Toronto; Canadá. Royal Ontario Museum; CanadáFil: Darski, Bianca. Universidade Federal do Rio Grande do Sul; BrasilFil: Freeman, Benjamin G.. University of British Columbia; CanadáFil: Bregman, Tom P.. University of Oxford; Reino Unido. Future-Fit Foundation; Reino UnidoFil: Cooney, Christopher R.. University Of Sheffield; Reino UnidoFil: Hughes, Emma C.. University Of Sheffield; Reino UnidoFil: Capp, Elliot J. R.. University Of Sheffield; Reino UnidoFil: Varley, Zoë K.. University Of Sheffield; Reino Unido. Natural History Museum; Reino UnidoFil: Friedman, Nicholas R.. Okinawa Institute of Science and Technology Graduate University; JapónFil: Korntheuer, Heiko. Johannes Gutenberg Universitat Mainz; AlemaniaFil: Corrales Vargas, Andrea. Universidad Nacional de Costa Rica; Costa RicaFil: García, Natalia Cristina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentin

Protocol for a feasibility study of a cohort embedded randomised controlled trial comparing NEphron Sparing Treatment (NEST) for small renal masses

Introduction: Small renal masses (SRMs; ≤4 cm) account for two-thirds of new diagnoses of kidney cancer, the majority of which are incidental findings. The natural history of the SRM seems largely indolent. There is an increasing concern regarding surgical overtreatment and the associated health burden in terms of morbidity and economy. Observational data support the safety and efficacy of percutaneous cryoablation but there is an unmet need for high-quality evidence on non-surgical management options and a head-to-head comparison with standard of care is lacking. Historical interventional trial recruitment difficulties demand novel study conduct approaches. We aim to assess if a novel trial design, the cohort embedded randomised controlled trial (RCT), will enable carrying out such a comparison. / Methods and analysis: Single-centre prospective cohort study of adults diagnosed with SRM (n=200) with an open label embedded interventional RCT comparing nephron sparing interventions. Cohort participants will be managed at patient and clinicians’ discretion and agree with longitudinal clinical data and biological sample collection, with invitation for trial interventions and participation in comparator control groups. Cohort participants with biopsy-proven renal cell carcinoma eligible for both percutaneous cryoablation and partial nephrectomy will be randomly selected (1:1) and invited to consider percutaneous cryoablation (n=25). The comparator group will be robotic partial nephrectomy (n=25). The primary outcome of this feasibility study is participant recruitment. Qualitative research techniques will assess barriers and recruitment improvement opportunities. Secondary outcomes are participant trial retention, health-related quality of life, treatment complications, blood transfusion rate, intensive care unit admission and renal replacement requirement rates, length of hospital stay, time to return to pre-treatment activities, number of work days lost, and health technologies costs. / Ethics and dissemination: Ethical approval has been granted (UK HRA REC 19/EM/0004). Study outputs will be presented and published. / Trial registration: ISRCTN18156881; Pre-results

Scrape Off Layer (SOL) transport and filamentary characteristics in high density tokamak regimes

A detailed cross-device investigation on the role of filamentary dynamics in high density regimes has been performed within the EUROfusion framework comparing ASDEX Upgrade (AUG) and TCV tokamaks. Both devices have run density ramp experiments at different levels of plasma current, keeping toroidal field or q95 constant in order to disentangle the role of parallel connection length and the current. During the scan at constant toroidal field, in both devices SOL profiles tend to develop a clear Scrape Off Layer (SOL) density shoulder at lower edge density whenever current is reduced. The different current behavior is substantially reconciled in terms of edge density normalized to Greenwald fraction. During the scan at constant q95 AUG exhibits a similar behaviour whereas in TCV no signature of upstream profile modification has been observed at lower level of currents. The latter behaviour has been ascribed to the lack of target density roll-over. The relation between upstream density profile modification and detachment condition has been investigated. For both devices the relation between blob-size and SOL density e-folding length is found independent of the plasma current, with a clear increase of blob-size with edge density normalized to Greenwald fraction observed. ASDEX Upgrade has also explored the filamentary behaviour in H-Mode. The experiments on AUG focused on the role of neutrals, performing discharges with and without the cryogenic pumps, highlighting how large neutral pressure not only in the divertor but at the midplane is needed in order to develop a H-Mode SOL profile shoulder in AUG