ALBERT

Description: An unusually deep (961 hPa) hurricane-like polar low over the Barents Sea during 18–21 December 2002 is studied by a series of fine-mesh (3 km) experiments using the Weather Research and Forecasting (WRF) model. The simulated polar low was similar to hurricanes and similar previous case-studies in that it had a clear, calm and warm eye structure surrounded by moist convection organized in spiral cloud bands, and the highest surface wind speeds were found in the eye wall. The proximity to the sea ice and the high surface wind speeds (about 25 m s −1 ) during the deepening stage triggered extremely high surface sensible and latent heat fluxes at the eye wall of about 1200 and 400 W m −2 , respectively. As the polar low moved eastward and weakened, maximum surface sensible and latent heat fluxes dropped to about 600 and 300 W m −2 , respectively. Two types of sensitivity experiments were designed to analyse the physical properties of the polar low. Firstly, physical processes such as condensational heating and sensible and/or latent heat fluxes were switched off–on throughout the simulation. In the second type, these processes were turned off–on after the polar low had reached its peak intensity, which minimized the deformation of the polar-low environment, making it suitable to study the direct effect of physical processes on the mature vortex. The experiments suggest that the deepening stage of the polar low was dominated by baroclinic growth and that upper-level potential vorticity forcing contributed throughout its life cycle. After the deepening stage, the baroclinicity vanished and the polar low was fuelled by surface sensible heat fluxes while latent heat fluxes played a minor role. Condensational heating was not essential for the energetics of the polar low. Surprisingly, in experiments where condensational heating was turned off throughout the simulation, the polar low intensified. Copyright © 2012 Royal Meteorological Society

Description: Correlation functions associated with the inverse covariances represented by polynomials of the homogeneous diffusion operator D are obtained analytically for an arbitrary polynomial of D, constrained by the positive-definiteness condition of the covariance operator. Copyright © 2012 Royal Meteorological Society

Description: The structure, evolution and dynamics of two lower stratospheric frontal zones are examined from a basic state variables perspective. The case studies highlight the asynchronous evolution of the lower stratospheric and upper tropospheric frontal portions of upper level jet-front (ULJF) systems, as well as some substantial differences in lower stratospheric frontal development that occur in southwesterly and northwesterly flow. The evolution of the ULJF in northwesterly flow was characterized by an initially intense but weakening lower stratospheric front along with an initially weak but intensifying upper tropospheric front. Throughout the evolution, geostrophic cold air advection in cyclonic shear characterized a substantial portion of the lower stratospheric front. This circumstance supported subsidence through the local jet core within the cold upper troposphere, weakening the lower stratospheric front via tilting. This subsidence extended downward below the jet core where it is suggested to have played a role in the early stages of upper tropospheric frontogenesis. In the southwesterly flow case, the evolution of the ULJF was characterized by a strengthening lower stratospheric front and a weakening upper tropospheric front. A deep column of upward vertical motion resulted from the superposition of lower tropospheric ascent associated with convection along a surface cold front and upper tropospheric-lower stratospheric (UTLS) ascent through the jet core coincident with geostrophic warm air advection in cyclonic shear along large sections of the lower stratospheric front. The UTLS ascent, located on the cold edge of the lower stratospheric baroclinicity, served to intensify the lower stratospheric frontal zone via tilting. The implications of these lower stratospheric frontal processes on the topography of the tropopause and downstream sensible weather are discussed. Copyright © 2012 Royal Meteorological Society

Description: Mitochondrial function is achieved through the cooperative interaction of two genomes: one nuclear (nuDNA) and the other mitochondrial (mtDNA). The unusual transmission of mtDNA, predominantly maternal without recombination is predicted to affect the fitness of male offspring. Recent research suggests the strong sexual dimorphism in aging is one such fitness consequence. The uniparental inheritance of mtDNA results in a selection asymmetry; mutations that affect only males will not respond to natural selection, imposing a male-specific mitochondrial mutation load. Prior work has implicated this male-specific mutation load in disease and infertility, but new data from fruit flies suggests a prominent role for mtDNA in aging; across many taxa males almost invariably live shorter lives than females. Here we discuss this new work and identify some areas of future research that might now be encouraged to explore what may be the underpinning cause of the strong sexual dimorphism in aging. Editor's suggested further reading in BioEssays: Mitonuclear match: Optimizing fitness and fertility over generations drives ageing within generations Abstract Mitochondrial manoeuvres: Latest insights and hypotheses on mitochondrial partitioning during mitosis in Saccharomyces cerevisiae Abstract Mitochondria and the culture of the Borg Abstract The maternal inheritance of mtDNA results in a selection asymmetry; natural selection cannot act on mutations that affect only males. This asymmetry imposes a male-specific mutation load previously implicated in male disease and infertility. New work suggests this asymmetry underpins the strong sexual dimorphism in aging observed across taxa.

Description: Observations of high spatio-temporal resolution from a precipitation network across Stord Island, located off the west coast of southern Norway, are compared to state-of-the-art numerical model simulations. The 12 week long observation period shows a clear orographic precipitation signal across the 10–15 km wide island (peak elevation 750 m). The model experiment designed to capture this signal is run with 9–3–1 km nested grid and results are compared with observations at different accumulation intervals. The total amount of precipitation over the 12 week period is underpredicted, even for the 1 km grid. The maximum precipitation intensity, however, is slightly overpredicted. Time-step (5 s) precipitation from the model is also compared with observed intensities at the highest possible temporal resolution permitted by the rain collection method. The observations indicate that most of the precipitation is formed at intensities from 5 to 20 mm h −1 . A smaller fraction of the precipitation is formed with intensities 〉20 mm h −1 . The simulated precipitation at the 3 km grid did not reproduce at the correct intensities. The 1 km grid showed an improved tendency to produce the precipitation at the right intensities, but had too high maximum intensities. A test simulation where the intermediate grid had no cumulus parametrization was performed. Even though effects such as undercatchment and unresolved terrain influenced, it was concluded that the test run performed better than the control run. The investigation concluded that, in general, a 1 km grid is sufficient for capturing the most intensive precipitation event in a satisfying way. Copyright © 2012 Royal Meteorological Society

Description: Line-shaped contrails arising from aircraft emissions affect radiative forcing. The magnitude of the radiative forcing from contrails depends strongly on their optical depth and their spatial and temporal variability caused by dynamical and microphysical processes. Here we investigate the significance of this variability, both for modelling contrail radiative forcing and estimating thresholds for the detection of contrails in satellite imagery. Ignoring the variability of contrail optical depth in models by prescribing a mean optical depth may overestimate mean net radiative forcing by 10−20%. Undersampling of optically thin line-shaped contrails by passive satellite remote sensing is linked to the inability to detect flux changes in the outgoing long-wave radiation below ≈3 W m −2 for conditions over the eastern North Pacific. Consideration of these findings aids efforts to better quantify uncertainties in aviation climate assessments. Copyright © 2012 Royal Meteorological Society

Description: In a previous study the author showed, using a toy model, that forecast performance using four-dimensional variational analysis (4D-Var) and an imperfect forecast model was dramatically improved by using a regularization matrix instead of a matrix estimating the true background-error covariance. This article carries out a theoretical analysis of this behaviour. The analysis first highlights the interpretation of short-window 4D-Var as a fixed lag smoother, which means that the control over model error growth exerted by observations late in the assimilation window is taken into account. It is then shown that, in a scalar case, the solution will converge to that of infinitely long-window weak-constraint 4D-Var where the same regularization constraint is applied at each subwindow. The optimum choice of regularization constraint is analyzed for the converged solution and is such that the regularization evolved by the model to the observation time equals the true error evolved to the observation time. The true error is controlled by the observation error regardless of the amount of model error provided that the optimum regularization is used. The same calculation is done for 3D-Var, showing that the true error is not so controlled and is typically larger. It is shown that the feedback between forecast-error growth and the choice of regularization constraint can have a strong effect on the optimal choice, as observed in the experiments. The results are consistent with setting the regularization equal to the background error calculated relative to the truth projected on to the model attractor, rather than the truth itself. In this context, the model attractor can be regarded as the model state closest to the truth that gives the correct time derivatives. Copyright © 2012 British Crown Copyright, the Met Office. Published by John Wiley & Sons, Ltd

Description: While innovations in modern microscopy, spectroscopy, and nanoscopy techniques have made single molecule observation a standard in many laboratories, the actual design of meaningful fluorescence reporter systems now hinders major scientific breakthroughs. Even though the field of chemical biology is supercharging the fluorescence toolbox, surprisingly few strategies exist that make the transition from model systems to biologically relevant applications. At the same time, the number of microscopy techniques is growing dramatically. We explain our view on how the impact of modern technologies is influenced not only by further hard- and software developments, but also by the availability and suitability of protein-engineering tools. We identify how the largely independent research fields of chemical biology and fluorescence nanoscopy can influence each other to synergistically drive future technology that can visualize the localization, structure, and dynamics of molecular function without constraints. Fluorescence technologies provide key to study molecular structure and dynamics with super spatial and temporal resolution. We discuss how synergistic developments of novel labeling technologies combined with optical engineering can make the biggest contribution to advance state of the art tools for both, in vitro and non-invasive in vivo measurements.

Description: A new incremental four-dimensional variational (4D-Var) data assimilation algorithm is introduced. The algorithm does not require the computationally expensive integrations with the nonlinear model in the outer loops. Nonlinearity is accounted for by modifying the linearization trajectory of the observation operator based on integrations with the tangent linear (TL) model. This allows us to update the linearization trajectory of the observation operator in the inner loops at negligible computational cost. As a result the distinction between inner and outer loops is no longer necessary. The key idea on which the proposed 4D-Var method is based is that by using Gaussian quadrature it is possible to get an exact correspondence between the nonlinear time evolution of perturbations and the time evolution in the TL model. It is shown that J -point Gaussian quadrature can be used to derive the exact adjoint-based observation impact equations and furthermore that it is straightforward to account for the effect of multiple outer loops in these equations if the proposed 4D-Var method is used. The method is illustrated using a three-level quasi-geostrophic model and the Lorenz (1996) model. Copyright © 2012 Royal Meteorological Society

Description: This article addresses the effects of cloud condensation nuclei on the evolution of an intense tropical convective system, known as Hector , using data taken from the ACTIVE and TWP-ICE field campaigns, which were conducted in 2005 and 2006. The Hector thunderstorms were observed in a variety of aerosol conditions so the data serve as an ideal dataset to test whether aerosols have a significant impact on the evolution of convective clouds and precipitation. We find evidence for an aerosol effect on the storm's properties, which are reproduced with a state-of-the-art mesoscale cloud-resolving model. Including the measured aerosol concentration within the model is shown to improve the fractions skill-score metric for every case presented in the article, thus giving us confidence that the deep convection observed during the period was indeed influenced by the aerosol entering the storm's inflow. However, we do not find a general relationship for the way aerosols affect properties such as cloud-top height, precipitation or radiative properties, as has been suggested in previous work. The reasons for this appear to be because of the nonlinearity of interactions between neighbouring cells and because of the variability in the meteorological profiles of temperature, wind and humidity. Copyright © 2013 Royal Meteorological Society

Description: New genes have frequently formed and spread to fixation in a wide variety of organisms, constituting abundant sets of lineage-specific genes. It was recently reported that an excess of primate-specific and human-specific genes were upregulated in the brains of fetuses and infants, and especially in the prefrontal cortex, which is involved in cognition. These findings reveal the prevalent addition of new genetic components to the transcriptome of the human brain. More generally, these findings suggest that genomes are continually evolving in both sequence and content, eroding the conservation endowed by common ancestry. Despite increasing recognition of the importance of new genes, we highlight here that these genes are still seriously under-characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes, taking advantage of functional and evolutionary genomic methods. We finally discuss how the refinement of new gene annotation will be important for the detection of evolutionary forces governing new gene origination. Regardless of recent findings that new genes are important for human brain functions, we highlight that new genes are still generally under-characterized in functional studies and that new gene annotation is inconsistent in current practice. We propose an integrative approach to annotate new genes based on functional and evolutionary genomics.

Description: A numerical comparison of the Lorenz and Charney–Phillips vertical grids for capturing the steady state of a set of equations that models the large-scale dynamics of the atmosphere and the planetary boundary layer (Part I of this article) has revealed important differences between the grids. Due to suppression of a negative feedback, Charney–Phillips grids that involve averaging of shear in the boundary-layer terms are not able to capture the structure of the boundary layer accurately. The Lorenz grid performs well in terms of capturing the boundary layer on its own, but the Charney–Phillips grids that use averaging of potential temperature gradient are generally preferred once dynamics are included. Any finite-difference approximation of the problem must be capable of accurately representing both the steady-state and time-dependent parts of the solution. In this Part II of the article, the ability of the Lorenz and Charney–Phillips configurations to capture the transient part of the system is considered. The configurations are compared in terms of their ability to capture the eigenmodes of the solution. Full comparison between Lorenz and Charney–Phillips grids is limited by non-normality of the linearised system, associated with the boundary layer. The Lorenz grid computational mode is examined. The structure is modified by the boundary layer but it still exists. For the modes that could be accurately examined, it is found that both grids perform well in terms of capturing spatial and temporal mode structure. Some Lorenz grid modes are identified that have spurious computational mode-like behaviour occurring near the top of the boundary layer. Copyright © 2012 Royal Meteorological Society

Description: The major scientific objective of the Megha-Tropiques (MT) satellite, an Indian Space Research Organisation (ISRO)–Centre National d'Études Spatiales (CNES) collaborative project, is to understand the energy and water cycles in the global tropical region. With its 20° inclined orbit, it will frequently measure radiation emitted by the Earth-Atmosphere System in the visible, infrared and microwave spectrum through its four sensors on board. Various geophysical parameters, namely water vapour, cloud liquid water and surface winds over oceanic regions, and the rainfall, humidity profile and top-of-atmosphere radiative fluxes over land as well as over oceanic regions will be derived from the measurements made by these instruments. This article deals with the efforts made by ISRO to develop algorithms for deriving these geophysical parameters from the microwave imager and sounder, mentioning the pre-launch specifications with prelude examples from existing space-borne sensors of similar types. The sensor-specific algorithms are presented in different sections. Copyright © 2012 Royal Meteorological Society

Description: We present idealized numerical model experiments to investigate the convective generation of vertical vorticity in a tropical depression. The ambient vertical vorticity is represented by a uniform solid-body rotation. The calculations are motivated by observations made during the Pre-Depression Investigation of Cloud-systems in the Tropics (PREDICT) experiment. A specific aim is to isolate and quantify the effects of low- to mid-level dry air on convective cells that form within a depression and, in particular, on the generation of vertical vorticity in these cells. The results do not support a common perception that dry air aloft produces stronger convective downdraughts and more intense, cold-air outflows therefrom. Indeed, we find that dry air aloft weakens both updraughts and downdraughts, corroborating the recent results of James and Markowski. As in the recent calculations of Wissmeier and Smith, the growing convective cells locally amplify the ambient rotation at low levels by more than an order of magnitude and this vorticity, which is produced by the stretching of existing ambient vorticity, persists long after the initial updraught has decayed. Moreover, significant amplification of vorticity occurs even for clouds of only moderate vertical extent. The maximum amplification of vorticity is relatively insensitive to the maximum updraught strength, or the height at which it occurs, and it is not unduly affected by the presence of dry air aloft. Thus the presence of dry air is not detrimental to the amplification of low-level vorticity, although it reduces the depth through which ambient vorticity is enhanced. Results for a limited number of different environmental soundings indicate that the maximum amplification of vorticity increases monotonically with the strength of the thermal perturbation that initiates the convection, but the amount of increase depends also on the thermodynamic structure of the sounding. Copyright © 2012 Royal Meteorological Society

Description: The frequency of occurrence and formation mechanisms of wave-cloud lines off the northwest coast of Australia are investigated. Prior to the present study, little was known about these wave-cloud lines. Apart from being spectacular atmospheric phenomenon in their own right, these wave clouds can have a role in the secondary initiation of convection and can be a hazard to low-flying aircraft. A climatology of wave clouds, produced from visible satellite imagery, suggests two main types of cloud lines form over northwest Australia. The first are bore-like waves, similar in structure to the ‘morning glory’ of northeast Australia, and occur at least 2 to 3 times per month throughout the entire year. The second type are convectively generated cloud lines, which are more circular in shape, appear to originate from convective storms and occur at least 0.5 to 1.5 times per month during the wet season. High-resolution, nested simulations are performed with the Met Office Unified Model for case-studies of each type of wave. The bore-like waves occurred in the presence of synoptic-scale, low-level southeasterly flow and a heat low along the northwest coast of Australia. At night, the offshore southeasterlies accelerate into the heat low and collide with the onshore sea breeze. The southeasterlies override the sea breeze and the wave-cloud lines form at the leading edge of this front. The convectively generated waves radiate outwards from the convective storms producing compensating subsidence and adiabatic warming. These waves take the form of n=2 mode wave fronts, which span the entire depth of the troposphere and are similar in structure to waves produced by deep convection which are described in previous studies. Copyright © 2012 Royal Meteorological Society

Description: Accurate coupling between the resolved-scale dynamics and the parametrised physics is essential for accurate modelling of the atmosphere. Previous emphasis has been on the temporal aspects of this so-called physics–dynamics coupling problem, with little attention on the spatial aspects. When designing a model for numerical weather prediction there is a choice for how to vertically arrange the predicted variables, namely the Lorenz and Charney–Phillips grids, and there is ongoing debate as to which is the optimal. The Charney–Phillips grid is considered good for capturing the potential vorticity dynamics and wave propagation, whereas the Lorenz grid is more suitable for conservation. However the Lorenz grid supports a computational mode. It is argued here that the Lorenz grid is preferred for modelling the stably stratified boundary layer. This presents the question: which grid will produce more accurate results when coupling the large-scale dynamics to the stably stratified planetary boundary layer? The question is addressed by examining the ability of both the Lorenz and Charney–Phillips grids to capture the steady state of a set of equations that simultaneously represents both large-scale dynamics and the planetary boundary layer. The results show that the Charney–Phillips grid is able to capture accurately the steady boundary-layer solution provided the Richardson number is calculated without vertically averaging the shear. Averaging the shear suppresses the negative feedback of the shear on the diffusion coefficient; the positive feedback, via the vertical gradient of potential temperature, then leads to the formation of unrealistic step-like features. Copyright © 2012 Royal Meteorological Society

Description: An analysis of the turbulence structure in a perturbed boundary layer and in low-wind regimes is presented. The study is based on 15 months of continuous wind and turbulence measurements gathered, within the framework of the Urban Turbulence Project, at three levels (5, 9 and 25 m) on a mast located in the outskirts of the city of Turin (Italy). The aim of the work is to investigate low-frequency processes in a perturbed boundary-layer. In fact, the urban canopy and the heat island, together with frequent low-wind conditions, interact with and modify the turbulence structure. In order to investigate this modification, the velocity Eulerian autocorrelation functions together with both the Eulerian and Lagrangian time-scales are shown and compared with the classical theory. The comparisons show that in low-wind cases the velocity autocorrelation functions are not simply exponential but present an oscillating behaviour. A method of normalization is proposed together with an analysis on the applicability of this function. The estimated Lagrangian time-scales are compared with two widely used parametrizations. It is found that the presence of the urban fabric influences the turbulence time-scales and suggests the development of new parametrizations. Finally, higher-order statistics are evaluated and the relationship between higher-order and lower-order moments are analysed, pointing out the effects due to the urban environment. Copyright © 2012 Royal Meteorological Society

Description: Recent studies of prostate cancer and other tumor types have revealed significant support, as well as unexpected complexities, for the application of concepts from normal stem cell biology to cancer. In particular, the cell of origin and cancer stem cell models have been proposed to explain the heterogeneity of tumors during the initiation, propagation, and evolution of cancer. Thus, a basis of intertumor heterogeneity has emerged from studies investigating whether stem cells and/or non-stem cells can serve as cells of origin for cancer and give rise to tumor subtypes that vary in disease outcome. Furthermore, analyses of putative cancer stem cells have revealed the genetically diverse nature of cancers and expanded our understanding of intratumor heterogeneity and clonal evolution. Overall, the principles that have emerged from these stem cell studies highlight the challenges to be surmounted to develop effective treatment strategies for cancer. Concepts from stem cell biology can explain the basis for intertumoral heterogeneity between different tumors of the same tissue type, as well as intratumoral heterogeneity within a single tumor. In this review, we discuss the cell of origin, cancer stem cells, and clonal evolution, with a focus on prostate cancer.

Description: How fast? How strong? How many? So what? Why do numbers matter in biology? Chromatin binding proteins are forever in motion, exchanging rapidly between bound and free pools. How do regulatory systems whose components are in constant flux ensure stability and flexibility? This review explores the application of quantitative and mathematical approaches to mechanisms of epigenetic regulation. We discuss methods for measuring kinetic parameters and protein quantities in living cells, and explore the insights that have been gained by quantifying and modelling dynamics of chromatin binding proteins. Current models for chromatin mediated gene regulation often describe molecules as binding, modifying or recruiting other molecules, but with little reference to the quantitative differences between them. In this review we explore how quantitative and mathematical approaches can give insights into mechanisms of epigenetic regulation.

Description: Evolutionary theory assumed that mutations occur constantly, gradually, and randomly over time. This formulation from the “modern synthesis” of the 1930s was embraced decades before molecular understanding of genes or mutations. Since then, our labs and others have elucidated mutation mechanisms activated by stress responses. Stress-induced mutation mechanisms produce mutations, potentially accelerating evolution, specifically when cells are maladapted to their environment, that is, when they are stressed. The mechanisms of stress-induced mutation that are being revealed experimentally in laboratory settings provide compelling models for mutagenesis that propels pathogen–host adaptation, antibiotic resistance, cancer progression and resistance, and perhaps much of evolution generally. We discuss double-strand-break-dependent stress-induced mutation in Escherichia coli. Recent results illustrate how a stress response activates mutagenesis and demonstrate this mechanism's generality and importance to spontaneous mutation. New data also suggest a possible harmony between previous, apparently opposed, models for the molecular mechanism. They additionally strengthen the case for anti-evolvability therapeutics for infectious disease and cancer. Stress-induced mutation molecular mechanism in Escherichia coli : repair of DNA double-strand breaks is switched to a mutagenic mode using DinB and other error-prone DNA polymerases during stress, by the RpoS stress response. This increases genetic diversity, and the ability to evolve, when cells are maladapted to their environment: when stressed.

Description: Scientists should learn to communicate effectively with their colleagues through long-term, sustained training instead of ad hoc, one-off “interventions” that may or may not occur during graduate school or postdoctoral work. Since such training may place unreasonable demands on research advisors, institutions should create career opportunities for “peer-peer communication teachers.”

Description: Hedgehog is an important morphogenic signal that directs pattern formation during embryogenesis, but its activity also remains present through adult life. It is now becoming increasingly clear that during the reproductive phase of life and beyond it continues to direct cell renewal (which is essential to combat the chronic environmental stress to which the body is constantly exposed) and counteracts vascular, osteolytic and sometimes oncological insults to the body. Conversely, down-regulation of hedgehog signalling is associated with ageing-related diseases such as type 2 diabetes, neurodegeneration, atherosclerosis and osteoporosis. Hence, in this essay we argue that hedgehog signalling is not only important at the start of life, but also constitutes an important anti-geriatric influence, and that enhanced understanding of its properties may contribute to developing rational strategies for healthy ageing and prevention of ageing-related diseases. Also watch the Video Abstract Hedgehog is a morphogenic signal during embryogenesis and adult life with many vital biological functions such as neuromodulators and anti-adipogenesis. Downregulation of Hedgehog signalling is associated with ageing-related diseases like Alzheimer/Parkinson and T2D diseases and upregulation of this signalling reduces risk of these diseases. Thus, Hedgehog signalling is antagonist of ageing.

Description: Control of osteogenesis by the canonical Wnt and BMP pathways in vivo: The cover image shows a transverse section through a Xenopus tropicalis metamorphosing tadpole phalange. This histological section was stained with Kernechtrot to reveal cell bodies (pink) and Alcian blue to show the cartilage (blue). The circular cartilaginous shaft is surrounded by a layer of bone mineralized matrix (grey ring) secreted by adjacent osteoblasts. On pages 953–962 Marcellini et al. review recent experimental evidence showing that the canonical Wnt and BMP pathways functionally interact as cells differentiate from osteochondroprogenitors to osteoblasts and osteocytes, in the context of the developing vertebrate embryo. BMP signalling specifies multipotent mesenchymal cells into osteochondroprogenitors which are subsequently driven towards the osteoblastic fate by the Wnt pathway. In osteoblasts, both pathways promote differentiation, albeit with notable mechanistic differences. Finally, in osteocytes, the Wnt and BMP pathways exert opposite effects on the control of bone resorption by osteoclasts. Cover by S. Marcellini.

Description: For data assimilation in numerical weather prediction, the initial forecast-error covariance matrix P f is required. For variational assimilation it is particularly important to prescribe an accurate initial matrix P f , since P f is either static (in the 3D-Var case) or constant at the beginning of each assimilation window (in the 4D-Var case). At large scales the atmospheric flow is well approximated by hydrostatic balance and this balance is strongly enforced in the initial matrix P f used in operational variational assimilation systems such as that of the Met Office. However, at convective scales this balance does not necessarily hold any more. Here we examine the extent to which hydrostatic balance is valid in the vertical forecast-error covariances for high-resolution models in order to determine whether there is a need to relax this balance constraint in convective-scale data assimilation. We use the Met Office Global and Regional Ensemble Prediction System (MOGREPS) and a 1.5 km resolution version of the Unified Model for a case study characterized by the presence of convective activity. An ensemble of high-resolution forecasts valid up to three hours after the onset of convection is produced. We show that at 1.5 km resolution hydrostatic balance does not hold for forecast errors in regions of convection. This indicates that in the presence of convection hydrostatic balance should not be enforced in the covariance matrix used for variational data assimilation at this scale. The results show the need to investigate covariance models that may be better suited for convective-scale data assimilation. Finally, we give a measure of the balance present in the forecast perturbations as a function of the horizontal scale (from 3–90 km) using a set of diagnostics. Copyright © 2012 Royal Meteorological Society and British Crown Copyright, the Met Office

Description: MHC II, a major feature of the adaptive immune system, is lacking in Atlantic cod, and there are different scenarios (metabolic cost hypothesis or functional shift hypothesis) that might explain this loss. The lack of MHC II coincides with an increased number of genes for MHC I and Toll-like receptors (TLRs).

Description: Fluorescence microscopy is the primary tool for studying complex processes inside individual living cells. Technical advances in both molecular biology and microscopy have made it possible to image cells from many genetic and environmental backgrounds. These images contain a vast amount of information, which is often hidden behind various sources of noise, convoluted with other information and stochastic in nature. Accessing the desired biological information therefore requires new tools of computational image analysis and modeling. Here, we review some of the recent advances in computational analysis of images obtained from fluorescence microscopy, focusing on bacterial systems. We emphasize techniques that are readily available to molecular and cell biologists but also point out examples where problem-specific image analyses are necessary. Thus, image analysis is not only a toolkit to be applied to new images but also an integral part of the design and implementation of a microscopy experiment.

Description: The use of super-resolution imaging techniques in cell biology has yielded a wealth of information regarding cellular elements and processes that were invisible to conventional imaging. Focusing on images obtained by stimulated emission depletion (STED) microscopy, we discuss how the new high-resolution data influence the ways in which we use and interpret images in cell biology. Super-resolution images have lent support to some of our current hypotheses. But, more significantly, they have revealed unexpectedly complex processes that cannot be accounted for by the simpler models based on diffraction-limited imaging. The super-resolution imaging data challenge cell biologists to change their theoretical framework, by including, for instance, interpretations that describe multiple functions, functional errors or lack of function for cellular elements. In this context, we argue that descriptive research using super-resolution microscopy is now as necessary as hypothesis-driven research.

Description: The current revolution in biological microscopy stems from the realisation that advances in optics and computational tools and automation make the modern microscope an instrument that can access all scales relevant to modern biology – from individual molecules all the way to whole tissues and organisms and from single snapshots to time-lapse recordings sampling from milliseconds to days. As these and more new technologies appear, the challenges of delivering them to the community grows as well. I discuss some of these challenges, and the examples where openly shared technology have made an impact on the field.

Description: The discovery and engineering of novel fluorescent proteins (FPs) from diverse organisms is yielding fluorophores with exceptional characteristics for live-cell imaging. In particular, the development of FPs for fluorescence (or Förster) resonance energy transfer (FRET) microscopy is providing important tools for monitoring dynamic protein interactions inside living cells. The increased interest in FRET microscopy has driven the development of many different methods to measure FRET. However, the interpretation of FRET measurements is complicated by several factors including the high fluorescence background, the potential for photoconversion artifacts and the relatively low dynamic range afforded by this technique. Here, we describe the advantages and disadvantages of four methods commonly used in FRET microscopy. We then discuss the selection of FPs for the different FRET methods, identifying the most useful FP candidates for FRET microscopy. The recent success in expanding the FP color palette offers the opportunity to explore new FRET pairs.

Description: Light sheet microscopy is an easy to implement and extremely powerful alternative to established fluorescence imaging techniques such as laser scanning confocal, multi-photon and spinning disk microscopy. By illuminating the sample only with a thin slice of light, photo-bleaching is reduced to a minimum, making light sheet microscopy ideal for non-destructive imaging of fragile samples over extended periods of time. Millimeter-sized samples can be imaged rapidly with high resolution and high depth penetration. A large variety of instruments have been developed and optimized for a number of different samples: Bessel beams form thin light sheets for single cells, and selective plane illumination microscopy (SPIM) offers multi-view acquisition to image entire embryos with isotropic resolution. This review explains how light sheet microscopy involves a conceptually new microscope design and how it changes modern imaging in biology.

Description: The role of the major histocompatibility complex (MHC) in mate choice in humans is controversial. Nowadays, the availability of genetic variation data at genomic scales allows for a careful assessment of this question. In 2008, Chaix et al. reported evidence for MHC-dependent mate choice among European American spouses from the HapMap 2 dataset. Recently, Derti et al. suggested that this observation was not robust. Furthermore, when Derti et al. applied similar analyses to the HapMap 3 European American samples, they did not see a significant effect. Although some of the points raised by Derti et al. are relevant, we disagree with the reported absence of evidence for MHC-dependent mate choice within the HapMap samples. More precisely, we show here that the MHC dissimilarity among HapMap 3 European American spouses is still extreme in comparison to the rest of the genome, even after multiple testing correction. This finding supports the hypothesis of MHC-dependent mate choice in some human populations. The MHC may influence mate choice in some human populations also depending on other variables such as socio-cultural factors, the level of genetic diversity and the strength of pathogenic pressures.

Description: Is a two-fold approach — preliminary studies based on small samples followed by a large-sample study to check reproducibility — in the search for biomarkers really prudent?

Description: Here we elucidate a paradox: how a single chemoattractant-receptor system in two individuals is used for communication despite the seeming inevitability of self-excitation. In the filamentous fungus Neurospora crassa , genetically identical cells that produce the same chemoattractant fuse via the homing of individual cell protrusions toward each other. This is achieved via a recently described “ping-pong” pulsatile communication. Using a generic activator-inhibitor model of excitable behavior, we demonstrate that the pulse exchange can be fully understood in terms of two excitable systems locked into a stable oscillatory pattern of mutual excitation. The most puzzling properties of this communication are the sudden onset of oscillations with final amplitude, and the absence of seemingly inevitable self-excitation. We show that these properties result directly from both the excitability threshold and refractory period characteristic of excitable systems. Our model suggests possible molecular mechanisms for the ping-pong communication. Fusion of genetically identical cells in Neurospora crassa is achieved by the cells taking turns in releasing a chemoattractant and sensing it.

Description: Food turns out to be not only the nutrient supplier for our body but also a carrier of regulatory information. Interestingly, a recent study made the discovery that some plant/food-derived microRNAs (miRNAs) accumulate in the serum of humans or plant-feeding animals, and regulate mammalian gene expression in a sequence-specific manner. The authors provided striking evidence that miRNAs could function as active signaling molecules to transport information across distinct species or even kingdoms. Although the mechanism of how miRNAs are shuttled between different organisms is still not well characterized, initial results point to the involvement of microvesicles and specific RNA-transporter-like proteins. These findings raise both speculation about the potential impact that plants may have on animal physiology at the molecular level, and an appealing possibility that food-derived miRNAs may offer us another means to deliver necessary nutrients or therapeutics to our bodies. There is recent evidence that microRNAs derived from ingested food sources can be taken up, packaged into microvesicles and, upon reaching the final recipient cells, regulate a target gene in a sequence-specific manner.

Description: Cancer is generally defined as uncontrollable growth of cells caused by genetic aberrations and/or environmental factors. Yet contagious cancers also occur. The recent emergence of a contagious cancer in Tasmanian devils has reignited interest in transmissible cancers. Two naturally occurring transmissible cancers are known: devil facial tumour disease and canine transmissible venereal tumour. Both cancers evolved once and have then been transmitted from one individual to another as clonal cell lines. The dog cancer is ancient; having evolved more than 6,000 years ago, while the devil disease was first seen in 1996. In this review I will compare and contrast the two diseases focusing on the life histories of the clonal cell lines, their evolutionary trajectories and the mechanisms by which they have achieved immune tolerance. A greater understanding of these contagious cancers will provide unique insights into the role of the immune system in shaping tumour evolution and may uncover novel approaches for treating human cancer. A better understanding of the two known transmissible cancers (Tasmanian devil facial tumour and canine transmissible venereal tumour) may provide unique insights into the role of the immune system in shaping tumour evolution and may uncover novel approaches for treating human cancer.

Description: Balancing self-renewal and differentiation of stem cells is an important issue in stem cell and cancer biology. Recently, the Drosophila neuroblast (NB), neural stem cell has emerged as an excellent model for stem cell self-renewal and tumorigenesis. It is of great interest to understand how defects in the asymmetric division of neural stem cells lead to tumor formation. Here, we review recent advances in asymmetric division and the self-renewal control of Drosophila NBs. We summarize molecular mechanisms of asymmetric cell division and discuss how the defects in asymmetric division lead to tumor formation. Gain-of-function or loss-of-function of various proteins in the asymmetric machinery can drive NB overgrowth and tumor formation. These proteins control either the asymmetric protein localization or mitotic spindle orientation of NBs. We also discuss other mechanisms of brain tumor suppression that are beyond the control of asymmetric division. Drosophila neuroblasts represent an excellent model system to study the molecular mechanisms of asymmetric divisions during stem cell self-renewal and how defects in this system lead to tumourigenesis.

Description: Cell interdivision periods (IDP) in homogenous cell populations vary stochastically. Another aspect of probabilistic cell behavior is randomness in cell differentiation. These features are suggested to result from competing stochastic events of assembly/disassembly of the transcription pre-initiation complex (PIC) at gene promoters. The time needed to assemble a proper PIC from different proteins, which must be numerous enough to make their combination gene specific, may be comparable to the IDP. Nascent mRNA visualization at defined genes and inferences from protein level fluctuations in single cells suggest that some genes do operate in this way. The onset of mRNA production by such genes may miss the time windows provided by the cell cycle, resulting in cells differentiating into those in which the respective mRNAs are either present or absent. This creates a way to generate cell phenotype diversity in multicellular organisms.

Description: For data assimilation in numerical weather prediction, the initial forecast-error covariance matrix P f is required. For variational assimilation it is particularly important to prescribe an accurate initial matrix P f , since P f is either static (in the 3D-Var case) or constant at the beginning of each assimilation window (in the 4D-Var case). At large scales the atmospheric flow is well approximated by hydrostatic balance and this balance is strongly enforced in the initial matrix P f used in operational variational assimilation systems such as that of the Met Office. However, at convective scales this balance does not necessarily hold any more. Here we examine the extent to which hydrostatic balance is valid in the vertical forecast-error covariances for high-resolution models in order to determine whether there is a need to relax this balance constraint in convective-scale data assimilation. We use the Met Office Global and Regional Ensemble Prediction System (MOGREPS) and a 1.5 km resolution version of the Unified Model for a case study characterized by the presence of convective activity. An ensemble of high-resolution forecasts valid up to three hours after the onset of convection is produced. We show that at 1.5 km resolution hydrostatic balance does not hold for forecast errors in regions of convection. This indicates that in the presence of convection hydrostatic balance should not be enforced in the covariance matrix used for variational data assimilation at this scale. The results show the need to investigate covariance models that may be better suited for convective-scale data assimilation. Finally, we give a measure of the balance present in the forecast perturbations as a function of the horizontal scale (from 3–90 km) using a set of diagnostics. Copyright © 2012 Royal Meteorological Society and British Crown Copyright, the Met Office

Description: There is no more challenging problem in computational science than that of estimating, as accurately as science and technology allows, the future evolution of Earth's climate; nor indeed is there a problem whose solution has such importance and urgency. Historically, the simulation tools needed to predict climate have been developed, somewhat independently, at a number of weather and climate institutes around the world. While these simulators are individually deterministic, it is often assumed that the resulting diversity provides a useful quantification of uncertainty in global or regional predictions. However, this notion is not well founded theoretically and corresponding ‘multi-simulator’ estimates of uncertainty can be prone to systemic failure. Separate to this, individual institutes are now facing considerable challenges in finding the human and computational resources needed to develop more accurate weather and climate simulators with higher resolution and full Earth-system complexity. A new approach, originally designed to improve reliability in ensemble-based numerical weather prediction, is introduced to help solve these two rather different problems. Using stochastic mathematics, this approach recognizes uncertainty explicitly in the parametrized representation of unresolved climatic processes. Stochastic parametrization is shown to be more consistent with the underlying equations of motion and, moreover, provides more skilful estimates of uncertainty when compared with estimates from traditional multi-simulator ensembles, on time-scales where verification data exist. Stochastic parametrization can also help reduce long-term biases which have bedevilled numerical simulations of climate from the earliest days to the present. As a result, it is suggested that the need to maintain a large ‘gene pool’ of quasi-independent deterministic simulators may be obviated by the development of probabilistic Earth-system simulators. Consistent with the conclusions of the World Summit on Climate Modelling, this in turn implies that individual institutes will be able to pool human and computational resources in developing future-generation simulators, thus benefitting from economies of scale; the establishment of the Airbus consortium provides a useful analogy here. As a further stimulus for such evolution, discussion is given to a potential new synergy between the development of dynamical cores, and stochastic processing hardware. However, it is concluded that the traditional challenge in numerical weather prediction, of reducing deterministic measures of forecast error, may increasingly become an obstacle to the seamless development of probabilistic weather and climate simulators, paradoxical as that may appear at first sight. Indeed, going further, it is argued that it may be time to consider focusing operational weather forecast development entirely on high-resolution ensemble prediction systems. Finally, by considering the exceptionally challenging problem of quantifying cloud feedback in climate change, it is argued that the development of the probabilistic Earth-system simulator may actually provide a route to reducing uncertainty in climate prediction. Copyright © 2012 Royal Meteorological Society

Description: Surface and upper-air observations of meteorological parameters at Gadanki (13.5°N, 79.2°E) are utilized to understand the thermal structure of the atmosphere in dry and wet spells and its effect on draught core statistics. The temperature and humidity variations from wet to dry spell are quite pronounced near the surface and in the atmospheric boundary layer (ABL), but not above the ABL. Interestingly, convective available potential energy (CAPE) is found to be higher during wet spells than during dry spells, in contrast to the earlier studies made elsewhere over warm oceans and tropical land masses. The stratified CAPE values based on rainfall occurrence are also larger during wet spells than during dry spells, irrespective of whether the sounding is made before, during or after the rain occurrence. Surprisingly, large CAPE values are observed after the rain occurrence in both spells. The high CAPE during wet spells (and also after rain occurrence) corresponds well with larger surface equivalent potential temperature ( θ e ). During wet spells, the positive buoyancy is not only larger but also vertically extended to higher altitudes. On the other hand, buoyancy profiles during dry spells are punctuated by several negative buoyancies (associated with stable layers), reducing CAPE values in those spells. A synthesis of all measurements reveals that favourable environmental conditions (high CAPE, humid atmosphere and weak stable layers) allow the convection to grow into a deep system in wet spells. On the other hand, strong stable layers, weak CAPE coupled with relatively less humidity above the ABL inhibits the growth of convective cloud during dry spells. These observations explain the differences in draught core statistics in wet and dry spells. Copyright © 2012 Royal Meteorological Society

Description: Understanding the combined effect of El Niño–Southern Oscillation (ENSO) and the North Atlantic Oscillation (NAO) is of great importance for climate seasonal prediction (extreme climate events in particular). Results in this study show that during the last hundred years (1900 to present), the ENSO–NAO connection experiences a notable interdecadal change in summer (June–August) according to a 21-year sliding correlation between them, namely, from no significant correlation (uncoupling) before the mid-1970s to a significant correlation (coupling) after the mid-1970s. Comparison analysis between the coupling epoch (1977–1997) and the uncoupling epoch (1958–1976) shows that the most pronounced circulation anomalies take place over the extratropical North Pacific. Further analysis and numerical experiments suggest that a poleward-propagating Rossby wave train, possibly enhanced by sea-surface-temperature anomalies in the extratropical North Pacific associated with the developing phases of ENSO during the later epoch, is responsible for connecting the ENSO signal with the NAO. © 2012 Crown in the right of Canada. Published by JohnWiley & Sons Ltd.

Description: The influence of soil moisture and atmospheric stability on mid-latitude diurnal convection and land–atmosphere exchange is investigated in an idealized cloud-resolving modelling framework using a full set of parametrization schemes. In each member of a series of month-long experiments, the model attains a state where deep, precipitating convection is triggered every day. This state is referred to as equilibrium diurnal convection. The triggering occurs via different mechanisms depending on the atmosphere–soil setting. In our framework latent heat fluxes comprise the primary control over the precipitation amounts. We find that evaporation is regulated by the availability of energy on the one hand and the availability of soil moisture and the near-surface saturation deficit of the atmosphere on the other. Increased cloud cover over wet soils reduces net short-wave radiation but increases net long-wave radiation, leading to a near-compensation of the two effects on available energy. Increased boundary layer moisture is removed by deep convection, thus increasing the near-surface saturation deficit and preventing a negative feedback of boundary layer moisture content on the latent heat fluxes. We also find that there is a spatial correlation between soil moisture and precipitation anomalies, suggesting that the soil moisture precipitation feedback acts on a scale of 10–50 km. Copyright © 2012 Royal Meteorological Society

Description: Correlation functions associated with the inverse covariances represented by polynomials of the homogeneous diffusion operator D are obtained analytically for an arbitrary polynomial of D, constrained by the positive-definiteness condition of the covariance operator. Copyright © 2012 Royal Meteorological Society

Description: Spectral nudging is a technique consisting in driving regional climate models (RCMs) on selected spatial scales corresponding to those produced by the driving global circulation model (GCM). This technique prevents large and unrealistic departures between the GCM driving fields and the RCM fields at the GCM spatial scales. Theoretically, the relaxation of the RCM towards the GCM should be infinitely strong provided thre are perfect large-scale fields. In practice, the nudging time is chosen based on trial and error. In this study, the physical parameters setting the optimal nudging coefficient are identified and their effects are discussed. In addition to the predictability time τ p , already analyzed in a companion article, the time interval τ a between consecutive GCM driving fields is a key controlling parameter, especially when spectral nudging is considered. Indeed, the driving GCM fields are interpolated in time at every RCM integration time step, which is much smaller than τ a . This produces an inaccurate evolution of the GCM fields. A nudging time close to zero (infinitly strong nudging) would thus produce a non-realistic evolution of the RCM large-scale field and consequently an inaccurate small-scale field. The optimum nudging coefficient thus differs from zero, but remains smaller than the predictability time τ p , as discussed elsewhere. Furthermore depending on the time interval τ a , all scales present in the driving fields may not be well time-resolved. It can then be beneficial to filter them out rather than driving the RCM with fields affected by time-sampling errors. Copyright © 2012 Royal Meteorological Society

Description: The continuous ranked probability score (CRPS) is a frequently used scoring rule. In contrast with many other scoring rules, the CRPS evaluates cumulative distribution functions. An ensemble of forecasts can easily be converted into a piecewise constant cumulative distribution function with steps at the ensemble members. This renders the CRPS a convenient scoring rule for the evaluation of ‘raw’ ensembles, obviating the need for sophisticated ensemble model output statistics or dressing methods prior to evaluation. In this article, a relation between the CRPS score and the quantile score is established. The evaluation of ‘raw’ ensembles using the CRPS is discussed in this light. It is shown that latent in this evaluation is an interpretation of the ensemble as quantiles but with non-uniform levels. This needs to be taken into account if the ensemble is evaluated further, for example with rank histograms. Copyright © 2012 Royal Meteorological Society

Description: The marine boundary layer is known to be influenced by fast long ocean swell waves travelling away from their generation area, where they were initiated by momentum transferred to the ocean wave field during storms. The atmospheric boundary layer during wind-following swell and various stability states has been investigated using large-eddy simulation (LES) data. The dominant energy-containing motions in the near-neutral atmospheric boundary layer over flat terrain are known to be dominated by near-ground shear-induced regions of high- and low-speed flow. Wind fields and momentum fluxes from LES for swell-dominated situations have been used to interpret field measurements suggesting that these motions are disrupted by effects related to the underlying wave field in the presence of swell waves. Statistical analysis and visualization are used to further describe the effects of stratification during swell for convective boundary-layer winds and fluxes. A mechanism for transport of momentum to the upper levels of the boundary layer is suggested from interpretation of LES data. Coherent detached eddies from the directly wave-induced motions near the surface are found to maintain an upward momentum transfer. This mechanism is found to strengthen during stronger swell conditions and also during slightly convective conditions. In this way, it is argued that processes related to both the wave field and surface convection can have a significant influence on the global structure of neutral and convective boundary layers during swell. This has implication for the turbulence length-scales during wind-following swell. Copyright © 2012 Royal Meteorological Society

Description: The structure, evolution and dynamics of two lower stratospheric frontal zones are examined from a basic state variables perspective. The case studies highlight the asynchronous evolution of the lower stratospheric and upper tropospheric frontal portions of upper level jet-front (ULJF) systems, as well as some substantial differences in lower stratospheric frontal development that occur in southwesterly and northwesterly flow. The evolution of the ULJF in northwesterly flow was characterized by an initially intense but weakening lower stratospheric front along with an initially weak but intensifying upper tropospheric front. Throughout the evolution, geostrophic cold air advection in cyclonic shear characterized a substantial portion of the lower stratospheric front. This circumstance supported subsidence through the local jet core within the cold upper troposphere, weakening the lower stratospheric front via tilting. This subsidence extended downward below the jet core where it is suggested to have played a role in the early stages of upper tropospheric frontogenesis. In the southwesterly flow case, the evolution of the ULJF was characterized by a strengthening lower stratospheric front and a weakening upper tropospheric front. A deep column of upward vertical motion resulted from the superposition of lower tropospheric ascent associated with convection along a surface cold front and upper tropospheric-lower stratospheric (UTLS) ascent through the jet core coincident with geostrophic warm air advection in cyclonic shear along large sections of the lower stratospheric front. The UTLS ascent, located on the cold edge of the lower stratospheric baroclinicity, served to intensify the lower stratospheric frontal zone via tilting. The implications of these lower stratospheric frontal processes on the topography of the tropopause and downstream sensible weather are discussed. Copyright © 2012 Royal Meteorological Society

Description: Forecasts provided by the THORPEX Interactive Grand Global Ensemble (TIGGE) project were compared with reforecast-calibrated ensemble predictions from the European Centre for Medium-Range Weather Forecasts (ECMWF) in extratropical regions. Considering the statistical performance of global probabilistic forecasts of 850 hPa and 2 m temperatures, a multimodel ensemble containing nine ensemble prediction systems (EPS) from the TIGGE archive did not improve on the performance of the best single-model, the ECMWF EPS. However, a reduced multimodel system, consisting of only the four best ensemble systems, provided by Canada, the USA, the United Kingdom and ECMWF, showed an improved performance. The multimodel ensemble provides a benchmark for the single-model systems contributing to the multimodel. However, reforecast-calibrated ECMWF EPS forecasts were of comparable or superior quality to the multimodel predictions, when verified against two different reanalyses or observations. This improved performance was achieved by using the ECMWF reforecast dataset to correct for systematic errors and spread deficiencies. The ECMWF EPS was the main contributor for the improved performance of the multimodel ensemble; that is, if the multimodel system did not include the ECMWF contribution, it was not able to improve on the performance of the ECMWF EPS alone. These results were shown to be only marginally sensitive to the choice of verification dataset. Copyright © 2012 Royal Meteorological Society

Description: In order to calculate unbiased microphysical and radiative quantities in the presence of a cloud, it is necessary to know not only the mean water content but also the distribution of this water content. This article describes a study of the in-cloud horizontal inhomogeneity of ice water content, based on CloudSat data. In particular, by focusing on the relations with variables that are already available in general circulation models (GCMs), a parametrization of inhomogeneity that is suitable for inclusion in GCM simulations is developed. Inhomogeneity is defined in terms of the fractional standard deviation (FSD), which is given by the standard deviation divided by the mean. The FSD of ice water content is found to increase with the horizontal scale over which it is calculated and also with the thickness of the layer. The connection to cloud fraction is more complicated; for small cloud fractions FSD increases as cloud fraction increases while FSD decreases sharply for overcast scenes. The relations to horizontal scale, layer thickness and cloud fraction are parametrized in a relatively simple equation. The performance of this parametrization is tested on an independent set of CloudSat data. The parametrization is shown to be a significant improvement on the assumption of a single-valued global FSD. Copyright © 2012 Royal Meteorological Society and British Crown Copyright, the Met Office

Description: The specification of a correct background-error covariance matrix is a key issue in data assimilation schemes. The Ensemble Kalman Filter (EnKF) aims at providing simulations of analysis and background errors and then gives a way to determine this background-error covariance matrix. The EnKF can be transposed to variational ensemble assimilation, where a set of perturbed variational analyses are performed. In this case, however, there is an evident important additional cost associated with the use of multiple minimizations. The aim of the paper is to investigate different techniques to reduce the cost of the multiple minimizations that have to be performed. In particular, the use is investigated of a preconditioning technique based on Ritz eigenpairs resulting from a first minimization performed by a combined Lanczos/conjugate-gradient algorithm. The possibility is also studied of improving the starting point of a new perturbed solution, with Lanczos vectors issued from a single prior unperturbed or perturbed minimization. This appears to provide a first significant reduction in the cost of the new minimization. Finally, a new approach is proposed to generalize the previous idea to the use of multiple sets of Lanczos vectors issued from an ensemble of perturbed assimilations. The application of this procedure to a simplified analysis problem shows encouraging results, as it appears to be a possible way for reducing the global cost of an ensemble variational assimilation. Moreover, this seems to provide an efficient strategy for parallelizing such an ensemble variational assimilation but also the deterministic variational assimilation itself. Copyright © 2012 Royal Meteorological Society

Description: Background-error variances estimated from a finite size ensemble of data assimilations are affected by sampling noise, which degrades the accuracy of the variance estimates. Previous work highlighted the close link between the spatial structures of background error and the associated sampling noise, and demonstrated the ability of local spatial averaging to remove this sampling noise. Existing filtering techniques commonly assume a homogeneous smoothing of the estimated variances. However, this assumption can be inadequate to represent error structures of varying scales, e.g. small-scale errors associated with localized severe weather events. To answer this problem, this article introduces and examines a heterogeneous filter based on the knowledge of the local spatial properties of the sampling noise. The filtering is realized with a diffusion process, and the diffusion coefficient is parametrized according to the local correlation length-scale of the sampling noise. This enables the diffusion coefficient to vary spatially in such a way as to encourage smoothing in regions where the background error is large scale in preference to regions where the error is small scale. A simulated 1D framework is considered to test the proposed approach. It is shown that the filtering using a spatially varying diffusion coefficient is able to preserve high-frequency variance structures, while this information tends to be smoothed with homogeneous filtering. The benefits of applying heterogeneous filtering are particularly pronounced with small ensemble sizes and in the vicinity of localized variance maxima. Copyright © 2012 Royal Meteorological Society

Description: Snow clouds forming directly over the ground and reaching depths of up to a kilometre have been observed with a W-band airborne radar. The phenomenon is referred to here as ‘ground-layer snow cloud’ (GSC). Most of the cases were observed over mountainous terrain but some were seen over nearly flat terrain. These snow clouds occurred over snow-covered ground. The temperature at their point of first appearance on rising slopes was in the range 0 to −10° C with humidity close to water saturation. GSCs form within windy and highly turbulent surface layers, with specific features linked to sudden rises or dips in terrain. The most plausible explanation for the formation of the GSC is that snow particles lofted from the surface grow in the ice-supersaturated environment and mix throughout the turbulent layer. Sufficiently high humidity for crystal growth distinguishes these clouds from blowing snow in dry air. On the downwind sides of mountains, the snow clouds precipitate and evaporate. As for blowing snow, visibility within GSCs is greatly reduced. The GSC represents a form of horizontal water mass transport. When a GSC forms with other clouds present above it, as is frequently the case, there is a clear potential for those clouds to be seeded from below, thereby altering their evolution, precipitation distribution, and other impacts. Copyright © 2012 Royal Meteorological Society

Description: Four operational numerical weather prediction (NWP) models were evaluated in winter conditions against (a) synoptic observations in Europe, (b) observations at a 48 m high micrometeorological mast in Sodankylä, northern Finland, and (c) observations at the Helsinki Testbed stations: (i) to evaluate the skills of the models to compute nocturnal 2 m air temperature (T2m) and the temperature inversion; and (ii) to distinguish between the T2m bias and the subgrid-scale spatial variability of T2m. The models were (1) the Integrated Forecast System (IFS) of the European Centre for Medium-Range Weather Forecasts (ECMWF), (2) the High Resolution Limited Area Model (HIRLAM), (3) the Applications of Research to Operations at Mesoscale (AROME) developed by Météo-France, and (4) the Global Forecasting System (GFS) of the US National Center for Environmental Predictions (NCEP). The results demonstrated a T2m bias increasing with decreasing temperature and strengthening temperature inversion. When a strong temperature inversion was observed in Sodankylä, the models underestimated it, whereas in near-neutral conditions the stratification was overestimated. Comparison of observed and modelled 3 h temperature tendencies showed that the T2m tendency in the models was on average only 17–20% of the observed one. The warm bias in T2m forecast in Sodankylä during periods of observed temperature inversion partly resulted from a warm bias in the initial conditions. This was due to problems in data assimilation in IFS and HIRLAM, in initialization in AROME, and in either or both procedures in GFS. In particular, the IFS data assimilation increased the T2m bias. Evaluation of modelled T2m against grid-averaged T2m observed at Helsinki Testbed demonstrated that the T2m model error dominated over the spatial variability of observed T2m. This suggests that over an almost flat terrain horizontal resolution is not a major factor for the accuracy of T2m forecast at low T2m typically associated with temperature inversions. Copyright © 2012 Royal Meteorological Society

Description: Observations from near-simultaneous atmospheric soundings released over contrasting land surfaces in the southwest of Western Australia during December 2005 (austral summer) and August 2007 (late austral winter or early spring) have shown higher planetary boundary layer (PBL) heights over native vegetation as compared to agricultural land. The large-eddy simulation technique is used to investigate the drivers behind these observed differences in PBL, and sensitivity tests are carried out with modified soil moisture and vegetation cover. It is shown that the differences in PBL for the December case are mainly driven by the change in vegetation cover, while a soil moisture gradient also played a role for the August case. The mixing diagram approach is used to further quantify the relative contributions of surface and entrainment fluxes on the growth of the PBL and it is shown that, while dry-air entrainment plays an important role in PBL development, it is the higher surface Bowen ratio which drives the more vigorous PBL development over the native vegetation. It is also shown that the enhanced PBL development over the native vegetation leads to the preferential formation of shallow convective clouds for the August case. Copyright © 2012 Royal Meteorological Society

Description: An unusually deep (961 hPa) hurricane-like polar low over the Barents Sea during 18–21 December 2002 is studied by a series of fine-mesh (3 km) experiments using the Weather Research and Forecasting (WRF) model. The simulated polar low was similar to hurricanes and similar previous case-studies in that it had a clear, calm and warm eye structure surrounded by moist convection organized in spiral cloud bands, and the highest surface wind speeds were found in the eye wall. The proximity to the sea ice and the high surface wind speeds (about 25 m s −1 ) during the deepening stage triggered extremely high surface sensible and latent heat fluxes at the eye wall of about 1200 and 400 W m −2 , respectively. As the polar low moved eastward and weakened, maximum surface sensible and latent heat fluxes dropped to about 600 and 300 W m −2 , respectively. Two types of sensitivity experiments were designed to analyse the physical properties of the polar low. Firstly, physical processes such as condensational heating and sensible and/or latent heat fluxes were switched off–on throughout the simulation. In the second type, these processes were turned off–on after the polar low had reached its peak intensity, which minimized the deformation of the polar-low environment, making it suitable to study the direct effect of physical processes on the mature vortex. The experiments suggest that the deepening stage of the polar low was dominated by baroclinic growth and that upper-level potential vorticity forcing contributed throughout its life cycle. After the deepening stage, the baroclinicity vanished and the polar low was fuelled by surface sensible heat fluxes while latent heat fluxes played a minor role. Condensational heating was not essential for the energetics of the polar low. Surprisingly, in experiments where condensational heating was turned off throughout the simulation, the polar low intensified. Copyright © 2012 Royal Meteorological Society

Description: The effect on deep convection of large-scale potential vorticity (PV) anomalies and their associated tropospheric stable layers is complex and not well understood. This article examines the meteorological events of 9 July 2007 (IOP7b of the Convective and Orographically-induced Precipitation Study (COPS)), which was dominated by an upper-level PV anomaly that stretched from the UK to southern France and as far northeast as Denmark. Three precipitation regions were identified from the case: lines of intense storms beneath the PV anomaly; less intense, more widespread convective precipitation to the east of the PV anomaly; and, in between, a region of no precipitation. The latter of these coincided with the high-resolution measurements and model analyses from COPS. The extensive and varied data analyzed in this investigation show that convective available potential energy (CAPE) was present in this region (the distribution of CAPE and convective inhibition (CIN) is presented via an innovative, pseudo-3D visualization that allows horizontal and vertical interactions to be considered). However, convection was capped by a complex arrangement of dry layers; the base of the key layer was at 750 hPa. These dry layers descended separately from the upper troposphere, moving around the PV anomaly as it developed from a breaking Rossby wave to the west during the seven days before the IOP. This case adds to other studies that show that descent of complex dry layers is an important mechanism for forming convection-inhibiting atmospheric lids in Western Europe. A simple conceptual model is developed that synthesizes the effect of large-scale PV anomalies on deep convection from a series of consistent case studies. This model has significant implications for storm forecasting and projections of storminess in future climates, as it highlights the importance of thin structures that can advect hundreds of km before having an impact. Copyright © 2012 Royal Meteorological Society

Description: Mass–wind and vorticity–divergence balance constraints based on the linearized Charney and quasi-geostrophic omega equations, respectively, are assessed in a developmental version of the global, three-dimensional variational data-assimilation system at Environment Canada. Unlike traditional balance constraints, which are averaged in time, the new constraints are flow-dependent and reflect a more complete set of dynamics. Single observation experiments demonstrate that the new covariance model leads to asymmetrical increments that are qualitatively aligned with the instantaneous background wind field. Data-assimilation experiments using real observations are performed for a period of five weeks during two different seasons, employing the control and experimental constraints. Subsequent forecast verification against radiosondes shows a definite benefit of the new covariances in the Tropics; however, the impact in the Extratropics is neutral or slightly negative. Verifications against analysis show virtually no change in the troposphere; however, a significant improvement is observed in the stratosphere at all lead times. Compared with the Charney mass–wind balance, the contribution of the quasi-geostrophic omega constraint is rather minimal, at least in its current adiabatic form. The new balance scheme requires a considerable amount of computational time in the context of our 3D-Var system, although the relative cost in a 4D-Var setting may be far less significant. Moreover, the present experiments are useful in elucidating several important aspects of covariance modelling, particularly the dependence of balance dynamics on spatial scale. © 2012 Crown in the right of Canada. Published by John Wiley & Sons Ltd.

Description: Ensemble forecasts of (u,v) -wind are of crucial importance for a number of decision-making problems related to e.g. air traffic control, ship routeing and energy management. The skill of these ensemble forecasts as generated by NWP-based models can be maximised by correcting for their lack of sufficient reliability. The original framework introduced here allows for an adaptive bivariate calibration of these ensemble forecasts. The originality of this methodology lies in the fact that calibrated ensembles still consist of a set of (space–time) trajectories, after translation and dilation. In parallel, the parameters of the models employed for improving the stochastic properties of the generating processes involved are adaptively and recursively estimated to accommodate smooth changes in the process characteristics and to lower computational costs. The approach is applied and evaluated based on the adaptive calibration of ECMWF ensemble forecasts of (u,v) -wind at 10 m above ground level over Europe over a three-year period between December 2006 and December 2009. Substantial improvements in (bivariate) reliability and in various deterministic/probabilistic scores are observed. Finally, the maps of translation and dilation factors are discussed. Copyright © 2012 Royal Meteorological Society

Description: An idealized ‘superparameterization’, or abbreviated but dynamically explicit representation of small-scale influences on the conventionally resolved larger scales of a dynamical model, is constructed within the Lorenz '96 system. The feasibility of abstracting the greater portion of its information content using computationally much faster statistical summaries, or emulators, is investigated through integration of a large number of ensemble forecasts. Even though based on an extremely small training-sample size, consistent with an assumed high computational expense for running a full superparameterization, some of the statistical emulator formulations perform nearly as well as the superparameterization forecast ensembles. As in previous studies, better forecast characteristics are generally achieved when autocorrelated random forcing is included, both in the otherwise deterministic superparameterization and in its statistical emulators. Copyright © 2012 Royal Meteorological Society

Description: In this article we show that entrainment during the developing stages of deep convection over land is much higher than convection at equilibrium. A series of idealised cloud-resolving model simulations are performed for a range of environmental conditions, and these show that the interaction with the environment via the entrainment and detrainment rates gradually decreases as the day progresses, reverting to the values found at equilibrium. The entrainment and detrainment rates are themselves found to depend on the environmental humidity and stability, and are also strongly linked to cloud size, suggesting that the representation of the horizontal growth of clouds in convective parametrizations is important for the representation of the diurnal cycle. We propose a simple new entrainment and detrainment formulation to take account of these findings, and show that this improves the representation of developing convection in a single-column model, providing a more gradual transition towards deep convection. Copyright © 2011 British Crown copyright, the Met Office. Published by John Wiley & Sons Ltd.

Description: A mechanism for amplification of mountain waves, and their associated drag, by parametric resonance is investigated using linear theory and numerical simulations. This mechanism, which is active when the Scorer parameter oscillates with height, was recently classified by previous authors as intrinsically nonlinear. Here it is shown that, if friction is included in the simplest possible form as a Rayleigh damping, and the solution to the Taylor–Goldstein equation is expanded in a power series of the amplitude of the Scorer parameter oscillation, linear theory can replicate the resonant amplification produced by numerical simulations with some accuracy. The drag is significantly altered by resonance in the vicinity of n/l 0 = 2, where l 0 is the unperturbed value of the Scorer parameter and n is the wave number of its oscillation. Depending on the phase of this oscillation, the drag may be substantially amplified or attenuated relative to its non-resonant value, displaying either single maxima or minima, or double extrema near n/l 0 = 2. Both non-hydrostatic effects and friction tend to reduce the magnitude of the drag extrema. However, in exactly inviscid conditions, the single drag maximum and minimum are suppressed. As in the atmosphere friction is often small but non-zero outside the boundary layer, modelling of the drag amplification mechanism addressed here should be quite sensitive to the type of turbulence closure employed in numerical models, or to computational dissipation in nominally inviscid simulations. Copyright © 2012 Royal Meteorological Society

Description: The technique of relaxation of the tropical atmosphere towards an analysis in a month-season forecast model has previously been successfully exploited in a number of contexts. Here it is shown that when tropical relaxation is used to investigate the possible origin of the observed anomalies in June–July 2007, a simple dynamical model is able to reproduce the observed component of the pattern of anomalies given by an ensemble of ECMWF forecast runs. Following this result, the simple model is used for a range of experiments on time-scales of relaxation, variables and regions relaxed based on a control model run with equatorial heating in a zonal flow. A theory based on scale analysis for the large-scale tropics is used to interpret the results. Typical relationships between scales are determined from the basic equations, and for a specified diabatic heating a chain of deductions for determining the dependent variables is derived. Different critical time-scales are found for tropical relaxation of different dependent variables to be effective. Vorticity has the longest critical time-scale, typically 1.2 days. For temperature and divergence, the time-scales are 10 hours and 3 hours, respectively. However not all the tropical fields, in particular the vertical motion, are reproduced correctly by the model unless divergence is heavily damped. To obtain the correct extra-tropical fields, it is crucial to have the correct rotational flow in the subtropics to initiate the Rossby wave propagation from there. It is sufficient to relax vorticity or temperature on a time-scale comparable or less than their critical time-scales to obtain this. However if the divergent advection of vorticity is important in the Rossby Wave Source then strong relaxation of divergence is required to accurately represent the tropical forcing of Rossby waves. Copyright © 2012 Royal Meteorological Society

Description: A combination of singular systems analysis and analytic phase techniques are used to investigate the possible occurrence in observations of coherent synchronization between quasi-biennial and semi-annual oscillations (QBOs; SAOs) in the stratosphere and troposphere. Time series of zonal mean zonal winds near the Equator are analysed from the ERA-40 and ERA-interim reanalysis datasets over a ∼ 50-year period. In the stratosphere, the QBO is found to synchronize with the SAO almost all the time, but with a frequency ratio that changes erratically between 4:1, 5:1 and 6:1. A similar variable synchronization is also evident in the tropical troposphere between semi-annual and quasi-biennial cycles (known as TBOs). Mean zonal winds from ERA-40 and ERA-interim, and also time series of indices for the Indian and West Pacific monsoons, are commonly found to exhibit synchronization, with SAO/TBO ratios that vary between 4:1 and 7:1. Coherent synchronization between the QBO and tropical TBO does not appear to persist for long intervals, however. This suggests that both the QBO and tropical TBOs may be separately synchronized to SAOs that are themselves enslaved to the seasonal cycle, or to the annual cycle itself. However, the QBO and TBOs are evidently only weakly coupled between themselves and are frequently found to lose mutual coherence when each changes its frequency ratio to its respective SAO. This suggests a need to revise a commonly cited paradigm that advocates the use of stratospheric QBO indices as a predictor for tropospheric phenomena such as monsoons and hurricanes. Copyright © 2012 Royal Meteorological Society

Description: The microwave payload of the Megha-Tropiques mission is explored to quantify the expected improvements in the retrieval of relative humidity profiles. Estimations of the profiles are performed using a generalized additive model that uses cubic smoothing splines to address the nonlinear dependencies between the brightness temperatures ( T B ) in the 183.31 GHz band and the relative humidity of specified tropospheric layers. Under clear-sky and oceanic situations, the six-channel configuration of the SAPHIR radiometer clearly improves the retrieval and reduces by a factor of two the variance of the residuals with respect to the current space-borne humidity sounders that have three channels in this band (AMSU-B, MHS). Additional information from the MADRAS radiometer (at 23.8 and 157 GHz) further improves the restitution with correlation coefficient higher than 0.89 throughout the troposphere. Copyright © 2011 Royal Meteorological Society

Description: The diagonal South Pacific Convergence Zone (SPCZ) is the major climatological precipitation feature over the Pacific region during the Northern Hemisphere winter. However, the basic mechanisms that control its structure and variability are only partly understood. Here, an analysis of the SPCZ is carried out in a multiscale framework. This identifies two modes that dominate: a (westward) shifted SPCZ and an enhanced SPCZ, which occur independently of each other. Within both modes, the primary mechanism for the initiation of precipitation is a transient synoptic wave propagating along the subtropical jet, which is then refracted by the basic state toward the westerly duct over the central equatorial Pacific. Individual vorticity centres in the wave become elongated, with a diagonal (northwest–southeast) tilt. Convection then occurs in a diagonal band in the poleward flow ahead of the cyclonic vorticity anomaly in the wave. However, latent heat release in the convection leads to upper-tropospheric divergence and anticyclonic vorticity forcing, which dissipates the wave, shutting off the convective forcing and stopping the precipitation. Hence, each individual wave or event only lasts a few days and contributes a discrete pulse of diagonally oriented precipitation to the region. The sum of these events leads to the diagonal climatological SPCZ. Event occurrence is a stochastic process, the probability of which is modified by lower-frequency variability of the basic state, including the Madden–Julian Oscillation (MJO) and El Niño–Southern Oscillation (ENSO). For example, during periods of enhanced convection over the eastern Indian Ocean to western Pacific (MJO phases 3–6 and La Niña) the westerly duct expands westwards, allowing synoptic waves to refract equatorwards earlier and increasing the probability of westward-shifted SPCZ events. Hence, both the existence and variability of the SPCZ depend fundamentally on scale interactions between dynamical processes on time-scales ranging from daily to interannual. Copyright © 2011 Royal Meteorological Society

Description: Many numerical models for weather prediction and climate studies are run at resolutions that are too coarse to resolve convection explicitly, but too fine to justify the local equilibrium assumed by conventional convective parametrizations. The Plant–Craig (PC) stochastic convective parametrization scheme, developed in this paper, solves this problem by removing the assumption that a given grid-scale situation must always produce the same sub-grid-scale convective response. Instead, for each time step and grid point, one of the many possible convective responses consistent with the large-scale situation is randomly selected. The scheme requires as input the large-scale state as opposed to the instantaneous grid-scale state, but must nonetheless be able to account for genuine variations in the large-scale situation. Here we investigate the behaviour of the PC scheme in three-dimensional simulations of radiative–convective equilibrium, demonstrating in particular that the necessary space–time averaging required to produce a good representation of the input large-scale state is not in conflict with the requirement to capture large-scale variations. The resulting equilibrium profiles agree well with those obtained from established deterministic schemes, and with corresponding cloud-resolving model simulations. Unlike the conventional schemes, the statistics for mass flux and rainfall variability from the PC scheme also agree well with relevant theory and vary appropriately with spatial scale. The scheme is further shown to adapt automatically to changes in grid length and in forcing strength. Copyright © 2011 Royal Meteorological Society

Description: The development of a polar low is simulated in an ideal baroclinic channel with the objective of studying the relative influence of different initial conditions on certain characteristics of the polar low. The basic state in the channel has a baroclinic jet at the tropopause level superposed by potential vorticity anomalies. The upper-level perturbation leads to the genesis of a polar low through baroclinic instability. During its growth, the polar low is driven by a combination of baroclinic and convective processes as the vertical motion associated with the polar low is found to be forced simultaneously by the adiabatic and diabatic omega-forcing terms in the quasi-geostrophic omega equation. The degree of baroclinicity, surface heating and the scale of the upper-level anomaly were each reduced, and static stability increased separately in a series of sensitivity experiments. The results show that the pattern of the vertical motion, the growth rate and phase speed of the polar low are highly sensitive to the modifications in the background conditions. In particular, the surface temperature and baroclinicity appear to be crucial in determining the strength of the vertical motion associated with the polar low. The scale and structure of the polar low are more vulnerable to the scale of the upper-level anomaly and initial baroclinicity than to the rest of the parameters tested. In all the sensitivity experiments, the formation of the polar low gets delayed and its intensity, in terms of the surface pressure, reduced due to the modified initial conditions. The reduced intensity suppresses the tendency for a vertical coupling of upper- and lower-level features of the polar low. Copyright © 2011 Royal Meteorological Society

Description: A 13-year (1998–2010) climatology of mesoscale convective characteristics associated with the West African monsoon are investigated using precipitation radar and passive microwave data from the NASA Tropical Rainfall Measuring Mission satellite. Seven regions defined as continental northeast and northwest, southeast and southwest, coastal, and maritime north and south are compared to analyse zonal and meridional differences. Data are categorized according to identified African easterly wave (AEW) phase and when no wave is present. While some enhancements are observed in association with AEW regimes, regional differences were generally more apparent than wave vs. no-wave differences. Convective intensity metrics confirm that land-based systems exhibit stronger characteristics, such as higher storm top and maximum 30 dBZ heights and significant 85 GHz brightness temperature depressions. Continental systems also contain a lower fraction of points identified as stratiform. Results suggest that precipitation processes also varied depending upon region and AEW regime, with warm-rain processes more apparent over the ocean and the southwest continental region and ice-based microphysics more dominant over land, including mixed-phase processes. AEW regimes did show variability in stratiform fraction and ice and liquid water content, suggesting modulation of mesoscale characteristics possibly through feedback with the synoptic environment. Copyright © 2011 Royal Meteorological Society

Description: The Convective and Orographically-driven Precipitation Study (COPS) carried out in summer 2007 over northeastern France and southwestern Germany provided a fairly comprehensive description of the low-troposphere water-vapour field, thanks in particular to the deployment of two airborne differential absorption lidar systems. These lidar observations were assimilated using the 3D-Var assimilation system of the Application of Research to Operations at MEsoscale (AROME) numerical weather prediction mesoscale model. The assimilation was carried out for the period 4 July–3 August by running a three-hour forward intermittent assimilation cycle. First, the impact of the lidar observations was assessed by comparing the analyses with a set of more than 200 independent soundings. The lidar observations were found to have a positive impact on the analyses by reducing the dry bias in the first 500 m above ground level and by diminishing the root-mean-square error by roughly 15% in the first km. Then the impact of the lidar observations was assessed by comparing the precipitation forecasts (obtained with and without the lidar observations for the period 15 July–2 August) with the gridded precipitation observations provided by the Vienna Enhanced Resolution Analysis. In general, the impact was found to be positive but not significant for the 24 h precipitation and positive and significant for the 6 h precipitation, with an improvement lasting up to 24 h. Some selected case studies show that the improvement was obtained through a better depiction of convection initiation or through a more accurate positioning of the precipitation systems. Copyright © 2011 Royal Meteorological Society

Description: The Met Office single-column model is used to examine the development phase of the diurnal cycle of tropical convection over land by comparing against previous results from an idealized cloud-resolving model study. Changing the deep convective parametrization over land to make the entrainment vary with the height of the lifting condensation level reduces the depth of the convection early in the day. The changes made to improve the early phase of diurnal cycle over land are tested in an atmosphere-only version of the Met Office Hadley Centre climate model and result in an improvement in the amplitude and timing of the diurnal peak in precipitation over land. Copyright © 2011 British Crown copyright, the Met Office. Published by John Wiley & Sons Ltd.

Description: The spectral predictability of the Met Office's Unified Model is examined using identical-twin experiments and the relative kinetic energy. In the troposphere, previous NWP results are recovered, namely the emergence of distinct regimes and the maximisation of the growth rate on synoptic scales at early times; in the middle atmosphere, the predictability decay is slower. This difference is attributed to the increase in the amplitude of gravity waves. The influence of small-scale motions is highlighted: improving their numerical representation by decreasing the timestep enhances predictability. Copyright © 2011 British Crown copyright, the MetOffice. Published by John Wiley & Sons Ltd.

Description: Observations providing three-dimensional information on clouds from space-borne active instruments on board CloudSat and CALIPSO are already available and new satellites, such as EarthCARE, should appear in the near future. This opens new possibilities for exploring the usefulness of this kind of observation, not only for improving model parametrizations but also for investigating their usage in data assimilation to extract information from the data so as to improve the initial atmospheric state. In this study, a 1D + 4D-Var technique has been selected to study the impact of observations related to clouds on 4D-Var analyses and subsequent forecasts. Using this two-step approach, temperature and specific humidity profiles retrieved from 1D-Var assimilation of CloudSat observations have been included in the 4D-Var system. Several experiments have been run for a couple of selected meteorological situations. Copyright © 2011 Royal Meteorological Society

Description: In this article, Northern Hemisphere winter midlatitude blocking is analysed through its wave-breaking characteristics. Rossby wave breaking is identified as a key process in blocking occurrence, as it provides the mechanism for the meridional reversal pattern typical of blocking. Two indices are designed to detect the major properties of wave breaking, i.e. the orientation (cyclonic/anticyclonic–direction of breaking or DB index) and the relative contribution of air masses (warm/cold–relative intensity or RI index). The use of the DB index differentiates between the anticyclonic cases over Europe and Asia and the cyclonic events over the oceanic basins. One of the three regions displaying cyclonic type was found over the Atlantic Ocean, the other two being over the Pacific Ocean. The first of these is located over the western side of the Pacific and is dominated by warm air extrusions, whereas the second is placed northward of the exit region of the jet stream, where the meridional θ gradient is much weaker. Two European blocking types have been detected using the RI index, which separates out the cases dominated by warm and cold air masses. The latter cases in particular exhibited a well-structured dipole, with associated strong anomalies in both temperature and precipitation. Copyright © 2011 Royal Meteorological Society

Description: This study investigates transient events of intense ocean evaporation with an amplitude exceeding 250 W m −2 , a duration of a few days, and a spatial extent of about 10ˆ6 km 2 over the eastern North Atlantic (referred to as ‘evaporation hot spots’) and their impact on southern Alpine heavy precipitation. First, moisture sources for a heavy precipitation event in the Piedmont in November 2002 are studied using a water-tagging simulation with a regional model. The results reveal three main moisture sources: land evapotranspiration, and evaporation from the Mediterranean and the North Atlantic, with the last source contributing the most. This was partly due to an evaporation hot spot that appeared along the western edge of a prominent upper-level trough about two days prior to the onset of heavy precipitation. In the hot spot area strong surface winds induced by the upper-level trough led to intense evaporation of water that was transported around the trough to the Piedmont region during subsequent days, where it contributed to the heavy precipitation. Secondly, analyses by the European Centre for Medium-Range Weather Forecasts (ECMWF) are used to investigate climatologically the potential relationship between eastern North Atlantic evaporation hot spots and southern Alpine precipitation. During a 10-year time period, 42 hot spots have been identified in the eastern North Atlantic. It is shown that they typically occur along the western flank of prominent upper-level troughs, and that the evaporating moisture is transported to Europe within one to four days. A climatological analysis of southern Alpine heavy precipitation events shows that they are frequently preceded by intense North Atlantic evaporation. Hence the climatological analysis further supports the conclusion from the Piedmont 2002 tagging experiment that intense evaporation over the North Atlantic and the subsequent moisture transport, both induced by the upper-level trough, are potential key factors for the development of southern Alpine heavy precipitation events. Copyright © 2011 Royal Meteorological Society

Description: An analytical model is developed for flow within and above a forest canopy with a slowly varying canopy density. Results are compared with existing analytical models for flow over a surface with slowly varying roughness length, and also with numerical simulations. The results show that the analytical solution is successful in capturing the behaviour of the flow for small and slowly changing variations in canopy density. Previous models which only vary the roughness length and neglect changes in displacement height fail to capture the near-surface flow accurately. Including changes in displacement height as well as roughness length changes gives results closer to those obtained with the full canopy model, but even then the flow induced in the canopy leads to significant differences. The analytical model also highlights the sensitivity of the results to the parametrization of the vertical component of the turbulent stress tensor, τ zz . For shorter wavelength variations in the canopy density, the analytical model breaks down as the more rapid changes in density induce larger flow perturbations which lead to increased flow into and out of the canopy. This kind of idealised analytical study provides important insights into the role of canopy heterogeneities on boundary-layer flow. This is important both for understanding near-surface winds and transport, and also for parametrizing the effects of surface heterogeneities in large-scale weather and climate models. Copyright © 2011 Royal Meteorological Society

Description: A non-hydrostatic model on the equatorial beta-plane is solved for the most basic solutions of vertically and zonally propagating internal plane waves. Solutions tilt in the vertical and propagate upward, with buoyancy as a principal restoring force. Results indicate that when frequency is of the same order of magnitude as a reduced buoyancy frequency, the shallow-water model equivalent depth depends on frequency. One consequence of this dependence is that Kelvin waves become dispersive at high frequencies. In a complementary observational analysis, linear regression and a space-time wavelet spectrum analysis of observed convectively coupled mixed Rossby gravity (MRG) waves are applied to estimate vertical wavelengths that are consistent with the strongest signals associated with observed convectively coupled waves at specific zonal wave numbers and frequencies. Substitution of these dispersion parameters into the model yields theoretical structures characterized by vertical and horizontal wavenumbers and frequencies similar to those observed in the lower and middle troposphere. These model solutions demonstrate that the Coriolis terms associated with the horizontal component of the earth's angular momentum explain substantial meridional tilts and phase shifts between quantities associated with observed convectively coupled waves, especially proximate to the surface of the Earth. Copyright © 2011 Royal Meteorological Society

Description: Three models with different discretizations for the shallow-water equations on a sphere are presented and compared using selected test cases. The first model is based on the global latitude–longitude grid system with a uniform Arakawa C grid and a two-time-level Crank–Nicolson iterative semi-Lagrangian method with an advecting wind interpolated in time. The second model uses the overset Yin–Yang grid, which is singularity-free and has quasi-uniform resolution. The local solver on each of the two component grids is based on the same time and space discretizations as in the first model. The positive-definite Helmholtz problem in the second model is solved using an optimized Schwarz-type domain-decomposition method with specific Robin or higher-order transmission conditions. The first and second models are obtained through the barotropic option incorporated into the Global Environmental Multiscale model used operationally at the Canadian Meteorological Center. The third model is discretized using the finite-volume methodology on a geodesic icosahedral grid. The time integration is performed with a fourth-order Runge–Kutta scheme. The tests employed to compare the three models are passive advection of a cosine bell, steady-state geostrophic flow, flow over an idealized mountain, a Rossby–Haurwitz wave, real-case 500 mb flow and evolution of a growing barotropic wave. When no analytic solution is available for a specific test, we compare the results with a high-resolution solution obtained from the first model in which all horizontal operations are evaluated in spectral space. © 2011 Crown in the right of Canada. Published by JohnWiley & Sons Ltd.

Description: Atmospheric tracers are often observed to be functionally related, and these relations can be physically or chemically significant. It is therefore highly desirable that the transport schemes used in chemistry and chemistry-climate models should not disrupt such functional relations in unphysical ways through numerical mixing or, indeed, unmixing. Here, diagnostics are proposed that quantify numerical mixing by a transport scheme for a single tracer, two tracers that are nonlinearly related, and three (or more) tracers that add up to a constant. For the two-tracer test, the question of how physically reasonable the numerical mixing is can be addressed by using scatter/correlation plots. Truncation errors will, in general, result in scatter points deviating from the preexisting functional curve and thereby introduce numerical mixing between the tracers. The proposed diagnostics quantify the mixing in terms of the normalized distances between the pre-existing functional curve and scatter points, and divide it into three categories: real mixing and two types of spurious numerical unmixing. For the three-tracer test, we quantify, in terms of standard error norms, how nearly a transport scheme can preserve the sum by transporting the individual tracers. The mixing diagnostics do not require the knowledge of the analytical solution to the transport problem for the individual tracers. However, using an idealized flow field and spatial distributions facilitates the use of the mixing diagnostics in transport scheme development. Hence we propose to exercise the new mixing diagnostics using an idealized but highly deformational analytical flow field. Example results using the CSLAM (Conservative Semi-LAgrangian Multi-tracer) scheme are presented. Copyright © 2011 Royal Meteorological Society

Description: An ensemble method combined with a four-dimensional variational data assimilation system is used to provide monthly estimates of the background error covariance matrix for global stratospheric and upper tropospheric ozone for the year 2008. The system is composed of the Mocage chemical transport model and the Valentina assimilation system. The ensemble was obtained from parallel analyses of perturbed data from the Microwave Limb Sounder (MLS) instrument. The monthly estimates of background error covariances have then been introduced in the assimilation suite. To assess the separate contribution of each of its components, a number of analyses were realized, using only some estimated components of the background error covariances and a basic model for the others. The evaluation is realized by comparing the analyses with independent ozone profiles (from ozonesondes) and total ozone columns (from the Ozone Monitoring Instrument). It demonstrates that using the estimated statistics compared to basic models for the background error covariance matrix globally slightly improves the analysis quality; however, using the estimated statistics more largely improves the analysis quality for special situations encountered in April and October. In these situations, the most important parameter for the analysis quality is the use of estimated correlations. Copyright © 2011 Royal Meteorological Society

Description: The effect of the relative orientation of the vertical wind shear to the surface wind on tropical cyclogenesis is explored in environments of radiative-convective equilibrium (RCE) through numerical simulation. This study serves as a companion paper to an earlier study on the thermodynamics of genesis in RCE. It is found, when the mean surface wind and shear are aligned, a negative surface wind anomaly arises from the superposition of the mean and vortex surface flows left of the shear vector. The resulting weak surface enthalpy fluxes and up-shear quasi-balanced subsidence leads to dry air being located cyclonically down-wind of the down-shear convective anomaly. Thus convection is inhibited from propagating cyclonically around the core leading to a large down-shear vortex tilt. Conversely, in a counter-aligned orientation, the negative surface wind anomaly and driest air is found right of the shear vector. Hence the driest air rotates into the down-shear flank where it moistened by shear-organized convection. Furthermore, the boundary layer is relatively moist left of shear due to the positive surface wind anomaly, therefore promoting the cyclonic propagation from down-shear and constraining the magnitude of the vortex tilt. Genesis is intimately tied to the magnitude of the tilt and is found to occur once the mid-level vortex has precessed into the up-shear flank. For smaller values of maximum tilt, vortex precession is comparatively rapid, aided by “showerhead” moistening provided by the up-shear advection of frozen condensate aloft. With the up-shear flank pre-moistened, rapid precession of the mid-level vortex, at smaller radii, leads to near saturation on the mesoscale and the onset of rapid intensification. When the magnitude of the tilt is quite large, precession is much slower and the showerhead effect is significantly reduced until just prior to the emergence of the mid-level vortex in the up-shear flank. Copyright © 2011 Royal Meteorological Society

Description: In early January 2011, southern China experienced another severe wintertime storm as in the winter of 2008. The storm consisted of a narrow east-west-oriented freezing rain band over central Guizhou with an extensive area of snow to the north and a rain swath to the south. This study investigates this event using conventional surface and radiosonde data as well as final (FNL) analyses data from the US National Center for Atmospheric Research/National Centers for Environmental Prediction(NCAR/NCEP). The results show that forcing by geostrophic and diabatic heating built up a positive direct secondary circulation perpendicular to the quasi-stationary front beneath 700 hPa to maintain the surface cold layer and warm layer aloft through surface cold advection and warm advection aloft. In addition, turbulence induced by strong wind shear in the middle and lower stratiform clouds with a low concentration of ice nuclei plays an important role in the growth of cloud drops and the enhancement of supercool raindrop precipitation over Guizhou. Copyright © 2011 Royal Meteorological Society

Description: This work tackles the problem of the automated detection of the atmospheric boundary layer (BL) height h , from aerosol lidar/ceilometer observations. A new method, the Bayesian selective method (BSM), is presented. It implements a Bayesian statistical inference procedure which combines in a statistically optimal way different sources of information. Firstly, atmospheric stratification boundaries are located from discontinuities in the ceilometer backscattered signal. The BSM then identifies the discontinuity edge that has the highest probability to effectively mark the BL height. Information from the contemporaneous physical boundary layer model simulations and a climatological dataset of BL height evolution are combined in the assimilation framework to assist this choice. The BSM algorithm has been tested for 4 months of continuous ceilometer measurements collected during the BASE:ALFA project, and is shown to realistically diagnose the BL depth evolution in many different weather conditions. A standard one-dimensional processing of the ceilometer signal without the a priori support of the dynamical and climatological BL models often fails to correctly detect h , with the greatest inaccuracies occurring at night-time when residual layers can generate very strong signals, which are then classified by an automated application of the gradient or of the wavelet analysis as the most probable BL height. The BSM approach instead carries information on the low climatological probability to find elevated BL depths at night and penalizes the selection of these points. Moreover, this method is able to correctly convey information along the temporal dimension, thus filling data gaps using earlier and subsequent ceilometer information for the retrieval. Copyright © 2011 Royal Meteorological Society

Description: The assimilation of observations with a forecast is often heavily influenced by the description of the error covariances associated with the forecast. When a temperature inversion is present at the top of the boundary layer (BL), a significant part of the forecast error may be described as a vertical positional error (as opposed to amplitude error normally dealt with in data assimilation). In these cases, failing to account for positional error explicitly is shown to result in an analysis for which the inversion structure is erroneously weakened and degraded. In this article, a new assimilation scheme is proposed to explicitly include the positional error associated with an inversion. This is done through the introduction of an extra control variable to allow position errors in the a priori to be treated simultaneously with the usual amplitude errors. This new scheme, referred to as the ‘floating BL scheme’, is applied to the one-dimensional (vertical) variational assimilation of temperature. The floating BL scheme is tested with a series of idealised experiments and with real data from radiosondes. For each idealised experiment, the floating BL scheme gives an analysis which has the inversion structure and position in agreement with the truth, and outperforms the assimilation which accounts only for forecast amplitude error. When the floating BL scheme is used to assimilate a large sample of radiosonde data, its ability to give an analysis with an inversion height in better agreement with that observed is confirmed. However, it is found that the use of Gaussian statistics is an inappropriate description of the error statistics of the extra control variable. This problem is alleviated by incorporating a non-Gaussian description of the new control variable in the new scheme. Anticipated challenges in implementing the scheme operationally are discussed towards the end of the article. Copyright © 2011 Royal Meteorological Society and British Crown Copyright, the Met Office

Description: A simple self-contained theory is proposed for describing the life cycles of convective systems as a discharge–recharge process. A closed description is derived for the dynamics of an ensemble of convective plumes based on an energy cycle. The system consists of prognostic equations for the cloud work function and the convective kinetic energy. The system can be closed by introducing a functional relationship between the convective kinetic energy and the cloud-base mass flux. The behaviour of this system is considered under a bulk simplification. Previous cloud-resolving models as well as bulk statistical theories for ensemble convective systems suggest that a plausible relationship would be to assume that the convective kinetic energy is linearly proportional to the cloud-base mass flux. As a result, the system reduces to a nonlinear dynamical system with two dependent variables, the cloud-base mass flux and the cloud work function. The fully nonlinear solution of this system always represents a periodic cycle regardless of the initial condition under constant large-scale forcing. Importantly, the inclusion of energy dissipation in this model does not in itself lead the system into equilibrium. Copyright © 2011 Royal Meteorological Society

Description: Successful quantitative precipitation forecasts under convectively unstable conditions depend on the ability of the model to capture the location, timing and intensity of convection. Ensemble forecasts of two mesoscale convective outbreaks over the UK are examined with a view to understanding the nature and extent of their predictability. In addition to a control forecast, twelve ensemble members are run for each case with the same boundary conditions but with perturbations added to the boundary layer. The intention is to introduce perturbations of appropriate magnitude and scale so that the large-scale behaviour of the simulations is not changed. In one case, convection is in statistical equilibrium with the large-scale flow. This places a constraint on the total precipitation, but the location and intensity of individual storms varied. In contrast, the other case was characterised by a large-scale capping inversion. As a result, the location of individual storms was fixed, but their intensities and the total precipitation varied strongly. The ensemble shows case-to-case variability in the nature of predictability of convection in a mesoscale model, and provides additional useful information for quantitative precipitation forecasting. Copyright © 2011 Royal Meteorological Society and British Crown Copyright, the Met Office

Description: The difference in turbulent transfer efficiency between momentum and scalars, represented by kB −1 , has been the subject of considerable interest in micrometeorology, and various parametrizations have been proposed to address this issue. The simple kB −1 parametrizations that are based on either empirical formulations or K-theory are still popularly used in the land surface models despite their theoretical deficiencies. Moreover, the impact of the uncertainty in this parameter on modelling surface carbon exchange has not been previously estimated. In this study, we examined the uncertainties of the simulated gross primary productivity (GPP), ecosystem respiration (RE), and net ecosystem exchange (NEE ≡ RE–GPP) for a forest canopy due to kB −1 parametrizations. The tested parametrizations included not only the schemes that set kB −1 as a constant or as a function of only the Reynolds number (popularly used in the land surface model), but also the schemes that express kB −1 as a function of plant phenology derived from the Lagrangian theory. Except for parametrizations that produced aerodynamic resistance as large as canopy resistance over a tall forest canopy, the variabilities of GPP and RE induced by kB −1 parametrizations were less than 2% of the annual GPP and RE, respectively. Nevertheless, the model produced approximately 10% variability of NEE values with changes in the kB −1 parametrizations (203±24 g C m −2 year −1 ) because the simulated RE was less sensitive to the kB −1 parametrizations than the simulated GPP due to the negative feedback among kB −1 , temperature, and RE. Our findings reveal that kB −1 parametrizations should be suitably applied in land surface modelling for better simulation of the global carbon cycle. Copyright © 2011 Royal Meteorological Society and British Crown Copyright, the Met Office

Description: Light Microscopy: From imaging probes to high resolution techniques andcomputational image analysis . On pages 333–340 Jason Swedlow gives a nice overview over the topics covered in this Special Issue. Advances in optics, automation, computational tools and imaging probes allow the visualization of ever smaller structures at increasing resolution. Furthermore, these techniques can be used for a wide variety of applications from basic research to clinical domains, e.g. by employing imaging techniques for screening. The image shows a section of mouse small intestine stained with DAPI (blue), anti-tubulin (red) and phalloidin (green).

Description: This article discusses a coupled water level forecasting system constructed for the River Dee (UK) using parsimonious, physically interpretable, time series models. Tidal forecasts, provided by a simple harmonic model, and observed water levels at the upstream boundary are used to drive a nonlinear hydrological model which forecasts water levels at three gauged sites on the flood plain. The assimilation of observed data and use of the model for real-time forecasting is presented. The results generated indicate that the forecasts of river water can be both timely and accurate except close to the tidal boundary where the the tide is affected by the weir at Chester. Copyright © 2012 Royal Meteorological Society

Description: The sensitivity of squall rainfall to changes in atmospheric temperature is investigated. For instantaneous rainrates and accumulations up to one hour, extreme rainfall scales with Clausius-Clapeyron (CC) for temperatures below 24°C and at up to twice CC above 24°C. For longer accumulation periods and higher temperatures the scaling breaks down due to increased propagation of the squall line. For all periods, the storm average rainfall is found to scale at approximately 1.5 times CC over the entire range of temperatures. These results have implications for design parameters for infrastructure that is vulnerable to flooding and for climate change projections. Copyright © 2012 Royal Meteorological Society

Description: Total cloud amount and cloud-base height are two quantities diagnosed from the vertical distribution of cloud in a model grid column. Together they form the basis of many cloud-based forecast products. Forecasts from four Met Office Unified Model (MetUM) horizontal resolution configurations are compared against manual and automated conventional synoptic (SYNOP) observations. The analysis shows that observation-type-dependent characteristics feed through to model forecast biases and skill scores, where manual and automated cloud observations produce biases of opposite kind. The mixing of observation types is therefore not recommended, as the ability to interpret results is compromised. This is especially relevant when tuning model physics. The effect of horizontal grid resolution is mixed on both bias and skill. Copyright © 2012 British Crown copyright, the Met Office Published by John Wiley & Sons Ltd.

Description: The structure of a tropical cyclone eye and eyewall plays an important role in intensification. While the eyewall is usually defined in terms of instantaneous velocity and derived quantities such as vorticity, or thermodynamic variables such as equivalent potential temperature, or pressure, a Lagrangian eyewall definition is based on the transport of particles. In this paper, we analyse a Lagrangian eye–eyewall interface (LEEI), which is defined as a surface that acts as barrier to particle motion. The surface is identified with a maximal ridge of a hyperbolic Lagrangian field, and varies with the initial time at which particles are seeded. Our study extends a previous LEEI construction (Rutherford B, Dangelmayr G. 2010. Q. J. R. Meteorol. Soc. 136: 1931–1944) as follows. First, the ridge extraction algorithm used in our previous work is fully automated over time and z -levels, and smoothed by representing the ridge curves on z -slices in terms of Fourier descriptors. Secondly, the ridge curves for varying z -levels are matched to vertical basis functions leading to a 3D spatially continuous and low-dimensional representation of the LEEI, by truncating the combined azimuthal and vertical expansion. The surface is then analysed over varying initial time, and structural differences in time and height show that differences in Lagrangian structure and the degree of axisymmetry correspond to changes in intensity. Copyright © 2012 Royal Meteorological Society

Description: Surface and upper-air observations of meteorological parameters at Gadanki (13.5°N, 79.2°E) are utilized to understand the thermal structure of the atmosphere in dry and wet spells and its effect on draught core statistics. The temperature and humidity variations from wet to dry spell are quite pronounced near the surface and in the atmospheric boundary layer (ABL), but not above the ABL. Interestingly, convective available potential energy (CAPE) is found to be higher during wet spells than during dry spells, in contrast to the earlier studies made elsewhere over warm oceans and tropical land masses. The stratified CAPE values based on rainfall occurrence are also larger during wet spells than during dry spells, irrespective of whether the sounding is made before, during or after the rain occurrence. Surprisingly, large CAPE values are observed after the rain occurrence in both spells. The high CAPE during wet spells (and also after rain occurrence) corresponds well with larger surface equivalent potential temperature ( θ e ). During wet spells, the positive buoyancy is not only larger but also vertically extended to higher altitudes. On the other hand, buoyancy profiles during dry spells are punctuated by several negative buoyancies (associated with stable layers), reducing CAPE values in those spells. A synthesis of all measurements reveals that favourable environmental conditions (high CAPE, humid atmosphere and weak stable layers) allow the convection to grow into a deep system in wet spells. On the other hand, strong stable layers, weak CAPE coupled with relatively less humidity above the ABL inhibits the growth of convective cloud during dry spells. These observations explain the differences in draught core statistics in wet and dry spells. Copyright © 2012 Royal Meteorological Society