The Role of Closed Gyres in Setting the Zonal Transport of the Antarctic Circumpolar Current

Eddy-permitting simulations are used to show that basinlike gyres can be observed in the large-scale barotropic flow of a wind-driven channel with a meridional topographic ridge. This is confirmed using both two-layer quasigeostrophic and 25-level primitive equation models at high horizontal resolution. Comparing results from simulations with and without the topographic ridge, it is shown that the zonal baroclinic transport in the channel increases with increasing wind stress when the bottom topography is flat but not when there is a meridional ridge. The saturation of transport for increasing wind occurs in conjunction with the development of recirculating gyres in the large-scale barotropic streamfunction. This suggests that the total circulation can be thought of as a superposition of a gyre mode (which has zero circumpolar transport) and a free circumpolar mode (which contains all of the transport). Basinlike gyres arise in the channel because the topography steers the barotropic streamlines and supports a frictional boundary layer similar to the more familiar ones observed along western boundaries. The gyre mode is thus closely linked with the bottom form stress exerted by the along-ridge flow and provides the sink for the wind momentum input. In this framework, any increase in wind forcing spins a stronger gyre as opposed to feeding the circumpolar transport. This hypothesis is supported with a suite of experiments where key parameters are carried over a wide range: wind stress, wind stress curl, ridge height, channel length, and bottom friction.Mathematics and Climate Research Network (Fellowship)National Science Foundation (U.S.) (Award OCE-1233832

Ribbon Turbulence

We investigate the non-linear equilibration of a two-layer quasi-geostrophic flow in a channel forced by an imposed unstable zonal mean flow, paying particular attention to the role of bottom friction. In the limit of low bottom friction, classical theory of geostrophic turbulence predicts an inverse cascade of kinetic energy in the horizontal with condensation at the domain scale and barotropization on the vertical. By contrast, in the limit of large bottom friction, the flow is dominated by ribbons of high kinetic energy in the upper layer. These ribbons correspond to meandering jets separating regions of homogenized potential vorticity. We interpret these result by taking advantage of the peculiar conservation laws satisfied by this system: the dynamics can be recast in such a way that the imposed mean flow appears as an initial source of potential vorticity levels in the upper layer. The initial baroclinic instability leads to a turbulent flow that stirs this potential vorticity field while conserving the global distribution of potential vorticity levels. Statistical mechanical theory of the 1-1/2 layer quasi-geostrophic model predict the formation of two regions of homogenized potential vorticity separated by a minimal interface. We show that the dynamics of the ribbons results from a competition between a tendency to reach this equilibrium state, and baroclinic instability that induces meanders of the interface. These meanders intermittently break and induce potential vorticity mixing, but the interface remains sharp throughout the flow evolution. We show that for some parameter regimes, the ribbons act as a mixing barrier which prevent relaxation toward equilibrium, favouring the emergence of multiple zonal jets

A discrete interaction numerical model for coagulation and fragmentation of marine detritic particulate matter (Coagfrag v.1)

A simplified model, representing the dynamics of marine organic particles in a given size range experiencing coagulation and fragmentation reactions, is developed. The framework is based on a discrete size spectrum on which reactions act to exchange properties between different particle sizes. The reactions are prescribed according to triplet interactions. Coagulation combines two particle sizes to yield a third one, while fragmentation breaks a given particle size into two (i.e. the inverse of the coagulation reaction). The complete set of reactions is given by all the permutations of two particle sizes associated with a third one. Since, by design, some reactions yield particle sizes that are outside the resolved size range of the spectrum, a closure is developed to take into account this unresolved range and satisfy global constraints such as mass conservation. In order to minimize the number of tracers required to apply this model to an ocean general circulation model, focus is placed on the robustness of the model to the particle size resolution. Thus, numerical experiments were designed to study the dependence of the results on (i) the number of particle size bins used to discretize a given size range (i.e. the resolution) and (ii) the type of discretization (i.e. linear vs. nonlinear). The results demonstrate that in a linearly size-discretized configuration, the model is independent of the resolution. However, important biases are observed in a nonlinear discretization. A first attempt to mitigate the effect of nonlinearity of the size spectrum is then presented and shows significant improvement in reducing the observed biases.Fil: Gremion, Gwenaëlle. Institut des Sciences de la Mer de Rimouski; CanadáFil: Nadeau, Louis Philippe. Institut des Sciences de la Mer de Rimouski; CanadáFil: Dufresne, Christiane. Institut des Sciences de la Mer de Rimouski; CanadáFil: Schloss, Irene Ruth. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; Argentina. Universidad Nacional de Tierra del Fuego. Instituto de Ciencias Polares, Recursos Naturales y Ambiente; ArgentinaFil: Archambault, Philippe. Laval University; CanadáFil: Dumont, Dany. Institut des Sciences de la Mer de Rimouski; Canad

A Model of the Ocean Overturning Circulation with Two Closed Basins and a Reentrant Channel

Zonally averaged models of the ocean overturning circulation miss important zonal exchanges of waters between the Atlantic and Indo-Pacific Oceans. A two-layer, two-basin model that accounts for these exchanges is introduced and suggests that in the present-day climate the overturning circulation is best described as the combination of three circulations: an adiabatic overturning circulation in the Atlantic Ocean associated with transformation of intermediate to deep waters in the north, a diabatic overturning circulation in the Indo- Pacific Ocean associated with transformation of abyssal to deep waters by mixing, and an interbasin circulation that exchanges waters geostrophically between the two oceans through the Southern Ocean. These results are supported both by theoretical analysis of the two-layer, two-basin model and by numerical simulations of a three-dimensional ocean model. Keywords: Ocean; Meridional overturning circulation; Ocean circulation; Mixing; Thermohaline circulationNational Science Foundation (U.S.) (Award OCE-1536515)National Science Foundation (U.S.) (Award OCE-1233832

Involvement of the Modifier Gene of a Human Mendelian Disorder in a Negative Selection Process

BACKGROUND:Identification of modifier genes and characterization of their effects represent major challenges in human genetics. SAA1 is one of the few modifiers identified in humans: this gene influences the risk of renal amyloidosis (RA) in patients with familial Mediterranean fever (FMF), a Mendelian autoinflammatory disorder associated with mutations in MEFV. Indeed, the SAA1 alpha homozygous genotype and the p.Met694Val homozygous genotype at the MEFV locus are two main risk factors for RA. METHODOLOGY/PRINCIPAL FINDINGS:HERE, WE INVESTIGATED ARMENIAN FMF PATIENTS AND CONTROLS FROM TWO NEIGHBORING COUNTRIES: Armenia, where RA is frequent (24%), and Karabakh, where RA is rare (2.5%). Sequencing of MEFV revealed similar frequencies of p.Met694Val homozygotes in the two groups of patients. However, a major deficit of SAA1 alpha homozygotes was found among Karabakhian patients (4%) as compared to Armenian patients (24%) (p = 5.10(-5)). Most importantly, we observed deviations from Hardy-Weinberg equilibrium (HWE) in the two groups of patients, and unexpectedly, in opposite directions, whereas, in the two control populations, genotype distributions at this locus were similar and complied with (HWE). CONCLUSIONS/SIGNIFICANCE:The excess of SAA1alpha homozygotes among Armenian patients could be explained by the recruitment of patients with severe phenotypes. In contrast, a population-based study revealed that the deficit of alpha/alpha among Karabakhian patients would result from a negative selection against carriers of this genotype. This study, which provides new insights into the role of SAA1 in the pathophysiology of FMF, represents the first example of deviations from HWE and selection involving the modifier gene of a Mendelian disorder

ARIA-EAACI statement on asthma and COVID-19 (June 2, 2020)

Non peer reviewe

Rhinitis associated with asthma is distinct from rhinitis alone: TARIA‐MeDALL hypothesis

Asthma, rhinitis, and atopic dermatitis (AD) are interrelated clinical phenotypes that partly overlap in the human interactome. The concept of “one-airway-one-disease,” coined over 20 years ago, is a simplistic approach of the links between upper- and lower-airway allergic diseases. With new data, it is time to reassess the concept. This article reviews (i) the clinical observations that led to Allergic Rhinitis and its Impact on Asthma (ARIA), (ii) new insights into polysensitization and multimorbidity, (iii) advances in mHealth for novel phenotype definitions, (iv) confirmation in canonical epidemiologic studies, (v) genomic findings, (vi) treatment approaches, and (vii) novel concepts on the onset of rhinitis and multimorbidity. One recent concept, bringing together upper- and lower-airway allergic diseases with skin, gut, and neuropsychiatric multimorbidities, is the “Epithelial Barrier Hypothesis.” This review determined that the “one-airway-one-disease” concept does not always hold true and that several phenotypes of disease can be defined. These phenotypes include an extreme “allergic” (asthma) phenotype combining asthma, rhinitis, and conjunctivitis.info:eu-repo/semantics/publishedVersio

Cabbage and fermented vegetables : From death rate heterogeneity in countries to candidates for mitigation strategies of severe COVID-19

Large differences in COVID-19 death rates exist between countries and between regions of the same country. Some very low death rate countries such as Eastern Asia, Central Europe, or the Balkans have a common feature of eating large quantities of fermented foods. Although biases exist when examining ecological studies, fermented vegetables or cabbage have been associated with low death rates in European countries. SARS-CoV-2 binds to its receptor, the angiotensin-converting enzyme 2 (ACE2). As a result of SARS-CoV-2 binding, ACE2 downregulation enhances the angiotensin II receptor type 1 (AT(1)R) axis associated with oxidative stress. This leads to insulin resistance as well as lung and endothelial damage, two severe outcomes of COVID-19. The nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is the most potent antioxidant in humans and can block in particular the AT(1)R axis. Cabbage contains precursors of sulforaphane, the most active natural activator of Nrf2. Fermented vegetables contain many lactobacilli, which are also potent Nrf2 activators. Three examples are: kimchi in Korea, westernized foods, and the slum paradox. It is proposed that fermented cabbage is a proof-of-concept of dietary manipulations that may enhance Nrf2-associated antioxidant effects, helpful in mitigating COVID-19 severity.Peer reviewe

Nrf2-interacting nutrients and COVID-19 : time for research to develop adaptation strategies

There are large between- and within-country variations in COVID-19 death rates. Some very low death rate settings such as Eastern Asia, Central Europe, the Balkans and Africa have a common feature of eating large quantities of fermented foods whose intake is associated with the activation of the Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) anti-oxidant transcription factor. There are many Nrf2-interacting nutrients (berberine, curcumin, epigallocatechin gallate, genistein, quercetin, resveratrol, sulforaphane) that all act similarly to reduce insulin resistance, endothelial damage, lung injury and cytokine storm. They also act on the same mechanisms (mTOR: Mammalian target of rapamycin, PPAR gamma:Peroxisome proliferator-activated receptor, NF kappa B: Nuclear factor kappa B, ERK: Extracellular signal-regulated kinases and eIF2 alpha:Elongation initiation factor 2 alpha). They may as a result be important in mitigating the severity of COVID-19, acting through the endoplasmic reticulum stress or ACE-Angiotensin-II-AT(1)R axis (AT(1)R) pathway. Many Nrf2-interacting nutrients are also interacting with TRPA1 and/or TRPV1. Interestingly, geographical areas with very low COVID-19 mortality are those with the lowest prevalence of obesity (Sub-Saharan Africa and Asia). It is tempting to propose that Nrf2-interacting foods and nutrients can re-balance insulin resistance and have a significant effect on COVID-19 severity. It is therefore possible that the intake of these foods may restore an optimal natural balance for the Nrf2 pathway and may be of interest in the mitigation of COVID-19 severity

Dynamics of a quasigeostrophic antarctic circumpolar current

The idea that basin-like dynamics may influence or control the Antarctic Circumpolar Current (ACC) is investigated with idealized analytic and numerical models. A simple 2-layer analytic model is developed to predict the transport evolution with the wind stress amplitude. At very low forcing, a non-zero minimum is predicted. This is followed by two distinct dynamical regimes for stronger forcing: a linearly increasing Stommel regime and a saturation regime in which the transport ceases to increase. The vertical distribution of the flow obtained using the geometry of the geostrophic contours (or characteristics) is key to predicting the occurrence of this transport saturation. Many eddy-permitting numerical simulations in large domains are carried over a wide range of parameters. The simulations using a reference zonal wind stress profile agree qualitatively with the analytic model. However, quantitative discrepancies are observed in the saturation regime: i) when a topographic continental ridge is added along the western boundary and ii) when the bottom drag is varied. When a continental ridge is added, eddy fluxes associated with zonal jets enhance the bottom layer recirculation and lower the saturation transport values. When the bottom drag is increased, the lower layer recirculation is suppressed, and this increases the saturation transport values. Experiments investigating the relative roles of the wind stress and wind stress curl in Drake Passage latitudes are also carried out. It is found that the transport is increased when adding a significant constant wind stress. In this regime dominated by the wind stress itself, there is an offset between the numerical results and what is predicted by the analytic model. The vertical momentum flux by mesoscale eddies can be used to distinguish between different regimes: an upward momentum transfer is observed when the dynamics is dominated by the wind stress curl and a downward flux is observed when it is not. In the regime where the wind stress curl dominates, Sverdrup circulation applies over most of the domain --- even in absence of meridional barriers. Also in this regime, transport is saturated, as suggested by the analytic model. The analytic model is also generalized to a continuous stratification and numerical experiments varying the vertical resolution are carried out to test its robustness. These simulations show that the 2-layer and 5-layer models give equivalent results when inertial effects are weak. However, in the 5-layer simulations, topographically-driven inertial recirculations blocking Drake Passage reduce the transport when inertial effects are strong. This behavior disapears, however, when realistic topography is used. In this context, the numerical results agree well with the predictions of the analytic model. It is also found that when the wind stress curl dominates, meridional walls play an important role in the dynamics at weak forcing but become less and less important as the forcing increases.Dans cette thèse, on étudié l'idée qu'une circulation de type bassin peut influencer et contrôler la dynamique du Courant Circumpolaire Antarctique (CCA) à l'aide de modèles analytique et numérique. Dans un premier temps, on développe un modèle analytique simple à deux couches pour estimer l'évolution du transport en fonction de l'amplitude du vent appliqué à la surface. À très faible amplitude, ce modèle prévoit un transport minimum non-nul. Deux régimes dynamique distincts succèdent à ce minimum: un régime de type "Stommel", dans lequel le transport augmente linéairement et un régime de "saturation" dans lequel le transport plafonne. On utilise la géométrie des "contours géostrophiques", pierre angulaire de la théorie, pour obtenir la distribution verticale de la circulation et estimer l'occurrence de ce régime de saturation.On effectue ensuite un grand nombre de simulations numériques à haute résolution spatiale, en variant la plupart des paramètres du modèle afin de tester la théorie analytique. On définit un profil de vent "référence" soufflant vers l'est suivant une fonction sin^2(y), où y est la latitude. Les simulations utilisant ce profil de référence correspondent qualitativement aux prévisions de la théorie analytique. Par contre, on observe des différences quantitatives dans le régime saturation: i) lorsqu'un plateau continental est ajouté à la frontière ouest et ii) lorsqu'on varie le coefficient de friction au fond. Lorsqu'on ajoute un plateau continental, les flux de tourbillons associés aux jets longitudinaux favorisent la circulation abyssale et baissent ainsi les valeurs de saturation du transport. Lorsqu'on augmente le coefficient de friction, la circulation abyssale est supprimée, ce qui augmente les valeurs de saturation du transport.Dans les expériences où l'on rajoute un vent constant au profil de référence, un décalage est observé entre les résultats des simulations numériques et les prévisions du modèle analytique. Cela définit un nouveau régime où le vent lui-même est fort en comparaison à son rotationnel. Le flux vertical de quantité de mouvement des tourbillons méso-échelle peut être utilisé afin de distinguer les différents régimes. En effet, ce flux est orienté vers le haut lorsque la dynamique est dominée par le rotationnel tandis qu'il est vers le bas lorsque le vent lui-même domine la dynamique. Dans le régime dominé par le rotationnel, une circulation de type Sverdrup est observée dans l'ensemble du bassin, même en absence de péninsules. De plus, le transport y est saturé, tel que suggéré par la théorie analytique.Le modèle analytique est ensuite généralisé au cas où la stratification est continue. On effectue des simulations numériques où la résolution verticale est variée afin de tester cette théorie généralisée. Ces simulations montrent que les modèles à 2 et 5 couches donnent des résultats similaires lorsque les effets d'inertie sont faibles. Par contre, d'intenses circulations générées au-dessus de la topographie bloquent le détroit de Drake et réduisent le transport lorsque les effets d'inertie sont importants. Cependant, ce comportement disparaît lorsqu'une topographie plus réaliste est utilisée. Dans ce contexte, les simulations numériques correspondent aux prévisions du modèle analytique. De plus, on observe que dans un régime où le rotationnel est dominant, les péninsules jouent un rôle important dans la dynamique lorsque le vent est faible tandis que leur rôle devient de plus en plus négligeable lorsque le vent augmente