Sensitivity of large-scale atmospheric analyses to humidity observations and its impact on the global water cycle and tropical and extratropical weather systems in ERA40

Reanalysis data obtained from data assimilation are increasingly used for diagnostic studies of the general circulation of the atmosphere, for the validation of modelling experiments and for estimating energy and water fluxes between the Earth surface and the atmosphere. Because fluxes are not specifically observed, but determined by the data assimilation system, they are not only influenced by the utilized observations but also by model physics and dynamics and by the assimilation method. In order to better understand the relative importance of humidity observations for the determination of the hydrological cycle, in this paper we describe an assimilation experiment using the ERA40 reanalysis system where all humidity data have been excluded from the observational data base. The surprising result is that the model, driven by the time evolution of wind, temperature and surface pressure, is able to almost completely reconstitute the large-scale hydrological cycle of the control assimilation without the use of any humidity data. In addition, analysis of the individual weather systems in the extratropics and tropics using an objective feature tracking analysis indicates that the humidity data have very little impact on these systems. We include a discussion of these results and possible consequences for the way moisture information is assimilated, as well as the potential consequences for the design of observing systems for climate monitoring. It is further suggested, with support from a simple assimilation study with another model, that model physics and dynamics play a decisive role for the hydrological cycle, stressing the need to better understand these aspects of model parametrization. .

An Integrated Assessment of changes in the thermohaline circulation

This paper discusses the risks of a shutdown of the thermohaline circulation (THC) for the climate system, for ecosystems in and around the North Atlantic as well as for fisheries and agriculture by way of an Integrated Assessment. The climate model simulations are based on greenhouse gas scenarios for the 21st century and beyond. A shutdown of the THC, complete by 2150, is triggered if increased freshwater input from inland ice melt or enhanced runoff is assumed. The shutdown retards the greenhouse gas-induced atmospheric warming trend in the Northern Hemisphere, but does not lead to a persistent net cooling. Due to the simulated THC shutdown the sea level at the North Atlantic shores rises by up to 80 cm by 2150, in addition to the global sea level rise. This could potentially be a serious impact that requires expensive coastal protection measures. A reduction of marine net primary productivity is associated with the impacts of warming rather than a THC shutdown. Regional shifts in the currents in the Nordic Seas could strongly deteriorate survival chances for cod larvae and juveniles. This could lead to cod fisheries becoming unprofitable by the end of the 21st century. While regional socioeconomic impacts might be large, damages would be probably small in relation to the respective gross national products. Terrestrial ecosystem productivity is affected much more by the fertilization from the increasing CO2 concentration than by a THC shutdown. In addition, the level of warming in the 22nd to 24th century favours crop production in northern Europe a lot, no matter whether the THC shuts down or not. CO2 emissions corridors aimed at limiting the risk of a THC breakdown to 10% or less are narrow, requiring departure from business-as-usual in the next few decades. The uncertainty about THC risks is still high. This is seen in model analyses as well as in the experts’ views that were elicited. The overview of results presented here is the outcome of the Integrated Assessment project INTEGRATION.

Discriminative pattern mining in software fault detection

We present a method to enhance fault localization for software systems based on a frequent pattern mining algorithm. Our method is based on a large set of test cases for a given set of programs in which faults can be detected. The test executions are recorded as function call trees. Based on test oracles the tests can be classified into successful and failing tests. A frequent pattern mining algorithm is used to identify frequent subtrees in successful and failing test executions. This information is used to rank functions according to their likelihood of containing a fault. The ranking suggests an order in which to examine the functions during fault analysis. We validate our approach experimentally using a subset of Siemens benchmark programs.

Effect of viral load on the outcome of herpes zoster

Varicella-zoster virus (VZV) is a member of the Herpesviridae family, primary infection with which causes varicella, more commonly known as chicken pox. Characteristic of members of the alphaherpesvirus subfamily, VZV is neurotropic and establishes latency in sensory neurons. Reactivation of VZV causes herpes zoster, also known as shingles. The most frequent complication following zoster is chronic and often debilitating pain called postherpetic neuralgia (PHN), which can last for months after the disappearance of a rash. During episodes of acute zoster, VZV viremia occurs in some, but not all, patients; however, the effect of the viral load on the disease outcome is not known. Here we describe the development of a highly specific, sensitive, and reproducible real-time PCR assay to investigate the factors that may contribute to the presence and levels of baseline viremia in patients with zoster and to determine the relationship between viremia and the development and persistence of PHN. VZV DNA was detected in the peripheral blood mononuclear cells (PBMCs) of 78% of patients with acute zoster and in 9% of healthy asymptomatic blood donors. The presence of VZV in the PBMCs of patients with acute zoster was independently associated with age and being on antivirals but not with gender, immune status, extent of rash, the age of the rash at the time of blood sampling, having a history of prodromal pain, or the extent of acute pain. Prodromal pain was significantly associated with higher baseline viral loads. Viral load levels were not associated with the development or persistence of PHN at 6, 12, or 26 weeks.

Multiple stressors on biotic interactions: how climate change and alien species interact to affect pollination

Global change may substantially affect biodiversity and ecosystem functioning but little is known about its effects on essential biotic interactions. Since different environmental drivers rarely act in isolation it is important to consider interactive effects. Here, we focus on how two key drivers of anthropogenic environmental change, climate change and the introduction of alien species, affect plant–pollinator interactions. Based on a literature survey we identify climatically sensitive aspects of species interactions, assess potential effects of climate change on these mechanisms, and derive hypotheses that may form the basis of future research. We find that both climate change and alien species will ultimately lead to the creation of novel communities. In these communities certain interactions may no longer occur while there will also be potential for the emergence of new relationships. Alien species can both partly compensate for the often negative effects of climate change but also amplify them in some cases. Since potential positive effects are often restricted to generalist interactions among species, climate change and alien species in combination can result in significant threats to more specialist interactions involving native species.

Humoral immunity following chickenpox is influenced by geography and ethnicity

Objectives To investigate the contribution of ethnicity and geographical location to varicella-zoster virus (VZV) serostatus and antibody concentrations. Methods The presence and concentrations of antibodies to VZV were measured in 639 Bangladeshi women born in Bangladesh (BBB), 94 Bangladeshi women born in the UK (BUK) and 262 White women born in the UK (WUK). The results were anaylsed in relation to demographic and social data. Results BBB women were significantly less likely to be VZV seropositive at all ages than both BUK and WUK women. However, the odds of a Bangladeshi-born woman being seropositive increased by 1.04 for each year under the age of 15 spent in the UK. In contrast, antibody concentrations were significantly lower in ethnic Bangladeshi women, irrespective of country of birth. White, but not Bangladeshi women, showed evidence of antibody boosting over time despite the latter having more exposure to children. Conclusion Geographical location during childhood is the major influence on age of primary infection with VZV while the level of antibody is related to ethnicity. Since the risk of re-infection with VZV following both natural infection and vaccination is increased as antibody concentrations fall, these results have implications for VZV vaccination programmes particularly in non-White populations.

Persistence of varicella-zoster virus viraemia in patients with herpes zoster.

BACKGROUND: Herpes zoster is caused by the reactivation of varicella-zoster virus from sensory neurons. The commonest complication following zoster is chronic pain termed post herpetic neuralgia. OBJECTIVES: To investigate the dynamics of VZV viraemia and viral load following the resolution of zoster and its relationship to PHN development. STUDY DESIGN: Blood samples were collected at baseline, 1 month, 3 months and 6 month from a prospective study of 63 patients with active zoster. Quantification of VZV DNA in whole blood was performed using a real-time PCR assay. RESULTS: During acute zoster, all patients had detectable VZV DNA in their blood. VZV DNA remained detectable in the blood of 91% of patients at 6 months although levels declined significantly (p<0.0001). A history of prodromal symptoms (p=0.005) and severity of pain at baseline (p=0.038) as well as taking antivirals (p=0.046) and being immunocompromised (p=0.043) were associated, with longer time to recovery from PHN. Viral DNA loads were consistently higher in patients with risk factors for PHN and higher viral DNA loads over time were associated with longer time to recovery (p=0.058 overall and 0.038 in immunocompetent). CONCLUSIONS: Based on these observations we hypothesise that VZV replication persists following acute shingles and that higher viral DNA loads contribute to the risk factors for PHN.

Evaluation of the time resolved fluorescence immunoassay (TRFIA) for the detection of varicella zoster virus (VZV) antibodies following vaccination of healthcare workers

Determination of varicella zoster virus (VZV) immunity in healthcare workers without a history of chickenpox is important for identifying those in need of vOka vaccination. Post immunisation, healthcare workers in the UK who work with high risk patients are tested for seroconversion. To assess the performance of the time-resolved fluorescence immunoassay (TRFIA) for the detection of antibody in vaccinated as well as unvaccinated individuals, a cut-off was first calculated. VZV-IgG specific avidity and titres six weeks after the first dose of vaccine were used to identify subjects with pre-existing immunity among a cohort of 110 healthcare workers. Those with high avidity (≥60%) were considered to have previous immunity to VZV and those with low or equivocal avidity (<60%) were considered naive. The former had antibody levels ≥400mIU/mL and latter had levels <400mIU/mL. Comparison of the baseline values of the naive and immune groups allowed the estimation of a TRFIA cut-off value of >130mIU/mL which best discriminated between the two groups and this was confirmed by ROC analysis. Using this value, the sensitivity and specificity of TRFIA cut-off were 90% (95% CI 79-96), and 78% (95% CI 61-90) respectively in this population. A subset of samples tested by the gold standard Fluorescence Antibody to Membrane Antigen (FAMA) test showed 84% (54/64) agreement with TRFIA.

A moving-mesh finite element method and its application to the numerical solution of phase-change problems

A distributed Lagrangian moving-mesh finite element method is applied to problems involving changes of phase. The algorithm uses a distributed conservation principle to determine nodal mesh velocities, which are then used to move the nodes. The nodal values are obtained from an ALE (Arbitrary Lagrangian-Eulerian) equation, which represents a generalization of the original algorithm presented in Applied Numerical Mathematics, 54:450--469 (2005). Having described the details of the generalized algorithm it is validated on two test cases from the original paper and is then applied to one-phase and, for the first time, two-phase Stefan problems in one and two space dimensions, paying particular attention to the implementation of the interface boundary conditions. Results are presented to demonstrate the accuracy and the effectiveness of the method, including comparisons against analytical solutions where available.

Initiation of deep convection at marginal instability in an ensemble of mesoscale models: a case-study from COPS

The present study investigates the initiation of precipitating deep convection in an ensemble of convection-resolving mesoscale models. Results of eight different model runs from five non-hydrostatic models are compared for a case of the Convective and Orographically-induced Precipitation Study (COPS). An isolated convective cell initiated east of the Black Forest crest in southwest Germany, although convective available potential energy was only moderate and convective inhibition was high. Measurements revealed that, due to the absence of synoptic forcing, convection was initiated by local processes related to the orography. In particular, the lifting by low-level convergence in the planetary boundary layer is assumed to be the dominant process on that day. The models used different configurations as well as different initial and boundary conditions. By comparing the different model performance with each other and with measurements, the processes which need to be well represented to initiate convection at the right place and time are discussed. Besides an accurate specification of the thermodynamic and kinematic fields, the results highlight the role of boundary-layer convergence features for quantitative precipitation forecasts in mountainous terrain.

Nitrogen processes in aquatic ecosystems

Executive summary Nature of the problem (science/management/policy) • Freshwater ecosystems play a key role in the European nitrogen (N) cycle, both as a reactive agent that transfers, stores and processes N loadings from the atmosphere and terrestrial ecosystems, and as a natural environment severely impacted by the increase of these loadings. Approaches • This chapter is a review of major processes and factors controlling N transport and transformations for running waters, standing waters, groundwaters and riparian wetlands. Key findings/state of knowledge • The major factor controlling N processes in freshwater ecosystems is the residence time of water, which varies widely both in space and in time, and which is sensitive to changes in climate, land use and management. • The effects of increased N loadings to European freshwaters include acidification in semi-natural environments, and eutrophication in more disturbed ecosystems, with associated loss of biodiversity in both cases. • An important part of the nitrogen transferred by surface waters is in the form of organic N, as dissolved organic N (DON) and particulate organic N (PON). This part is dominant in semi-natural catchments throughout Europe and remains a significant component of the total N load even in nitrate enriched rivers. • In eutrophicated standing freshwaters N can be a factor limiting or co-limiting biological production, and control of both N and phosphorus (P) loading is oft en needed in impacted areas, if ecological quality is to be restored. Major uncertainties/challenges • The importance of storage and denitrifi cation in aquifers is a major uncertainty in the global N cycle, and controls in part the response of catchments to land use or management changes. In some aquifers, the increase of N concentrations will continue for decades even if efficient mitigation measures are implemented now. • Nitrate retention by riparian wetlands has oft en been highlighted. However, their use for mitigation must be treated with caution, since their effectiveness is difficult to predict, and side effects include increased DON emissions to adjacent open waters, N2O emissions to the atmosphere, and loss of biodiversity. • In fact, the character and specific spatial origins of DON are not fully understood, and similarly the quantitative importance of indirect N2O emissions from freshwater ecosystems as a result of N leaching losses from agricultural soils is still poorly known at the regional scale. • These major uncertainties remain due to the lack of adequate monitoring (all forms of N at a relevant frequency), especially – but not only – in the southern and eastern EU countries. Recommendations (research/policy) • The great variability of transfer pathways, buffering capacity and sensitivity of the catchments and of the freshwater ecosystems calls for site specific mitigation measures rather than standard ones applied at regional to national scale. • The spatial and temporal variations of the N forms, the processes controlling the transport and transformation of N within freshwaters, require further investigation if the role of N in influencing freshwater ecosystem health is to be better understood, underpinning the implementation of the EU Water Framework Directive for European freshwaters.