Mountain wave breaking in atmospheric flows with directional wind shear

In this thesis, mountain wave breaking triggered by directional wind shear is investigated using numerical simulations of idealized and semi-idealized orographic flows. Idealized simulations are used to produce a regime diagram to diagnose conditions for wave breaking in Richardson number-dimensionless mountain height parameter space. It is found that, in the presence of directional shear, wave breaking can occur over lower mountains than in a constant-wind case. Furthermore, the extent of regions within the simulation domain where Clear-Air Turbulence (CAT) is expected increases with terrain elevation and background wind shear intensity. Analysis of the model output, supported by theoretical arguments, suggest the existence of a link between wave breaking and the relative orientations of the incoming wind vector and the horizontal velocity perturbation vector. This condition provides a possible diagnostic for CAT forecast in directional shear flows. The stability of the flow to wave breaking in the transition from hydrostatic to nonhydrostatic mountain waves is also investigated. Wave breaking seems to be inhibited by non-hydrostatic effects for weak wind shear, but enhanced for stronger wind shear. In the second part of the thesis, a turbulence encounter observed over the Rocky Mountains (in Colorado, USA) is studied. The role of directional shear in causing wave breaking is isolated from other possible wave breaking mechanisms through various sensitivity tests. The existence of an asymptotic wake, as predicted by Shutts for directional shear flows, is hypothesized to be responsible for a significant downwind transport of unstable air detected in cross-sections of the flow. Finally, critical levels induced by directional shear are studied by spectral analysis of the horizontal velocity wave perturbations. This is done for a fully idealized flow and for the more realistic flow corresponding to the investigated turbulence encounter. In these 2D power spectra, a rotation of the most energetic wave modes with the background wind and their selective absorption can be found. Such behaviour is consistent with the mechanism leading to wave breaking in directional shear flows

Machine dependence and reproducibility for coupled climate simulations: the HadGEM3-GC3.1 CMIP Preindustrial simulation

When the same weather or climate simulation is run on different high-performance computing (HPC) platforms, model outputs may not be identical for a given initial condition. While the role of HPC platforms in delivering better climate projections is to some extent discussed in the literature, attention is mainly focused on scalability and performance rather than on the impact of machine-dependent processes on the numerical solution. Here we investigate the behaviour of the Preindustrial (PI) simulation prepared by the UK Met Office for the forthcoming CMIP6 (Coupled Model Intercomparison Project Phase 6) under different computing environments. Discrepancies between the means of key climate variables were analysed at different timescales, from decadal to centennial. We found that for the two simulations to be statistically indistinguishable, a 200-year averaging period must be used for the analysis of the results. Thus, constant-forcing climate simulations using the HadGEM3-GC3.1 model are reproducible on different HPC platforms provided that a sufficiently long duration of simulation is used. In regions where El Niño–Southern Oscillation (ENSO) teleconnection patterns were detected, we found large sea surface temperature and sea ice concentration differences on centennial timescales. This indicates that a 100-year constant-forcing climate simulation may not be long enough to adequately capture the internal variability of the HadGEM3-GC3.1 model, despite this being the minimum simulation length recommended by CMIP6 protocols for many MIP (Model Intercomparison Project) experiments. On the basis of our findings, we recommend a minimum simulation length of 200 years whenever possible

Mountain wave turbulence in the presence of directional wind shear over the Rocky Mountains

Mountain wave turbulence in the presence of directional wind shear over the Rocky Mountains in Colorado is investigated. Pilot Reports (PIREPs) are used to select cases in which moderate or severe turbulence encounters were reported in combination with significant directional wind shear in the upstream sounding from Grand Junction, CO (GJT). For a selected case, semi-idealized numerical simulations are carried out using the WRF-ARW atmospheric model, initialized with the GJT atmospheric sounding and a realistic but truncated orography profile. In order to isolate the role of directional wind shear in causing wave breaking, sensitivity tests are performed to exclude the variation of the atmospheric stability with height, the speed shear, and the mountain amplitude as dominant wave breaking mechanisms. Significant downwind transport of instabilities is detected in horizontal flow cross-sections, resulting in mountain-wave-induced turbulence occurring at large horizontal distances from the first wave breaking point (and from the orography that generates the waves). The existence of an asymptotic wake, as predicted by Shutts for directional shear flows, is hypothesized to be responsible for this downwind transport. Critical levels induced by directional wind shear are further studied by taking 2D power spectra of the magnitude of the horizontal velocity perturbation field. In these spectra, a rotation of the most energetic wave modes with the background wind, as well as perpendicularity between the background wind vector and the wave-number vector of those modes at critical levels, can be found, which is consistent with the mechanism expected to lead to wave breaking in directional shear flows

Model-data comparison of Antarctic winter sea-ice extent and Southern Ocean sea-surface temperatures during Marine Isotope Stage 5e

Marine Isotope Stage (MIS) 5e (130-116 ka) represents a ‘laboratory’ for evaluating climate model performance under warmer-than-present conditions. Climate model simulations for MIS 5e have previously failed to produce Southern Ocean sea-surface temperatures (SST) and sea-ice extent reconstructed from marine sediment core proxy records. Here we compare state of the art HadGEM3 and HadCM3 simulations of Peak MIS 5e Southern Ocean summer SST and September sea-ice concentrations with the latest marine sediment core proxy data. The model outputs and proxy records show the least consistency in the regions located near the present-day Southern Ocean gyre boundaries, implying the possibility that model simulations are currently unable to fully realise changes in gyre extent and position during MIS 5e. Including Heinrich 11 meltwater forcing in Peak MIS 5e climate simulations improves the likeness to proxy data but it is clear that longer (3-4 ka) run times are required to fully test the consistency between models and data

Spike S1 domain interactome in non-pulmonary systems: A role beyond the receptor recognition

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19), which, since 2019 in China, has rapidly become a worldwide pandemic. The aggressiveness and global spread were enhanced by the many SARS-CoV-2 variants that have been isolated up to now. These mutations affect mostly the viral glycoprotein Spike (S), the capsid protein mainly involved in the early stages of viral entry processes, through the recognition of specific receptors on the host cell surface. In particular, the subunit S1 of the Spike glycoprotein contains the Receptor Binding Domain (RBD) and it is responsible for the interaction with the angiotensin-converting enzyme 2 (ACE2). Although ACE2 is the primary Spike host receptor currently studied, it has been demonstrated that SARS-CoV-2 is also able to infect cells expressing low levels of ACE2, indicating that the virus may have alternative receptors on the host cells. The identification of the alternative receptors can better elucidate the pathogenicity and the tropism of SARS-CoV-2. Therefore, we investigated the Spike S1 interactomes, starting from host membrane proteins of non-pulmonary cell lines, such as human kidney (HK-2), normal colon (NCM460D), and colorectal adenocarcinoma (Caco-2). We employed an affinity purification-mass spectrometry (AP-MS) to pull down, from the membrane protein extracts of all cell lines, the protein partners of the recombinant form of the Spike S1 domain. The purified interactors were identified by a shotgun proteomics approach. The lists of S1 potential interacting proteins were then clusterized according to cellular localization, biological processes, and pathways, highlighting new possible S1 intracellular functions, crucial not only for the entrance mechanisms but also for viral replication and propagation processes

CMIP6/PMIP4 simulations of the mid-Holocene and Last Interglacial using HadGEM3: comparison to the pre-industrial era, previous model versions and proxy data

Results for these simulations are assessed firstly against the same model's pre-industrial control simulation (a simulation comparison, to describe and understand the differences between the pre-industrial – PI – and the two palaeo simulations) and secondly against previous versions of the same model relative to newly available proxy data (a model–data comparison, to compare all available simulations from the same model with proxy data to assess any improvements due to model advances). The introduction of this newly available proxy data adds further novelty to this study. Globally, for metrics such as 1.5 m temperature and surface rainfall, whilst both the recent palaeoclimate simulations are mostly capturing the expected sign and, in some places, magnitude of change relative to the pre-industrial, this is geographically and seasonally dependent. Compared to newly available proxy data (including sea surface temperature – SST – and rainfall) and also incorporating data from previous versions of the model shows that the relative accuracy of the simulations appears to vary according to metric, proxy reconstruction used for comparison and geographical location. In some instances, such as mean rainfall in the mid-Holocene, there is a clear and linear improvement, relative to proxy data, from the oldest to the newest generation of the model. When zooming into northern Africa, a region known to be problematic for models in terms of rainfall enhancement, the behaviour of the West African monsoon in both recent palaeoclimate simulations is consistent with current understanding, suggesting a wetter monsoon during the mid-Holocene and (more so) the Last Interglacial, relative to the pre-industrial era. However, regarding the well-documented “Saharan greening” during the mid-Holocene, results here suggest that the most recent version of the UK's physical model is still unable to reproduce the increases suggested by proxy data, consistent with all other previous models to date

Galacto-Oligosaccharide/Polidextrose Enriched Formula Protects against Respiratory Infections in Infants at High Risk of Atopy: A Randomized Clinical Trial

Early nutrition affects the risk of atopy and infections through modifications of intestinal microbiota. The Prebiotics in the Prevention of Atopy (PIPA) study was a 24-month randomised, double-blind, placebo-controlled trial. It aimed to evaluate the effects of a galacto-oligosaccharide/polydextrose (GOS/PDX)-formula (PF) on atopic dermatitis (AD) and common infections in infants who were born to atopic parents and to investigate the relationship among early nutrition, gut microbiota and clinical outcomes

Agreement between reconstructed and modeled boreal precipitation of the Last Interglacial

The last extended time period when climate may have been warmer than today was during the Last Interglacial (LIG; ca. 129 to 120 thousand years ago). However, a global view of LIG precipitation is lacking. Here, seven new LIG climate models are compared to the first global database of proxies for LIG precipitation. In this way, models are assessed in their ability to capture important hydroclimatic processes during a different climate. The models can reproduce the proxy-based positive precipitation anomalies from the preindustrial period over much of the boreal continents. Over the Southern Hemisphere, proxy-model agreement is partial. In models, LIG boreal monsoons have 42% wider area than in the preindustrial and produce 55% more precipitation and 50% more extreme precipitation. Austral monsoons are weaker. The mechanisms behind these changes are consistent with stronger summer radiative forcing over boreal high latitudes and with the associated higher temperatures during the LIG

Turbulence generation by mountain wave breaking in flows with directional wind shear

Mountain wave breaking, and the resulting potential for the generation of turbulence in the atmosphere, is investigated using numerical simulations of idealized, nearly hydrostatic atmospheric flows with directional wind shear over an axisymmetric isolated mountain. These simulations, which use the WRF-ARWmodel, differ in degree of flow non-linearity and shear intensity, quantified through the dimensionless mountain height and the Richardson number of the incoming flow, respectively. The aim is to diagnose wave breaking based on large-scale flow variables. The simulation results have been used to produce a regime diagram giving a description of the wave breaking behaviour in Richardson number–dimensionless mountain height parameter space. By selecting flow overturning occurrence as a discriminating factor, it was possible to split the regime diagram into sub-regions with and without wave breaking. When mountain waves break, the associated convective instability leads to turbulence generation (which is one of the known forms of Clear Air Turbulence, also known as CAT). Thus, regions within the simulation domain where wave breaking and the development of CAT are expected have been identified. The extent of these regions increases with terrain elevation and background wind shear intensity. Analysis of the model output, supported by theoretical arguments, suggest the existence of a link between wave breaking and the relative orientations of the incoming wind vector and the horizontal velocity perturbation vector. More specifically, in a wave breaking event, due to the effect of critical levels, the background wind vector and the wave-number vector of the dominant mountain waves are perpendicular. It is shown that, at least for the wind profile employed in the present study, this corresponds to a situation where the background wind vector and the velocity perturbation vector are also approximately perpendicular

Effect of synbiotic supplementation in children and adolescents with cystic fibrosis: a randomized controlled clinical trial

BACKGROUND/OBJECTIVES:Cystic fibrosis (CF) is characterized by excessive activation of immune processes. The aim of this study was to evaluate the effect of synbiotic supplementation on the inflammatory response in children/adolescents with CF. SUBJECTS/METHODS:A randomized, placebo-controlled, double-blind, clinical-trial was conducted with control group (CG, n = 17), placebo-CF-group (PCFG, n = 19), synbiotic CF-group (SCFG, n = 22), PCFG negative (n = 8) and positive (n = 11) bacteriology, and SCFG negative (n = 12) and positive (n = 10) bacteriology. Markers of lung function (FEV1), nutritional status [body mass index-for age (BMI/A), height-for-age (H/A), weight-for-age (W/A), upper-arm fat area (UFA), upper-arm muscle area (UMA), body fat (%BF)], and inflammation [interleukin (IL)-12, tumor necrosis factor-alpha (TNF-α), IL-10, IL-6, IL-1β, IL-8, myeloperoxidase (MPO), nitric oxide metabolites (NOx)] were evaluated before and after 90-day of supplementation with a synbiotic. RESULTS:No significance difference was found between the baseline and end evaluations of FEV1 and nutricional status markers. A significant interaction (time vs. group) was found for IL-12 (p = 0.010) and myeloperoxidase (p = 0.036) between PCFG and SCFG, however, the difference was not maintained after assessing the groups individually. NOx diminished significantly after supplementation in the SCFG (p = 0.030). In the SCFG with positive bacteriology, reductions were found in IL-6 (p = 0.033) and IL-8 (p = 0.009) after supplementation. CONCLUSIONS: Synbiotic supplementation shown promise at diminishing the pro-inflammatory markers IL-6, IL-8 in the SCFG with positive bacteriology and NOx in the SCFG in children/adolescents with CF