Chaotic advection, mixing, and property exchange in three-dimensional ocean eddies and gyres

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2018This work investigates how a Lagrangian perspective applies to models of two oceanographic flows: an overturning submesoscale eddy and the Western Alboran Gyre. In the first case, I focus on the importance of diffusion as compared to chaotic advection for tracers in this system. Three methods are used to quantify the relative contributions: scaling arguments including a Lagrangian Batchelor scale, statistical analysis of ensembles of trajectories, and Nakamura effective diffusivity from numerical simulations of dye release. Through these complementary methods, I find that chaotic advection dominates over turbulent diffusion in the widest chaotic regions, which always occur near the center and outer rim of the cylinder and sometimes occur in interior regions for Ekman numbers near 0.01. In thin chaotic regions, diffusion is at least as important as chaotic advection. From this analysis, it is clear that identified Lagrangian coherent structures will be barriers to transport for long times if they are much larger than the Batchelor scale. The second case is a model of the Western Alboran Gyre with realistic forcing and bathymetry. I examine its transport properties from both an Eulerian and Lagrangian perspective. I find that advection is most often the dominant term in Eulerian budgets for volume, salt, and heat in the gyre, with diffusion and surface fluxes playing a smaller role. In the vorticity budget, advection is as large as the effects of wind and viscous diffusion, but not dominant. For the Lagrangian analysis, I construct a moving gyre boundary from segments of the stable and unstable manifolds emanating from two persistent hyperbolic trajectories on the coast at the eastern and western extent of the gyre. These manifolds are computed on several isopycnals and stacked vertically to construct a three-dimensional Lagrangian gyre boundary. The regions these manifolds cover is the stirring region, where there is a path for water to reach the gyre. On timescales of days to weeks, water from the Atlantic Jet and the northern coast can enter the outer parts of the gyre, but there is a core region in the interior that is separate. Using a gate, I calculate the continuous advective transport across the Lagrangian boundary in three dimensions for the first time. A Lagrangian volume budget is calculated, and challenges in its closure are described. Lagrangian and Eulerian advective transports are found to be of similar magnitudes.Funding for this work was provided by Woods Hole Oceanographic Institution and the Office of Naval Research. The ONR support was through the MURI on Dynamical Systems Theory and Lagrangian Data Assimilation in 4D and the CALYPSO project

The role of whitecapping in thickening the ocean surface boundary layer

Author Posting. © American Meteorological Society, 2015. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 45 (2015): 2006–2024, doi:10.1175/JPO-D-14-0234.1.The effects of wind-driven whitecapping on the evolution of the ocean surface boundary layer are examined using an idealized one-dimensional Reynolds-averaged Navier–Stokes numerical model. Whitecapping is parameterized as a flux of turbulent kinetic energy through the sea surface and through an adjustment of the turbulent length scale. Simulations begin with a two-layer configuration and use a wind that ramps to a steady stress. This study finds that the boundary layer begins to thicken sooner in simulations with whitecapping than without because whitecapping introduces energy to the base of the boundary layer sooner than shear production does. Even in the presence of whitecapping, shear production becomes important for several hours, but then inertial oscillations cause shear production and whitecapping to alternate as the dominant energy sources for mixing. Details of these results are sensitive to initial and forcing conditions, particularly to the turbulent length scale imposed by breaking waves and the transfer velocity of energy from waves to turbulence. After 1–2 days of steady wind, the boundary layer in whitecapping simulations has thickened more than the boundary layer in simulations without whitecapping by about 10%–50%, depending on the forcing and initial conditions.We thank Skidmore College for financial and infrastructure support, and Skidmore and the National Science Foundation for funding travel to meetings where early versions of this work were presented. We also thank the National Science Foundation, Oregon State University, Jonathan Nash, and Joe Jurisa for funding and hosting a workshop on River Plume Mixing in October, 2013, where ideas and context for this paper were developed.2016-02-0

The Western Alboran Gyre: an analysis of its properties and its exchange with surrounding water

Author Posting. © American Meteorological Society, 2020. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 50(12), (2020): 3379-3402, https://do.org/10.1175/JPO-D-20-0028.1.One of the largest and most persistent features in the Alboran Sea is the Western Alboran Gyre (WAG), an anticyclonic recirculation bounded by the Atlantic Jet (AJ) to the north and the Moroccan coast to the south. Eulerian budgets from several months of a high-resolution model run are used to examine the exchange of water across the Eulerian WAG’s boundary and the processes affecting the salinity, temperature, and vorticity of the WAG. The volume transport across the sides of the WAG is found to be related to vertical isopycnal movement at the base of the gyre. Advection is found to drive a decay in the salinity minimum and anticyclonic vorticity of the Eulerian WAG. Given the large contributions of advection, a Lagrangian analysis is performed, revealing geometric aspects of the exchange that are hidden in an Eulerian view. In particular, stable and unstable manifolds identify a stirring region around the outer reaches of the gyre where water is exchanged with the WAG on a time scale of weeks. Its complement is an inner core that expands with depth and exchanges water with its surroundings on much longer time scales. The 3D evolution of one parcel, or lobe, of water as it enters the WAG is also described, identifying a general Lagrangian subduction pathway.This work was supported on DOD (MURI) Grant N000141110087, ONR Grant N000141812417, and NSF Grant OCE-1558806.2021-05-1

Surprise responses in the human brain demonstrate statistical learning under high concurrent cognitive demand

The ability to learn about regularities in the environment and to make predictions about future events is fundamental for adaptive behaviour. We have previously shown that people can implicitly encode statistical regularities and detect violations therein, as reflected in neuronal responses to unpredictable events that carry a unique prediction error signature. In the real world, however, learning about regularities will often occur in the context of competing cognitive demands. Here we asked whether learning of statistical regularities is modulated by concurrent cognitive load. We compared electroencephalographic metrics associated with responses to pure-tone sounds with frequencies sampled from narrow or wide Gaussian distributions. We showed that outliers evoked a larger response than those in the centre of the stimulus distribution (i.e., an effect of surprise) and that this difference was greater for physically identical outliers in the narrow than in the broad distribution. These results demonstrate an early neurophysiological marker of the brain’s ability to implicitly encode complex statistical structure in the environment. Moreover, we manipulated concurrent cognitive load by having participants perform a visual working memory task while listening to these streams of sounds. We again observed greater prediction error responses in the narrower distribution under both low and high cognitive load. Furthermore, there was no reliable reduction in prediction error magnitude under high-relative to low cognitive load. Our findings suggest that statistical learning is not a capacity limited process, and that it proceeds automatically even when cognitive resources are taxed by concurrent demands

The Web of Legal Protections for Participants in Genomic Research

The identification and arrest of the Golden State Killer using DNA uploaded to an ancestry database occurred shortly before recruitment for the National Institutes of Health’s (NIH) All of Us Study commenced, with a goal of enrolling and collecting DNA, health, and lifestyle information from one million Americans. It also highlighted the need to ensure prospective research participants that their confidentiality will be protected and their materials used appropriately. But there are questions about how well current law protects against these privacy risks. This article is the first to consider comprehensively and simultaneously all the federal and state laws offering protections to participants in genomic research. The literature typically focuses on the federal laws in isolation, questioning the strengths of federal legal protections for genomic research participants provided in the Common Rule, the HIPAA Privacy Rule, or the Genetic Information Nondiscrimination Act. Nevertheless, we found significant numbers and surprising variety among state laws that provide greater protections than federal laws, often filling in federal gaps by broadening the applicability of privacy or nondiscrimination standards or by providing important remedies for individuals harmed by breaches. Identifying and explaining the protections these laws provide is significant both to allow prospective participants to accurately weigh the risks of enrolling in these studies and as models for how federal legal protections could be expanded to fill known gaps

Innovative package for frontline maternal, newborn and child health workers in South Sudan

Improving maternal, newborn, and child health is a leading priority worldwide. It is a particularly urgent issue in South Sudan, which suffers from the world’s worst maternal mortality and among the worst newborn and child mortalities. A leading barrier to improving these health indices is limited frontline health worker capacity. In partnership with the Ministry of Health, the Division of Global Health and Human Rights (Department of Emergency Medicine, Massachusetts General Hospital, Boston, USA) has developed and is currently implementing its novel Maternal, Newborn, and Child Survival (MNCS) Initiative throughout much of South Sudan. The purpose of MNCS is to build frontline health worker capacity through a training package that includes:1. A participatory training course2. Pictorial checklists to guide prevention, care, and referral3. Re-useable medical equipment and commodities.Program implementation began in November 2010 utilizing a training-of-trainers model. To date, 72 local trainers and 632 frontline health workers have completed the training and received their MNCS checklists and commodities. Initial monitoring and evaluation results are encouraging as further evaluation continues. This innovative training package may also serve as a model for building capacity for maternal, newborn, and child health in other resource limited settings beyond South Sudan

Identification and functional characterization of an N-terminal oligomerization domain for polycystin-2*

Autosomal dominant polycystic kidney disease (ADPKD), the most common inherited cause of kidney failure, is caused by mutations in either PKD1 (85%) or PKD2 (15%). The PKD2 protein, polycystin-2 (PC2 or TRPP2), is a member of the transient receptor potential (TRP) superfamily and functions as a non-selective calcium channel. PC2 has been found to form oligomers in native tissues suggesting that it may form functional homo- or heterotetramers with other subunits, similar to other TRP channels. Our experiments unexpectedly revealed that PC2 mutant proteins lacking the known C-terminal dimerization domain were still able to form oligomers and co-immunoprecipitate full-length PC2, implying the possible existence of a proximal dimerization domain. Using yeast two-hybrid and biochemical assays, we have mapped an alternative dimerization domain to the N terminus of PC2 (NT2-1-223, L224X). Functional characterization of this domain demonstrated that it was sufficient to induce cyst formation in zebrafish embryos and inhibit PC2 surface currents in mIMCD3 cells probably by a dominant-negative mechanism. In summary, we propose a model for PC2 assembly as a functional tetramer which depends on both C- and N-terminal dimerization domains. These results have significant implications for our understanding of PC2 function and disease pathogenesis in ADPKD and provide a new strategy for studying PC2 function

Reflecting to Rebuild and Strengthen Professional Development A Collection of ‘Post-Online’ Conversations

The file attached to this record is the author's versionThis monograph is a multi-authored collection consisting of our faculty’s post-online reflections. The objective was to gather thoughts and discussion around teaching and research during COVID-19. We aim to build and explore around ‘lived experiences’ to provide a reference point to help Continuous Professional Learning and Development (CPLD) activities. The section on ‘digital diaries’ consists of dialogues from staff categorised into varied themes. In the testimonies, staff have reflected around their challenges, targets, strengths, familiarity and how they managed to overcome difficulties and achieve goals. A special section, from the Centre for Urban Research on Austerity (CURA), is devoted to identifying how pandemic has intensified research challenges, highlighting the funding, time and location constraints on academic research

IL-13 is a driver of COVID-19 severity

Immune dysregulation is characteristic of the more severe stages of SARS-CoV-2 infection. Understanding the mechanisms by which the immune system contributes to COVID-19 severity may open new avenues to treatment. Here, we report that elevated IL-13 was associated with the need for mechanical ventilation in 2 independent patient cohorts. In addition, patients who acquired COVID-19 while prescribed Dupilumab, a mAb that blocks IL-13 and IL-4 signaling, had less severe disease. In SARS-CoV-2–infected mice, IL-13 neutralization reduced death and disease severity without affecting viral load, demonstrating an immunopathogenic role for this cytokine. Following anti–IL-13 treatment in infected mice, hyaluronan synthase 1 (Has1) was the most downregulated gene, and accumulation of the hyaluronan (HA) polysaccharide was decreased in the lung. In patients with COVID-19, HA was increased in the lungs and plasma. Blockade of the HA receptor, CD44, reduced mortality in infected mice, supporting the importance of HA as a pathogenic mediator. Finally, HA was directly induced in the lungs of mice by administration of IL-13, indicating a new role for IL-13 in lung disease. Understanding the role of IL-13 and HA has important implications for therapy of COVID-19 and, potentially, other pulmonary diseases. IL-13 levels were elevated in patients with severe COVID-19. In a mouse model of the disease, IL-13 neutralization reduced the disease and decreased lung HA deposition. Administration of IL-13–induced HA in the lung. Blockade of the HA receptor CD44 prevented mortality, highlighting a potentially novel mechanism for IL-13–mediated HA synthesis in pulmonary pathology