Grey zone simulations of the morning convective boundary layer development

Numerical simulations of two cases of morning boundary layer development are conducted to investigate the impact of grid resolution on mean profiles and turbulent kinetic energy (TKE) partitioning from the large eddy simulation (LES) to the mesoscale limit. Idealized LES, using the 3-D Smagorinsky scheme, is shown to be capable of reproducing the boundary layer evolution when compared against measurements. However, increasing grid spacing results in the damping of resolved TKE and the production of superadiabatic temperature profiles in the boundary layer. Turbulence initiation is significantly delayed, exhibiting an abrupt onset at intermediate resolutions. Two approaches, the bounding of vertical diffusion coefficient and the blending of the 3-D Smagorinsky with a nonlocal 1D scheme, are used to model subgrid diffusion at grey zone resolutions. Simulations are compared against the coarse-grained fields from the validated LES results for each case. Both methods exhibit particular strengths and weaknesses, indicating the compromise that needs to be made currently in high-resolution numerical weather prediction. The blending scheme is able to reproduce the adiabatic profiles although turbulence is underestimated in favor of the parametrized heat flux, and the spin-up of TKE remains delayed. In contrast, the bounding approach gives an evolution of TKE that follows the coarse-grained LES very well, relying on the resolved motions for the nonlocal heat flux. However, bounding gives unrealistic static instability in the early morning temperature profiles (similar to the 3-D Smagorinsky scheme) because model dynamics are unable to resolve TKE when the boundary layer is too shallow compared to the grid spacing.This work has been funded by the Natural Environment Research Council (NERC) GREYBLS (Modelling Grey Zone Boundary Layers) project (grant NE/K011456/1). We acknowledge the use of the MONSooN system, a collaborative facility supplied under the Joint Weather and Climate Research Programme, which is a strategic partnership between the Met Office and the Natural Environment Research Council

So near and yet so far: harmonic radar reveals reduced homing ability of Nosema infected honeybees.

© 2014 Wolf et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Citation: Wolf S, McMahon DP, Lim KS, Pull CD, Clark SJ, et al. (2014) So Near and Yet So Far: Harmonic Radar Reveals Reduced Homing Ability of Nosema Infected Honeybees. PLoS ONE 9(8): e103989. doi:10.1371/journal.pone.0103989Pathogens may gain a fitness advantage through manipulation of the behaviour of their hosts. Likewise, host behavioural changes can be a defence mechanism, counteracting the impact of pathogens on host fitness. We apply harmonic radar technology to characterize the impact of an emerging pathogen--Nosema ceranae (Microsporidia)--on honeybee (Apis mellifera) flight and orientation performance in the field. Honeybees are the most important commercial pollinators. Emerging diseases have been proposed to play a prominent role in colony decline, partly through sub-lethal behavioural manipulation of their hosts. We found that homing success was significantly reduced in diseased (65.8%) versus healthy foragers (92.5%). Although lost bees had significantly reduced continuous flight times and prolonged resting times, other flight characteristics and navigational abilities showed no significant difference between infected and non-infected bees. Our results suggest that infected bees express normal flight characteristics but are constrained in their homing ability, potentially compromising the colony by reducing its resource inputs, but also counteracting the intra-colony spread of infection. We provide the first high-resolution analysis of sub-lethal effects of an emerging disease on insect flight behaviour. The potential causes and the implications for both host and parasite are discussed.Biotechnology and Biological Sciences Research Council (BBSRC)Department for Environment Food & Rural Affairs (DEFRA)Natural Environment Research Council (NERC)The Scottish GovernmentWellcome Trus

Control of Single Molecule Fluorescence Dynamics by Stimulated Emission Depletion

The feasibility of manipulating the single molecule absorption-emission cycle using picosecond stimulated emission depletion (STED) is investigated using a stochastic computer simulation. In the simulation the molecule is subjected to repeated excitation and depletion events using time delayed pairs of excitation (PUMP) and depletion (DUMP) pulses derived from a high repetition rate pulsed laser system. The model is used to demonstrate that a significant and even substantial reduction in the occurrence of 'dark states' in the fluorescence emission can be achieved using stimulated emission depletion. Variation in the PUMP-DUMP window allows precise control of the fluorescence yield with substantial increases in the fluorescence intensity observed at early PUMP-DUMP delays

Radar tracking and motion-sensitive cameras on flowers reveal the development of pollinator multi-destination routes over large spatial scales.

PublishedJournal ArticleResearch Support, Non-U.S. Gov'tCentral place foragers, such as pollinating bees, typically develop circuits (traplines) to visit multiple foraging sites in a manner that minimizes overall travel distance. Despite being taxonomically widespread, these routing behaviours remain poorly understood due to the difficulty of tracking the foraging history of animals in the wild. Here we examine how bumblebees (Bombus terrestris) develop and optimise traplines over large spatial scales by setting up an array of five artificial flowers arranged in a regular pentagon (50 m side length) and fitted with motion-sensitive video cameras to determine the sequence of visitation. Stable traplines that linked together all the flowers in an optimal sequence were typically established after a bee made 26 foraging bouts, during which time only about 20 of the 120 possible routes were tried. Radar tracking of selected flights revealed a dramatic decrease by 80% (ca. 1500 m) of the total travel distance between the first and the last foraging bout. When a flower was removed and replaced by a more distant one, bees engaged in localised search flights, a strategy that can facilitate the discovery of a new flower and its integration into a novel optimal trapline. Based on these observations, we developed and tested an iterative improvement heuristic to capture how bees could learn and refine their routes each time a shorter route is found. Our findings suggest that complex dynamic routing problems can be solved by small-brained animals using simple learning heuristics, without the need for a cognitive map.This research was supported by a combined grant from the Wellcome Trust, the Biotechnology and Biological Sciences Research Council, and the Engineering and Physical Sciences Research Council (BB/F52765X/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

The 2019 Raikoke volcanic eruption - Part 1: Dispersion model simulations and satellite retrievals of volcanic sulfur dioxide

Abstract. Volcanic eruptions can cause significant disruption to society, and numerical models are crucial for forecasting the dispersion of erupted material. Here we assess the skill and limitations of the Met Office's Numerical Atmospheric-dispersion Modelling Environment (NAME) in simulating the dispersion of the sulfur dioxide (SO2) cloud from the 21–22 June 2019 eruption of the Raikoke volcano (48.3∘ N, 153.2∘ E). The eruption emitted around 1.5±0.2 Tg of SO2, which represents the largest volcanic emission of SO2 into the stratosphere since the 2011 Nabro eruption. We simulate the temporal evolution of the volcanic SO2 cloud across the Northern Hemisphere (NH) and compare our model simulations to high-resolution SO2 measurements from the TROPOspheric Monitoring Instrument (TROPOMI) and the Infrared Atmospheric Sounding Interferometer (IASI) satellite SO2 products. We show that NAME accurately simulates the observed location and horizontal extent of the SO2 cloud during the first 2–3 weeks after the eruption but is unable, in its standard configuration, to capture the extent and precise location of the highest magnitude vertical column density (VCD) regions within the observed volcanic cloud. Using the structure–amplitude–location (SAL) score and the fractional skill score (FSS) as metrics for model skill, NAME shows skill in simulating the horizontal extent of the cloud for 12–17 d after the eruption where VCDs of SO2 (in Dobson units, DU) are above 1 DU. For SO2 VCDs above 20 DU, which are predominantly observed as small-scale features within the SO2 cloud, the model shows skill on the order of 2–4 d only. The lower skill for these high-SO2-VCD regions is partly explained by the model-simulated SO2 cloud in NAME being too diffuse compared to TROPOMI retrievals. Reducing the standard horizontal diffusion parameters used in NAME by a factor of 4 results in a slightly increased model skill during the first 5 d of the simulation, but on longer timescales the simulated SO2 cloud remains too diffuse when compared to TROPOMI measurements. The skill of NAME to simulate high SO2 VCDs and the temporal evolution of the NH-mean SO2 mass burden is dominated by the fraction of SO2 mass emitted into the lower stratosphere, which is uncertain for the 2019 Raikoke eruption. When emitting 0.9–1.1 Tg of SO2 into the lower stratosphere (11–18 km) and 0.4–0.7 Tg into the upper troposphere (8–11 km), the NAME simulations show a similar peak in SO2 mass burden to that derived from TROPOMI (1.4–1.6 Tg of SO2) with an average SO2 e-folding time of 14–15 d in the NH. Our work illustrates how the synergy between high-resolution satellite retrievals and dispersion models can identify potential limitations of dispersion models like NAME, which will ultimately help to improve dispersion modelling efforts of volcanic SO2 clouds. </jats:p

HER2 testing in breast cancer: Opportunities and challenges

Human epidermal growth factor receptor 2 (HER2) is overexpressed in 15-25% of breast cancers, usually as a result of HER2 gene amplification. Positive HER2 status is considered to be an adverse prognostic factor. Recognition of the role of HER2 in breast cancer growth has led to the development of anti-HER2 directed therapy, with the humanized monoclonal antibody trastuzumab (Herceptin (R)) having been approved for the therapy of HER2-positive metastatic breast cancer. Clinical studies have further suggested that HER2 status can provide important information regarding success or failure of certain hormonal therapies or chemotherapies. As a result of these developments, there has been increasing demand to perform HER2 testing on current and archived breast cancer specimens. This article reviews the molecular background of HER2 function, activation and inhibition as well as current opinions concerning its role in chemosensitivity and interaction with estrogen receptor biology. The different tissue-based assays used to detect HER2 amplification and overexpression are discussed with respect to their advantages and disadvantages, when to test (at initial diagnosis or pre-treatment), where to test (locally or centralized) and the need for quality assurance to ensure accurate and valid testing results

Optimal search patterns in honeybee orientation flights are robust against emerging infectious diseases.

Published onlineJournal ArticleLévy flights are scale-free (fractal) search patterns found in a wide range of animals. They can be an advantageous strategy promoting high encounter rates with rare cues that may indicate prey items, mating partners or navigational landmarks. The robustness of this behavioural strategy to ubiquitous threats to animal performance, such as pathogens, remains poorly understood. Using honeybees radar-tracked during their orientation flights in a novel landscape, we assess for the first time how two emerging infectious diseases (Nosema sp. and the Varroa-associated Deformed wing virus (DWV)) affect bees' behavioural performance and search strategy. Nosema infection, unlike DWV, affected the spatial scale of orientation flights, causing significantly shorter and more compact flights. However, in stark contrast to disease-dependent temporal fractals, we find the same prevalence of optimal Lévy flight characteristics (μ ≈ 2) in both healthy and infected bees. We discuss the ecological and evolutionary implications of these surprising insights, arguing that Lévy search patterns are an emergent property of fundamental characteristics of neuronal and sensory components of the decision-making process, making them robust against diverse physiological effects of pathogen infection and possibly other stressors.This study was funded jointly by a grant from BBSRC, Defra, NERC, the Scottish Government and the Wellcome Trust, under the Insect Pollinators Initiative (grant numbers BB/I00097/1 and BB/I000100/1). Additional support came from the Deutsche Forschungsgemeinschaft (DFG, grant number WO 1745/2-1) to S.W. Rothamsted Research is a national institute of bioscience strategically funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC)

Macro-Climatic Distribution Limits Show Both Niche Expansion and Niche Specialization among C4 Panicoids

Grasses are ancestrally tropical understory species whose current dominance in warm open habitats is linked to the evolution of C4 photosynthesis. C4 grasses maintain high rates of photosynthesis in warm and water stressed environments, and the syndrome is considered to induce niche shifts into these habitats while adaptation to cold ones may be compromised. Global biogeographic analyses of C4 grasses have, however, concentrated on diversity patterns, while paying little attention to distributional limits. Using phylogenetic contrast analyses, we compared macro-climatic distribution limits among ~1300 grasses from the subfamily Panicoideae, which includes 4/5 of the known photosynthetic transitions in grasses. We explored whether evolution of C4 photosynthesis correlates with niche expansions, niche changes, or stasis at subfamily level and within the two tribes Paniceae and Paspaleae. We compared the climatic extremes of growing season temperatures, aridity, and mean temperatures of the coldest months. We found support for all the known biogeographic distribution patterns of C4 species, these patterns were, however, formed both by niche expansion and niche changes. The only ubiquitous response to a change in the photosynthetic pathway within Panicoideae was a niche expansion of the C4 species into regions with higher growing season temperatures, but without a withdrawal from the inherited climate niche. Other patterns varied among the tribes, as macro-climatic niche evolution in the American tribe Paspaleae differed from the pattern supported in the globally distributed tribe Paniceae and at family level.Fil: Aagesen, Lone. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Biganzoli, Fernando. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Métodos Cuantitativos y Sistemas de Información; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Bena, María Julia. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Godoy Bürki, Ana Carolina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Reinheimer, Renata. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; ArgentinaFil: Zuloaga, Fernando Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentin