Mitigating masked pixels in climate-critical datasets

Remote sensing observations of the Earth's surface are frequently stymied by clouds, water vapour, and aerosols in our atmosphere. These degrade or preclude the measurementof quantities critical to scientific and, hence, societal applications. In this study, we train a natural language processing (NLP) algorithm with high-fidelity ocean simulations in order to accurately reconstruct masked or missing data in sea surface temperature (SST)--i.e. one of 54 essential climate variables identified by the Global Climate Observing System. We demonstrate that the Enki model repeatedly outperforms previously adopted inpainting techniques by up to an order-of-magnitude in reconstruction error, while displaying high performance even in circumstances where the majority of pixels are masked. Furthermore, experiments on real infrared sensor data with masking fractions of at least 40% show reconstruction errors of less than the known sensor uncertainty (RMSE < ~0.1K). We attribute Enki's success to the attentive nature of NLP combined with realistic SST model outputs, an approach that may be extended to other remote sensing variables. This study demonstrates that systems built upon Enki--or other advanced systems like it--may therefore yield the optimal solution to accurate estimates of otherwise missing or masked parameters in climate-critical datasets sampling a rapidly changing Earth.Comment: 21 pages, 6 main figure, 3 in Appendix; submitte

The role of curvature in modifying frontal instabilities. Part I: Review of theory and presentation of a nondimensional instability criterion

In this study, we examine the role of curvature in modifying frontal stability. We first evaluate the classical criterion that the Coriolis parameter, f, multiplied by the Ertel potential vorticity (PV), q, is positive for stable flow and that instability is possible when this quantity is negative. The first portion of this statement can be deduced from Ertel’s PV theorem, assuming an initially positive fq. Moreover, the full statement is implicit in the governing equation for the mean flow, as the discriminant, fq, changes sign. However, for curved fronts in cyclo-geostrophic or gradient wind balance (GWB), an additional term enters the discriminant owing to conservation of absolute angular momentum, L. The resulting expression, Lq < 0, simultaneously generalizes Rayleigh’s (1917) criterion by accounting for baroclinicity and Hoskins’ (1974) criterion by accounting for centrifugal effects. In particular, changes in the front’s vertical shear and stratification owing to curvature tilt the absolute vorticity vector away from its thermal wind state; in an effort to conserve the product of absolute angular momentum and Ertel PV, this modifies gradient Rossby and Richardson numbers permitted for stable flow. This forms the basis of a non-dimensional expression valid for inviscid, curved fronts on the f -plane, which can be used to classify frontal instabilities. In conclusion, the classical criterion, fq < 0, should be replaced by the more general criterion, Lq < 0, for studies involving gravitational, centrifugal, and symmetric instabilities at curved density fronts. In Part 2 of the study, we examine interesting outcomes of the criterion applied to low-Richardson number fronts and vortices in GWB

The role of curvature in modifying frontal instabilities. Part II: Application of the criterion to curved density fronts at low Richardson numbers

We continue our study of the role of curvature in modifying frontal stability. In Part 1, we obtained an instability criterion valid for curved fronts and vortices in gradient wind balance (GWB): Φ′ = L′q′ < 0, where L′ and q′ are the non-dimensional absolute angular momentum and Ertel potential vorticity (PV), respectively. In Part 2, we investigate this criterion in a parameter space representative of low-Richardson number fronts and vortices in GWB. An interesting outcome is that, for Richardson numbers near one, anticyclonic flows increase in q′, while cyclonic flows decrease in q′, tending to stabilize anticyclonic and de-stabilize cyclonic flow. Although stability is marginal or weak for anticyclonic flow (owing to multiplication by L′), the de-stabilization of cyclonic flow is pronounced, and may help to explain an observed asymmetry in the distribution of small-scale, coherent vortices in the ocean interior. We are referring mid-latitude submesoscale and polar mesoscale vortices that are generated by friction and/or buoyancy forcing within boundary layers but that are often documented outside these layers. A comparison is made between several documented vortices and predicted stability maps, providing support for the proposed mechanism. Finally, a simple expression, which is a root of the stability discriminant, Φ′, explains the observed asymmetry in the distribution of vorticity. In conclusion, the generalized criterion is consistent with theory, observations and recent modeling studies, and demonstrates that curvature in low-stratified environments can de-stabilize cyclonic and stabilize anticyclonic fronts and vortices to symmetric instability. The results may have implications for Earth system models

The contribution of surface and submesoscale processes to turbulence in the open ocean surface boundary layer

The ocean surface boundary layer is a critical interface across which momentum, heat, and trace gases are exchanged between the oceans and atmosphere. Surface processes (winds, waves, and buoyancy forcing) are known to contribute significantly to fluxes within this layer. Recently, studies have suggested that submesoscale processes, which occur at small scales (0.1–10 km, hours to days) and therefore are not yet represented in most ocean models, may play critical roles in these turbulent exchanges. While observational support for such phenomena has been demonstrated in the vicinity of strong current systems and littoral regions, relatively few observations exist in the open‐ocean environment to warrant representation in Earth system models. We use novel observations and simulations to quantify the contributions of surface and submesoscale processes to turbulent kinetic energy (TKE) dissipation in the open‐ocean surface boundary layer. Our observations are derived from moorings in the North Atlantic, December 2012 to April 2013, and are complemented by atmospheric reanalysis. We develop a conceptual framework for dissipation rates due to surface and submesoscale processes. Using this framework and comparing with observed dissipation rates, we find that surface processes dominate TKE dissipation. A parameterization for symmetric instability is consistent with this result. We next employ simulations from an ocean front‐resolving model to reestablish that dissipation due to surface processes exceeds that of submesoscale processes by 1–2 orders of magnitude. Together, these results suggest submesoscale processes do not dramatically modify vertical TKE budgets, though such dynamics may be climatically important owing to their ability to remove energy from the ocean

Seasonality of submesoscale flows in the ocean surface boundary layer

A signature of submesoscale flows in the upper ocean is skewness in the distribution of relative vorticity. Expected to result for high Rossby-number flows, such skewness has implications for mixing, dissipation and stratification within the upper ocean. An array of moorings deployed in the Northeast Atlantic for one year as part of the OSMOSIS experiment reveals that relative vorticity is positively skewed during winter even though the scale of the Rossby number is less than 0.5. Furthermore, this skewness is reduced to zero during spring and autumn. There is also evidence of modest seasonal variations in the gradient Rossby number. The proposed mechanism by which relative vorticity is skewed is that the ratio of lateral to vertical buoyancy gradients, as summarized by the inverse gradient Richardson number, restricts its range during winter but less so at other times of the year. These results support recent observations and model simulations suggesting the upper ocean is host to a seasonal cycle in submesoscale turbulence

An annual cycle of submesoscale vertical flow and restratification in the upper ocean

Numerical simulations suggest that submesoscale turbulence may transform lateral buoyancy gradients into vertical stratification, and thus restratify the upper ocean via vertical flow. However, the observational evidence for this restratifying process has been lacking due to the difficulty in measuring such ephemeral phenomena, particularly over periods of months to years. This study presents an annual cycle of the vertical velocity and associated restratification estimated from two nested clusters of meso- and submesoscale-resolving moorings, deployed in a typical mid-ocean area of the Northeast Atlantic. Vertical velocities inferred using the non-diffusive density equation are substantially stronger at submesoscales (horizontal scales of 1-10 km) than at mesoscales (horizontal scales of 10-100 km), with respective root mean square values of 38.0 ± 6.9 m/day and 22.5 ± 3.3 m/day. The largest submesoscale vertical velocities and rates of restratification occur in events of a few days’ duration in winter and spring, and extend down to at least 200 m below the mixed layer base. These events commonly coincide with the enhancement of submesoscale lateral buoyancy gradients, which is itself associated with persistent mesoscale frontogenesis. This suggests that mesoscale frontogenesis is a regular precursor of the submesoscale turbulence that restratifies the upper ocean. The upper-ocean restratification induced by submesoscale motions integrated over the annual cycle is comparable in magnitude to the net destratification driven by local atmospheric cooling, indicating that submesoscale flows play a significant role in determining the climatological upper-ocean stratification in the study area

Collagen concentration and biomechanical properties of samples from the lower uterine cervix in relation to age and parity in non-pregnant women

<p>Abstract</p> <p>Background</p> <p>During normal pregnancy the cervix has a load bearing function. The cervical tissue consists mainly of an extracellular matrix (ECM) rich in collagen; important for the biomechanical properties. The aim of the present study was to evaluate how the biomechanical strength of samples from the distal cervix is associated with collagen content in relation to age and parity. This study demonstrates a method to investigate cervical tissue from women who still have their uterus in situ.</p> <p>Methods</p> <p>Cervical punch biopsies (2 × 15 mm) were obtained from 57 healthy women (median age: 39 years, range: 29-49 years). Biomechanical tensile testing was performed, and collagen concentration (as % of dry defatted weight (DDW)) and content (mg of collagen per mm of specimen length) was determined. Histomorphometry was used to determine the volume densities of extracellular matrix and smooth muscle cells. Smooth muscle cells were identified by immunohistochemistry. Finally, orientation of collagen fibers was estimated. Data are given as mean +/- SD.</p> <p>Results</p> <p>The mean collagen concentration (62.2 +/- 6.6%) increased with age (0.5% per year, r = 0.45, p = 0.003) and decreased with parity (1.7% per birth, r = -0.45, p = 0.033). Maximum load was positively correlated with collagen content (mg of collagen per mm of specimen length) (r = 0.76, p < 0.001). Normalized maximum stiffness was increased with age (r = 0.32, p = 0.017), whereas no correlation was found with regard to parity. In tissue samples with a length of approximately one cm, volume density of smooth muscle cells increased gradually from 8.9% in the distal part near the epithelium, to 15.5% in the proximal part (p < 0.001).</p> <p>Conclusions</p> <p>The present study shows that cervical collagen concentration increases with age and decreases with parity in non-pregnant women. In addition, collagen stiffness increased with age, whereas no change in collagen tensile strength with respect to age and parity was found. These results show that collagen contributes to cervical tissue tensile strength and age and parity should be considered confounding factors.</p

On critical behaviour in systems of Hamiltonian partial differential equations

We study the critical behaviour of solutions to weakly dispersive Hamiltonian systems considered as perturbations of elliptic and hyperbolic systems of hydrodynamic type with two components. We argue that near the critical point of gradient catastrophe of the dispersionless system, the solutions to a suitable initial value problem for the perturbed equations are approximately described by particular solutions to the Painlev\ue9-I (PI) equation or its fourth-order analogue P2I. As concrete examples, we discuss nonlinear Schr\uf6dinger equations in the semiclassical limit. A numerical study of these cases provides strong evidence in support of the conjecture

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead