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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.

Purpose This study aims to address the lack of spatial dose comparisons of planned and delivered rectal doses during prostate radiotherapy by using dose‐surface maps (DSMs) to analyze dose delivery accuracy and comparing these results to those derived using DVHs. Methods Two independent cohorts were used in this study: twenty patients treated with 36.25 Gy in five fractions (SBRT) and 20 treated with 60 Gy in 20 fractions (IMRT). Daily delivered rectum doses for each patient were retrospectively calculated using daily CBCT images. For each cohort, planned and average‐delivered DVHs were generated and compared, as were planned and accumulated DSMs. Permutation testing was used to identify DVH metrics and DSM regions where significant dose differences occurred. Changes in rectal volume and position between planning and delivery were also evaluated to determine possible correlation to dosimetric changes. Results For both cohorts, DVHs and DSMs reported conflicting findings on how planned and delivered rectum doses differed from each other. DVH analysis determined average‐delivered DVHs were on average 7.1% ± 7.6% (p ≤ 0.002) and 5.0 ± 7.4% (p ≤ 0.021) higher than planned for the IMRT and SBRT cohorts, respectively. Meanwhile, DSM analysis found average delivered posterior rectal wall dose was 3.8 ± 0.6 Gy (p = 0.014) lower than planned in the IMRT cohort and no significant dose differences in the SBRT cohort. Observed dose differences were moderately correlated with anterior‐posterior rectal wall motion, as well as PTV superior‐inferior motion in the IMRT cohort. Evidence of both these relationships were discernable in DSMs. Conclusion DSMs enabled spatial investigations of planned and delivered doses can uncover associations with interfraction motion that are otherwise masked in DVHs. Investigations of dose delivery accuracy in radiotherapy may benefit from using DSMs over DVHs for certain organs such as the rectum.

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.

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.

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.

Radiomics-based machine learning classifiers have shown potential for detecting bone metastases (BM) and for evaluating BM response to radiotherapy (RT). However, current radiomics models require large datasets of images with expert-segmented 3D regions of interest (ROIs). Full ROI segmentation is time consuming and oncologists often outline just RT treatment fields in clinical practice. This presents a challenge for real-world radiomics research. As such, a method that simplifies BM identification but does not compromise the power of radiomics is needed. The objective of this study was to investigate the feasibility of radiomics models for BM detection using lesion-center-based geometric ROIs. The planning-CT images of 170 patients with non-metastatic lung cancer and 189 patients with spinal BM were used. The point locations of 631 BM and 674 healthy bone (HB) regions were identified by experts. ROIs with various geometric shapes were centered and automatically delineated on the identified locations, and 107 radiomics features were extracted. Various feature selection methods and machine learning classifiers were evaluated. Our point-based radiomics pipeline was successful in differentiating BM from HB. Lesion-center-based segmentation approach greatly simplifies the process of preparing images for use in radiomics studies and avoids the bottleneck of full ROI segmentation.

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.

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.

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.

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.