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Species differences in the structure and function of the immune system of laboratory animals are known to exist and have been reviewed extensively. However, the number and diversity of wild and exotic species, along with their associated viruses, that come into contact with humans has increased worldwide sometimes with lethal consequences. Far less is known about the immunobiology of these exotic and wild species. Data suggest that species differences of the mechanisms of inflammation, innate immunity and adaptive immunity are all involved in the establishment and maintenance of viral infections across reservoir hosts. The current review attempts to collect relevant data concerning the basics of innate and adaptive immune functions of exotic and wild species followed by identification of those differences that may play a role in the maintenance of viral infections in reservoir hosts.

Deep-sea polymetallic nodule mining research activity has substantially increased in recent years, but the expected level of environmental impact is still being established. One environmental concern is the discharge of a sediment plume into the midwater column. We performed a dedicated field study using sediment from the Clarion Clipperton Fracture Zone. The plume was monitored and tracked using both established and novel instrumentation, including acoustic and turbulence measurements. Our field studies reveal that modeling can reliably predict the properties of a midwater plume in the vicinity of the discharge and that sediment aggregation effects are not significant. The plume model is used to drive a numerical simulation of a commercial-scale operation in the Clarion Clipperton Fracture Zone. Key takeaways are that the scale of impact of the plume is notably influenced by the values of environmentally acceptable threshold levels, the quantity of discharged sediment, and the turbulent diffusivity in the Clarion Clipperton Fracture Zone.

We derive conservative time-dependent structured discretizations and two-way embedded (nested) schemes for multiscale ocean dynamics governed by primitive equations (PEs) with a nonlinear free surface. Our multiscale goal is to resolve tidal-to-mesoscale processes and interactions over large multiresolution telescoping domains with complex geometries including shallow seas with strong tides, steep shelfbreaks, and deep ocean interactions. We first provide an implicit time-stepping algorithm for the nonlinear free-surface PEs and then derive a consistent time-dependent spatial discretization with a generalized vertical grid. This leads to a novel time-dependent finite volume formulation for structured grids on spherical or Cartesian coordinates, second order in time and space, which preserves mass and tracers in the presence of a time-varying free surface. We then introduce the concept of two-way nesting, implicit in space and time, which exchanges all of the updated fields values across grids, as soon as they become available. A class of such powerful nesting schemes applicable to telescoping grids of PE models with a nonlinear free surface is derived. The schemes mainly differ in the fine-to-coarse scale transfers and in the interpolations and numerical filtering, specifically for the barotropic velocity and surface pressure components of the two-way exchanges. Our scheme comparisons show that for nesting with free surfaces, the most accurate scheme has the strongest implicit couplings among grids. We complete a theoretical truncation error analysis to confirm and mathematically explain findings. Results of our discretizations and two-way nesting are presented in realistic multiscale simulations with data assimilation for the middle Atlantic Bight shelfbreak region off the east coast of the USA, the Philippine archipelago, and the Taiwan-Kuroshio region. Multiscale modeling with two-way nesting enables an easy use of different sub-gridscale parameterizations in each nested domain. The new developments drastically enhance the predictive capability and robustness of our predictions, both qualitatively and quantitatively. Without them, our multiscale multiprocess simulations either were not possible or did not match ocean data.

We consider the interactions of internal tides (ITs) with a dynamic, rotational and heterogeneous ocean, and spatially varying topography. The IT fields are expanded using vertical modal basis functions, whose amplitudes vary horizontally and temporally. We obtain the evolution equations of modal amplitudes and energy including simultaneous three-way interactions with the mean flow, buoyancy and topography. We apply these equations to a set of idealized and two realistic data-assimilative primitive equation simulations. These simulations reveal that significant interactions of ITs with the background fields occur at topographic features and strong currents, in particular when the scales of the background and ITs are similar. In local hot spots, the new three-way interaction terms, when compared to the total modal conversion, are found to reach up to 10 %–30 % at steep topography and approximately 50 % in the Gulf Stream. We provide a dimensional analysis to guide the diagnosis of such strong interactions. When IT interactions are with a large-scale barotropic current (without topographic effects), our modal energy equation reduces to the conservation of modal wave action under a Wentzel–Kramers–Brillouin consideration. We further derive analytical solutions of the modulation of wavenumber and energy of an IT propagating into a collinear current. For ITs propagating along the flow direction, the wavelength is stretched and the amplitude is reduced, with the degree of modulation determined by $|\\,f/\\omega _0|$, the ratio of inertial to tidal frequencies. For ITs propagating opposite to the flow direction, a critical value of $|\\,f/\\omega _0|$ exists, below and above which the waves show remarkably different behaviours. The critical opposing current speed which triggers the wave focusing/blocking phenomenon is obtained and its implication for the propagation and dissipation of ITs is discussed.

We develop an accurate partial differential equation-based methodology that predicts the time-optimal paths of autonomous vehicles navigating in any continuous, strong, and dynamic ocean currents, obviating the need for heuristics. The goal is to predict a sequence of steering directions so that vehicles can best utilize or avoid currents to minimize their travel time. Inspired by the level set method, we derive and demonstrate that a modified level set equation governs the time-optimal path in any continuous flow. We show that our algorithm is computationally efficient and apply it to a number of experiments. First, we validate our approach through a simple benchmark application in a Rankine vortex flow for which an analytical solution is available. Next, we apply our methodology to more complex, simulated flow fields such as unsteady double-gyre flows driven by wind stress and flows behind a circular island. These examples show that time-optimal paths for multiple vehicles can be planned even in the presence of complex flows in domains with obstacles. Finally, we present and support through illustrations several remarks that describe specific features of our methodology.

A hydrostatic, coupled-mode, shallow-water model (CSW) is described and used to diagnose and simulate tidal dynamics in the greater Mid-Atlantic Bight region. The reduced-physics model incorporates realistic stratification and topography, internal tide forcing from a priori estimates of the surface tide, and advection terms that describe first-order interactions of internal tides with slowly varying mean flow and mean buoyancy fields and their respective shear. The model is validated via comparisons with semianalytic models and nonlinear primitive equation models in several idealized and realistic simulations that include internal tide interactions with topography and mean flows. Then, 24 simulations of internal tide generation and propagation in the greater Mid-Atlantic Bight region are used to diagnose significant internal tide interactions with the Gulf Stream. The simulations indicate that locally generated mode-one internal tides refract and/or reflect at the Gulf Stream. The redirected internal tides often reappear at the shelf break, where their onshore energy fluxes are intermittent (i.e., noncoherent with surface tide) because meanders in the Gulf Stream alter their precise location, phase, and amplitude. These results provide an explanation for anomalous onshore energy fluxes that were previously observed at the New Jersey shelf break and linked to the irregular generation of nonlinear internal waves.

Where, when, and what to sample, and how to optimally reach the sampling locations, are critical questions to be answered by autonomous and Lagrangian platforms and sensors. For a reproducible scientific sampling approach, answers should be quantitative and provided using fundamental principles. This article reviews concepts and recent progress toward this principled approach, focusing on reachability, path planning, and adaptive sampling, and presents results of a real-time forecasting and planning experiment completed during February–April 2017 for the Northern Arabian Sea Circulation-autonomous research program. The predictive skill, layered fields, and uncertainty estimates obtained using the MIT MSEAS multi-resolution ensemble ocean modeling system are first studied. With such inputs, deterministic and probabilistic three-dimensional reachability forecasts issued daily for gliders and floats are then showcased and validated. Finally, a Bayesian adaptive sampling framework is shown to forecast in real time the observations that are most informative for estimating classic ocean fields and also secondary variables such as Lagrangian coherent structures.

The level set methodology for time-optimal path planning is employed to predict collision-free and fastest-time trajectories for swarms of underwater vehicles deployed in the Philippine Archipelago region. To simulate the multiscale ocean flows in this complex region, a data-assimilative primitive-equation ocean modeling system is employed with telescoping domains that are interconnected by implicit two-way nesting. These data-driven multiresolution simulations provide a realistic flow environment, including variable large-scale currents, strong jets, eddies, wind-driven currents, and tides. The properties and capabilities of the rigorous level set methodology are illustrated and assessed quantitatively for several vehicle types and mission scenarios. Feasibility studies of all-to-all broadcast missions, leading to minimal time transmission between source and receiver locations, are performed using a large number of vehicles. The results with gliders and faster propelled vehicles are compared. Reachability studies, i.e., determining the boundaries of regions that can be reached by vehicles for exploratory missions, are then exemplified and analyzed. Finally, the methodology is used to determine the optimal strategies for fastest-time pick up of deployed gliders by means of underway surface vessels or stationary platforms. The results highlight the complex effects of multiscale flows on the optimal paths, the need to utilize the ocean environment for more efficient autonomous missions, and the benefits of including ocean forecasts in the planning of time-optimal paths.

During the Costa Concordia emergency case, regional, subregional, and relocatable ocean models have been used together with the oil spill model, MEDSLIK-II, to provide ocean currents forecasts, possible oil spill scenarios, and drifters trajectories simulations. The models results together with the evaluation of their performances are presented in this paper. In particular, we focused this work on the implementation of the Interactive Relocatable Nested Ocean Model (IRENOM), based on the Harvard Ocean Prediction System (HOPS), for the Costa Concordia emergency and on its validation using drifters released in the area of the accident. It is shown that thanks to the capability of improving easily and quickly its configuration, the IRENOM results are of greater accuracy than the results achieved using regional or subregional model products. The model topography, and to the initialization procedures, and the horizontal resolution are the key model settings to be configured. Furthermore, the IRENOM currents and the MEDSLIK-II simulated trajectories showed to be sensitive to the spatial resolution of the meteorological fields used, providing higher prediction skills with higher resolution wind forcing.

The North Equatorial Current (NEC) transports water westward around numerous islands and over submarine ridges in the western Pacific. As the currents flow over and around this topography, the central question is: how are momentum and energy in the incident flow transferred to finer scales? At the south point of Peleliu Island, Palau, a combination of strong NEC currents and tides flow over a steep, submarine ridge. Energy cascades suddenly from the NEC via the 1 km scale lee waves and wake eddies to turbulence. These submesoscale wake eddies are observed every tidal cycle, and also in model simulations. As the flow in each eddy recirculates and encounters the incident flow again, the associated front contains interleaving temperature (T) structures with 1–10 m horizontal extent. Turbulent dissipation (ε) exceeds 10−5 W kg−1 along this tilted and strongly sheared front. A train of such submesoscale eddies can be seen at least 50 km downstream. Internal lee waves with 1 km wavelengths are also observed over the submarine ridge. The mean form drag exerted by the waves (i.e., upward transport of eastward momentum) of about 1 Pa is sufficient to substantially reduce the westward NEC, if not for other forcing, and is greater than the turbulent bottom drag of about 0.1 Pa. The effect on the incident flow of the form drag from only one submarine ridge may be similar to the bottom drag along the entire coastline of Palau. The observed ε is also consistent with local dissipation of lee wave energy. The circulation, including lee waves and wake eddies, was simulated by a datadriven primitive equation ocean model. The model estimates of the form drags exerted by pressure drops across the submarine ridge and due to wake eddies were found to be about 10 times higher than the lee wave and turbulent bottom drags. The ridge form drag was correlated to both the tidal flow and winds while the submesoscale wake eddy drag was mainly tidal.