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Sarcopenia is an increasingly recognized complication of cirrhosis that is associated with morbidity and mortality. Differences in the prevalence and prognosis of sarcopenia between men and women have been reported in other patient groups, but there is insufficient understanding of how sex impacts the prognostic value of sarcopenia in cirrhosis. A search of MEDLINE and Embase was conducted from earliest entries to April 2021. Studies were included if they examined sex‐stratified mortality impact of reduced muscle function or mass in outpatient populations with cirrhosis. We identified 700 studies of which 6 were deemed relevant for inclusion in this narrative review. Studies of interest were heterogeneous, precluding pooling of data and making interpretation of the literature challenging. Muscle mass was assessed in five studies (n= 2566, 1730 men, 836 women) and was reduced in 36–50% of men and 24–43% of women. All five studies found that reduced muscle mass determined by computed tomography, dual‐energy X‐ray absorptiometry, and bioelectrical impedance analysis was associated with increased mortality in men. Of these, two studies identified a corresponding relationship in women; reduced muscle mass defined by computed tomography was associated with increased mortality [hazard ratio (HR) 2.82, P= 0.001], while increasing muscle mass by bioelectrical impedance analysis likewise conferred a survival benefit (HR 0.45, P= 0.0016). Only one study assessed the relationship of muscle function with sex‐stratified mortality (n= 1405, 827 men, 578 women), concluding that reduced muscle function predicted mortality in both men and women (HR 1.65, P< 0.001 and HR 1.54, P< 0.001, respectively). Reduced muscle mass in cirrhosis is consistently associated with mortality in men, but lack of sex‐stratification of mortality analyses limits the ability to make strong conclusions about the impact of sarcopenia specifically in women, with even fewer data available for analysing muscle function. Improved understanding of the sex‐specific impacts of sarcopenia may help address patient deterioration and mortality while awaiting liver transplantation and allow for early intervention to mitigate mortality risk. Large, multicentre studies with adequate female participation and sex‐stratified mortality analyses are warranted.

An accurate representation of physical and biological processes is crucial to resolve larval dispersal pathways and characterize connectivity of coral reef ecosystems. We investigate how hydrodynamic forcings drive larval retention rates during the bi‐annual mass coral spawning of the coral genus Acroporawithin a coral reef atoll (Mermaid Reef), located off northwestern Australia. By analyzing hydrodynamic conditions during 41 yr of historical spring and autumn coral spawning events, we identify typical and extreme hydrodynamic forcing conditions. Particle tracking using the output from a fine‐scale coupled wave‐flow hydrodynamic model forced with typical hydrodynamic conditions during coral spawning, revealed a mean transport of larvae eastward across the atoll. Transport was mainly driven by a combination of wave and tidal currents, where the residual tidal flow and unidirectional wave flow increased the net export of particles, and the oscillatory tidal (non‐residual) flow reduced the net export of particles from the reef. Importantly, however, numerical simulations forced with extreme hydrodynamic conditions generated by episodic tropical cyclones (11 out of 41 yr) showed large deviations from the typical eastward flow during autumn spawning, generating different connectivity pathways within the reef. Considering the substantial time larvae can be retained within reef systems, overlooking fine‐scale hydrodynamic processes may greatly overestimate larval transport distances between adjacent coral reef atolls. As a result, we emphasize the need to consider fine‐scale hydrodynamic processes within regional connectivity predictions, which is generally not considered yet critical to understand the capacity of reefs to recover following disturbances.

A field experiment study of flow transport around a coral reef was conducted at Scott Reef, an offshore atoll in the Timor Sea. A drifter deployment was designed based on the insight derived from two Lagrangian data analysis approaches, the finite‐time Lyapunov exponent method and the optimized‐parameter spectral clustering method, which were used to analyze the predictions of a numerical model. This analysis predicted the formation of a key transport barrier during a critical time of the tidal cycle that separated two bodies of water, one remaining trapped within the lagoon, and one advected offshore; this transport structure had no clear signature upon inspection of the velocity fields and thus the use of Lagrangian methods was crucial. The observed drifter trajectories confirmed the predictions, with the drifters separating into two clusters, one on each side of the transport barrier. The results demonstrate how Lagrangian approaches elucidate the processes governing connectivity and water exchanges between atolls and the surrounding ocean.

Coastal habitats have faced decades of loss caused by urbanization. Global recognition of the ecosystem services that coastal habitats provide has led to an emphasis on cities to adopt nature-based solutions (NBS). However, a broad assessment of urban areas and their potential to conserve remaining coastal habitat has not been undertaken. Here we apply spatial analytics to investigate 5,096 coastal urban areas in tropical and subtropical regions within the distribution of mangroves, tidal flats, seagrass meadows, and coral reefs, and find <50% of urban areas have natural coastal habitats within their extent. Large conservation opportunities for urban areas exist within an adjacent 50 km buffer zone where a significant proportion (93%) of urban-influenced coastal habitat lies and where 26% is currently protected. Potential high-conservation areas across the globe provide a unique opportunity to increase the resilience of urbanizing coasts and NBS for long-term socioeconomic and conservation goals.

Scott Reef is a remote yet biodiverse coral reef atoll, rising from depths > 1000 m on the edge of the continental shelf of northwestern Australia. An intensive 2‐week field study was conducted to assess how physical oceanographic processes influence reef communities in South Scott's deep (~ 50 m) and expansive (~ 300 km2) semi‐enclosed lagoon. The study covered a spring–neap tidal cycle, during which moored instruments measured temperature and velocities at a lagoon entrance and ship‐based vertical profilers measured water quality parameters. Tidally driven internal bores advected cooler and deeper offshore waters (up to 4.5°C, mean 2.4°C) into the lagoon, which were also richer in nutrients and chlorophyll athan lagoon waters. This offshore water originated from approximately 75 m depth. We used the strong observed relationship between in situ measurements of nitrate and temperature to estimate nitrate concentrations from high temporally and spatially resolved temperature measurements at the lagoon entrance, and then estimated the horizontal nitrate fluxes into the lagoon using the velocity measurements. The depth‐integrated, time‐averaged nitrate flux during spring tides (1.46 kg m−1d−1) was over three times larger than during neap tides (0.46 kg m−1d−1), despite a passing tropical storm that temporarily deepened the offshore thermocline and reduced the magnitude of the fluxes. Our observations indicate that colder, deeper, and nutrient‐rich water associated with internal tidal bores during spring tide is likely to be the primary mechanism through which allochtonous nutrients are delivered to benthic and pelagic communities within the lagoon of this isolated atoll.

Shear stresses on vegetated beds play an important role in driving a wide range of processes at the sediment‐water interface, including sediment transport. Existing methods for the estimation of bed shear stress are not applicable to vegetated beds due to the significant alteration of the near‐bed velocity profile and turbulence intensities by the vegetation. In addition, bed shear stress distributions are highly spatially variable in the presence of vegetation. In this study, computational fluid dynamics simulations were used to investigate the spatial variability of bed shear stresses in the presence of emergent vegetation (modeled as arrays of circular cylinders) and the variation of bed stress with characteristics of both the bulk flow and the array. A recently proposed model that assumes a linear variation of stress in the viscous layer immediately above the bed is shown to be a reliable tool for estimating the spatially averaged bed shear stress over a wide range of flow conditions and vegetation densities. However, application of this model is found to be restrictive due to the lack of a reliable predictive tool for the thickness of the viscous layer. Based on a balance between turbulent kinetic energy production in the vegetation stem wakes and the viscous dissipation of turbulent kinetic energy at the bed, an enhanced formulation is proposed to predict the thickness of the viscous layer, which significantly improves the accuracy of model predictions. This improved model enhances the predictive capability for important benthic processes (such as sediment transport) in vegetated aquatic systems. The presence of aquatic vegetation significantly alters the magnitude and spatial variability of bed shear stresses in channel flowsThe Linear Stress Model is found to be a reliable tool for estimating bed stresses within vegetation, modeled as arrays of rigid cylindersModel performance is significantly improved through a new approach for estimating the thickness of the viscous layer immediately above the bed

The hydrodynamics of a tidally forced semi‐enclosed coral reef atoll (North Scott) at the edge of the continental shelf of northwestern Australia were investigated by combining field observations and numerical modeling. The observations revealed that the spring tidal range outside the atoll reaches 4 m, and as the water level drops below mean sea level, the reef rim surrounding the shallow (~10–15 m) lagoon becomes exposed. During this time, the lagoon can only exchange with the open ocean through two narrow channels, resulting in highly asymmetric water levels and velocities that were most pronounced during spring tide. On average, the ebb tide duration was ~2 hr longer than the flood, with rapid flood velocities in the channel reaching 2 m/s. We applied an unstructured grid model Delft3D‐Flexible Mesh to simulate the atoll hydrodynamics and were able to replicate the asymmetric water levels and complex velocities in the lagoon. The results revealed that at higher tidal stages, a dominant momentum balance exists between the pressure gradient (established by the propagation of the tide on the shelf) and the local flow acceleration of water throughout the interior of the atoll. At lower tidal stages, which coincided with a reversal of the offshore tidal pressure gradient, the lagoon became isolated from offshore dynamics and all momentum terms were negligible. This resulted in a tidally averaged residual westward flow within the lagoon that drove an asymmetric flushing pattern within the atoll, which we propose would be a common flushing mechanism within other tide‐dominated atolls worldwide. The hydrodynamics of a tide‐dominated atoll reef system were assessed with field observations and numerical modelingThe semi‐enclosed atoll morphology and large tidal range resulted in highly asymmetric water levels, velocities, and residual flowsA residual east‐west flow, caused by interactions between the phasing of the ocean tide and lagoon water levels, dominated flushing

Similar to the construction of physical ships and laboratory buildings, scientific knowledge is built incrementally and requires solid components of data, theory, and methodology at each phase of the “construction.” The peer‐review process provides the necessary “inspection” and the assurance that every step of the construction is solid, particularly in regard to the proper use of the scientific method. The peer‐review process helps improve the published work by providing constructive suggestions and by safeguarding against scientific work that could later be found to be built on shaky foundations. Because no single scientist has intimate knowledge of today's many aspects of the Ocean Sciences, we rely on each other's expertise to serve as unbiased “inspectors” of published articles. Your considerable time and effort, spent reviewing JGR‐Oceansmanuscript(s) during 2017, are sincerely appreciated by our editorial board and by the Ocean Science community at large. We thank you for rising to this professional challenge and for your wisdom, commitment, skill, and service. Similar to the construction of physical ships and laboratory buildings, scientific knowledge is built incrementally and requires solid components of data, theory, and methodology at each phase of the "construction". The peer review process provides the necessary "inspection" and the assurance that every step of the construction is solid, particularly in regard to the proper use of the scientific method. The peer‐review process helps improve the published work by providing constructive suggestions, and by safe‐guarding against scientific work that could later found to be built on shaky foundations. Because no single scientist has intimate knowledge of today's many aspects of the Ocean Sciences, we rely on each other's expertise to serve as unbiased "inspectors" of published articles. Your considerable time and effort, spent reviewing JGR‐Oceans manuscript(s) during 2017, are sincerely appreciated by our editorial board, and by the Ocean Science community at large. We thank you for rising to this professional challenge, and for your wisdom, commitment, skill, and service. The JGR‐Oceans Editors thank all the peer reviewers from 2017

Owing to their strong forcing of the ocean surface, tropical cyclones strongly modify the hydrodynamics of Australia's North West Shelf (one of the world's tropical cyclone hot spots), which in turn plays a dominant role in its sediment dynamics. Previous modeling studies have focused on describing the short‐term sediment dynamics during individual tropical cyclones but have lacked validation of the responses using field observations. As a consequence, the long‐term cumulative impact of the tropical cyclones on the residual sediment transport pathways at the shelf scale remains unclear. In this study we apply a sediment transport model over the North West Shelf, validate its performance using an extensive field data set, and implement a 14‐year‐long model simulation to assess the sediment fluxes. The model results confirm the overwhelming role tropical cyclones play on sediment transport processes over most of the shelf, despite each cyclone only influencing a small portion of the shelf at a particular time. Overall, we identified 19 tropical cyclone events over the 14‐year period, which, despite accounting for less than 5% of time, were found to drive the majority of both the suspended sediment alongshore and seaward cross‐shore transport. The results revealed significant interannual variability of the tropical cyclone‐induced sediment dynamics with greater suspended transport during the three consecutive Ningaloo Niño years (2011–2013) where sea surface temperatures off northwestern Australia were anomalously warm with elevated tropical cyclone activity. The Australia's North West Shelf ROMS‐COAWST model reproduced the suspended sediment dynamics observed during historical tropical cyclonesOver a 14‐year period tropical cyclones dominate the overall sediment dynamics of the entire shelf despite being relatively infrequentInterannual variability of the sediment dynamics is simulated with increased cyclone activity during three consecutive warm Ningaloo Nino years

Benthic fluxes of chlorophyll a(Chl a) and particulate organic carbon (POC) and nitrogen (PON) were quantified on Tallon reef, a strongly tide‐dominated (spring range > 8 m) reef located in the Kimberley region of northwestern Australia, over a 2‐week period. Extensive hydrodynamic observations were used to construct a reef‐scale mass balance to estimate material exchange between the reef and ocean over individual tidal cycles. Additionally, a one‐dimensional control volume approach was used to estimate fluxes of Chl ain waters traversing the reef platform. Particulate material was delivered to the reef platform in a pulse during flood tide, and benthic uptake of Chl adeclined to negligible values toward the end of ebb tide. On the scale of tidal cycles, a net uptake of Chl awas observed on the reef platform (on average 1.3 mg Chl am−2d−1), which was lower than previous studies of many reef communities. Fluxes showed variability depending on the magnitude of individual tidal cycles, which was likely related to volumes of oceanic Chl ainputs. Tallon reef was a net source of detrital POC and PON to the surrounding coastal ocean, with average POC exports ∼ 3% of the reef's benthic gross primary production. Seasonal measurements of water quality reported here are among the first records for the coastal Kimberley, and suggest that reefs in the west Kimberley may experience naturally elevated levels of phytoplankton and particulate nutrients, especially during the wet season.

Sediment produced on fringing coral reefs that is transported along the bed or in suspension affects ecological reef communities as well as the morphological development of the reef, lagoon, and adjacent shoreline. This study quantified the physical process contribution and relative importance of sea‐swell waves, infragravity waves, and mean currents to the spatial and temporal variability of sediment in suspension. Estimates of bed shear stresses demonstrate that sea‐swell waves are the key driver of the suspended sediment concentration (SSC) variability spatially (reef flat, lagoon, and channels) but cannot fully describe the SSC variability alone. The comparatively small but statistically significant contribution to the bed shear stress by infragravity waves and currents, along with the spatial availability of sediment of a suitable size and volume, is also important. Although intratidal variability in SSC occurs in the different reef zones, the majority of the variability occurs over longer slowly varying (subtidal) timescales, which is related to the arrival of large swell waves at a reef location. The predominant flow pathway, which can transport suspended sediment, consists of cross‐reef flow across the reef flat that diverges in the lagoon and returns offshore through channels. This pathway is primarily due to subtidal variations in wave‐driven flows but can also be driven alongshore by wind stresses when the incident waves are small. Higher frequency (intratidal) current variability also occurs due to both tidal flows and variations in the water depth that influence wave transmission across the reef and wave‐driven currents. Sea‐swell waves drive most suspended sediment variability but infragravity waves and/or mean currents contribute to subtidal variabilityReduced bed stresses within large bottom roughness are still greater than those on a sandy bed within the lagoon without roughnessLimited sediment availability on a reef flat reduces suspended sediment concentrations compared to within reef lagoon and channels

Two marine heat wave events along Western Australia (WA) during the alternate austral summer periods of 2010/2011 and 2012/2013, both linked to La Niña conditions, severely impacted marine ecosystems over more than 12° of latitude, which included the unprecedented bleaching of many coral reefs. Although these two heat waves were forced by similar large‐scale climate drivers, the warming patterns differed substantially between events. The central coast of WA (south of 22°S) experienced greater warming in 2010/2011, whereas the northwestern coast of WA experienced greater warming in 2012/2013. To investigate how oceanic and atmospheric heat exchange processes drove these different spatial patterns, an analysis of the ocean heat budget was conducted by integrating remote sensing observations, in situ mooring data, and a high‐resolution (∼1 km) ocean circulation model (Regional Ocean Modeling System). The results revealed substantial spatial differences in the relative contributions made by heat advection and air‐sea heat exchange between the two heat wave events. During 2010/2011, anomalous warming driven by heat advection was present throughout the region but was much stronger south of 22°S where the poleward‐flowing Leeuwin Current strengthens. During 2012/2013, air‐sea heat exchange had a much more positive (warming) influence on sea surface temperatures (especially in the northwest), and when combined with a more positive contribution of heat advection in the north, this can explain the regional differences in warming between these two La Niña‐associated marine heat wave events. Two marine heat waves affected northwestern Australia during La Nina conditions in the austral summers of 2010/2011 and 2012/2013Substantial spatial differences in the warming patterns occurred due to how heat advection and air‐sea heat exchange differed between eventsAnomalous heat advection drove higher warming in the south in 2010/2011; in 2012/2013 air‐sea heat exchange led to greater warming in the north

Owing to their strong forcing at the air‐sea interface, tropical cyclones are a major driver of hydrodynamics and sediment dynamics of continental shelves, strongly impacting marine habitats and offshore industries. Despite the North West Shelf of Australia being one of the most frequently impacted tropical cyclone regions worldwide, there is limited knowledge of how tropical cyclones influence the sediment dynamics of this shelf region, including the significance of these episodic extreme events to the normal background conditions that occur. Using an extensive 2 year data set of the in situ sediment dynamics and 14 yearlong calibrated satellite ocean‐color data set, we demonstrate that alongshore propagating cyclones are responsible for simultaneously generating both strong wave‐induced sediment resuspension events and significant southwestward subtidal currents. Over the 2 year study period, two particular cyclones (Iggy and Narelle) dominated the sediment fluxes resulting in a residual southwestward sediment transport over the southern part of the shelf. By analyzing results from a long‐term (37 year) wind and wave hindcast, our results suggest that at least 16 tropical cyclones had a strong potential to contribute to that southwestward sediment pathway in a similar way to Iggy and Narelle. Over Australia's North West Shelf, tropical cyclones are the main drivers of suspended sediment dynamicsSuspended sediment during cyclone events results from wave resuspension rather than advection of terrigenous material over most of the shelfThe overall residual shelf sediment pathway is dominated by episodic tropical cyclone events generating southwestward wind‐induced transport spanning the entire shelf

Benthic dissolved oxygen fluxes were measured on the reef flat of Tallon Island, an intertidal reef platform in the Kimberley region of northwestern Australia, for periods of 2 weeks in the wet and dry seasons. This reef flat is strongly tidally forced by semidiurnal tides (spring range > 8 m) and experiences highly asymmetric water level variability, with ebb durations lasting ∼10 h; this results in diel variations in water temperature and dissolved oxygen (DO) concentration (up to ∼11°C and 440 μM, respectively) that are among the most extreme recorded for reefs worldwide. Given the consistent tidal flow patterns, a one‐dimensional control volume approach was used to make continuous Eulerian measurements of net production and community respiration from observed changes in DO within two zones: an inner zone dominated by seagrass and an outer zone dominated by macroalgae. Community respiration (R) was controlled primarily by DO concentration; however, fluxes approached the limits of DO mass transfer at low flow speeds. Estimates of gross primary production (P) suggested that reef communities were able to fix carbon at rates comparable to other tropical seagrass and mixed reef flat communities despite short‐term (∼hours) extremes in light (up to 1800 μmol m−2s−1) and temperature (> 35°C). Daily net community production fluctuated between net autotrophy and heterotrophy over a ∼15 d period depending on the phase difference between the solar and tidal cycles but was nonetheless metabolically balanced on time scales greater than weeks (P : R= 1.0–1.1).

The influence of vegetation canopies on the flow structure in streams, rivers, and floodplains is heavily dependent on the cumulative drag forces exerted by the vegetation. The drag coefficients of vegetation elements within a canopy have been shown to be significantly different from the well‐established value for a single element in isolation. This study investigates the mechanisms that determine canopy flow resistance and proposes a new model for predicting canopy drag coefficients. Large Eddy Simulations were used to investigate the fine‐scale hydrodynamics within emergent canopies with solid area fractions ( λ) ranging from 0.016 to 0.25. The influences of three mechanisms in modifying canopy drag, namely, blockage, sheltering, and delayed separation, were investigated. While the effects of sheltering and delayed separation were found to slightly reduce the drag of very sparse canopies, the blockage effect significantly increased the drag of denser canopies ( λ≳0.04). An analogy between canopy flow and wall‐confined flow around bluff bodies is used to identify an alternative reference velocity in the definition of the canopy drag coefficient; namely, the constricted cross‐section velocity (Uc). Through comparison with both prior experimental data and the present numerical simulations, typical formulations for the drag coefficient of a single cylinder are shown to accurately predict the drag coefficient of staggered emergent canopies when Ucis used as the reference velocity. Finally, it is shown that this new model can be extended to predict the bulk drag coefficient of randomly arranged vegetation canopies. Drag coefficients of vegetation canopies in aquatic flows can significantly exceed those of the canopy elements in isolationThis drag increase is due to the blockage effect, where high velocities adjacent to canopy elements reduce the wake pressureA new formulation for canopy drag coefficients is presented and validated against numerical simulations

During 2015–2016, record temperatures triggered a pan-tropical episode of coral bleaching, the third global-scale event since mass bleaching was first documented in the 1980s. Here we examine how and why the severity of recurrent major bleaching events has varied at multiple scales, using aerial and underwater surveys of Australian reefs combined with satellite-derived sea surface temperatures. The distinctive geographic footprints of recurrent bleaching on the Great Barrier Reef in 1998, 2002 and 2016 were determined by the spatial pattern of sea temperatures in each year. Water quality and fishing pressure had minimal effect on the unprecedented bleaching in 2016, suggesting that local protection of reefs affords little or no resistance to extreme heat. Similarly, past exposure to bleaching in 1998 and 2002 did not lessen the severity of bleaching in 2016. Consequently, immediate global action to curb future warming is essential to secure a future for coral reefs.

The presence of large bottom roughness, such as that formed by benthic organisms on coral reef flats, has important implications for the size, concentration, and transport of suspended sediment in coastal environments. A 3 week field study was conducted in approximately 1.5 m water depth on the reef flat at Ningaloo Reef, Western Australia, to quantify the cross‐reef hydrodynamics and suspended sediment dynamics over the large bottom roughness (∼20–40 cm) at the site. A logarithmic mean current profile consistently developed above the height of the roughness; however, the flow was substantially reduced below the height of the roughness (canopy region). Shear velocities inferred from the logarithmic profile and Reynolds stresses measured at the top of the roughness, which are traditionally used in predictive sediment transport formulations, were similar but much larger than that required to suspend the relatively coarse sediment present at the bed. Importantly, these stresses did not represent the stresses imparted on the sediment measured in suspension and are therefore not relevant to the description of suspended sediment transport in systems with large bottom roughness. Estimates of the bed shear stresses that accounted for the reduced near‐bed flow in the presence of large roughness vastly improved the relationship between the predicted and observed grain sizes that were in suspension. Thus, the impact of roughness, not only on the overlying flow but also on bed stresses, must be accounted for to accurately estimate suspended sediment transport in regions with large bottom roughness, a common feature of many shallow coastal ecosystems. Shear stresses imposed by roughness on the flow are much larger than those acting on bed sedimentSuspended sediment concentrations and fluxes are suppressed by the large reef roughnessAccounting for reduced shear stresses within the roughness improves sediment transport predictions

Nearshore rocky reefs with scales of order 10–100 m are common along the world's coastline and often shape wave‐driven hydrodynamics and shoreline morphology in their lee. The interaction of waves with these reefs generally results in either two or four‐cell mean circulation systems (2CC and 4CC, respectively), with diverging flows behind the reefs and at the shoreline in the 2CC case and flows that diverge in the lee and converge at the shoreline in the 4CC case. By applying a phase‐resolving wave‐flow model to conduct a detailed analysis of mean momentum balances for waves interacting with nearshore reefs, we develop an understanding of the drivers of 2CC and 4CC flow dynamics and how they vary for different reef geometries and wave and water level conditions. The 2CC or 4CC patterns were primarily driven by alongshore pressure gradients toward the exposed (nonreef fronted) or reef‐fronted beach. These alongshore pressure gradients were dependent on the cross‐shore setup dynamics governed by the balance between pressure (i.e., related to the setup) and radiation stress gradients, and mean bottom stresses exerted on the water column. If shoreline wave setup in the lee of the reef was less than the exposed beach, a 4CC pattern developed with convergent flow at the shoreline in the lee of the reef; otherwise, a 2CC emerged with divergent flow at the shoreline. Across the parameter space investigated, reef roughness, distance to the shoreline, and beach slope were the three parameters most likely to change the flow patterns between 2CC and 4CC. Small‐scale nearshore rocky reefs are found worldwide along a variety of sandy and rocky coastlines. Wave breaking over small reefs drives mean alongshore circulation patterns in their lee that may cause shoreline accretion or erosion. In this study, we apply a wave‐flow model to investigate the physical drivers of the mean currents in the lee of small reefs. The alongshore circulation was primarily driven by the differences of the mean water levels between the lee and the adjacent nonreef fronted beaches. Mean water levels increased by wave breaking; however, the onshore‐directed mean flows over the reef created offshore‐directed bottom stresses that reduced the mean water levels in the reef lee. If the shoreline mean water levels in the lee were less than the adjacent beach, alongshore currents that converged from the adjacent beaches toward the reefs were developed. If the shoreline mean water levels in the lee of the reef exceeded the adjacent beach, alongshore currents that diverged from the reef toward the adjacent beach occurred. The improved understanding of the circulation drivers developed in this study enhances our ability to characterize and predict wave‐driven flows in small‐scale nearshore reef systems. Phase‐resolved model simulations were used to understand circulation patterns that occur in the lee of small‐scale reefsTwo‐cell and four‐cell circulation patterns were primarily driven by alongshore pressure gradients, which depend on the setup dynamicsA four‐cell pattern generally developed if the shoreline wave setup in the lee of the reef was less than the adjacent nonreef fronted beach Phase‐resolved model simulations were used to understand circulation patterns that occur in the lee of small‐scale reefs Two‐cell and four‐cell circulation patterns were primarily driven by alongshore pressure gradients, which depend on the setup dynamics A four‐cell pattern generally developed if the shoreline wave setup in the lee of the reef was less than the adjacent nonreef fronted beach

A feedback between seagrass presence, suspended sediment and benthic light can induce bistability between two ecosystem states: one where the presence of seagrass reduces suspended sediment concentrations to increase benthic light availability thereby favoring growth, and another where seagrass absence increases turbidity thereby reducing growth. This literature review identifies (1) how the environmental and seagrass meadow characteristics influence the strength and direction (stabilizing or destabilizing) of the seagrass-sediment-light feedback, and (2) how this feedback has been incorporated in ecosystem models proposed to support environmental decision making. Large, dense seagrass meadows in shallow subtidal, non-eutrophic systems, growing in sediments of mixed grain size and subject to higher velocity flows, have the greatest potential to generate bistability via the seagrass-sediment-light feedback. Conversely, seagrass meadows of low density, area and height can enhance turbulent flows that interact with the seabed, causing water clarity to decline. Using a published field experiment as a case study, we show that the seagrass-sediment-light feedback can induce bistability only if the suspended sediment has sufficient light attenuation properties. The seagrass-sediment-light feedback has been considered in very few ecosystem models. These models have the potential to identify areas where bistability occurs, which is information that can assist in spatial prioritization of conservation and restoration efforts. In areas where seagrass is present and bistability is predicted, recovery may be difficult once this seagrass is lost. Conversely, bare areas where seagrass presence is predicted (without bistability) may be better targets for seagrass restoration than bare areas where bistability is predicted.

Here we synthesize data from previous field and laboratory studies describing how rates of nutrient uptake and metabolite exchange (mass transfer) are related to form drag and bottom stresses (momentum transfer). Reanalysis of this data shows that rates of mass transfer are highly correlated (r2≥ 0.9) with the root of the bottom stress τbot0.4under both waves and currents and only slightly higher under waves (~10%). The amount of mass transfer that can occur per unit bottom stress (or form drag) is influenced by morphological features ranging anywhere from millimeters to meters in scale; however, surface‐scale roughness (millimeters) appears to have little effect on actual nutrient uptake by living reef communities. Although field measurements of nutrient uptake by natural reef communities agree reasonably well with predictions based on existing mass‐momentum transfer relationships, more work is needed to better constrain these relationships for more rugose and morphologically complex communities. Mass‐momentum relationships describing nutrient uptake and metabolite exchange in reef communities are similar under waves and currentsRates of mass transfer per unit bottom stress are likely lower for more morphologically heterogeneous reef communitiesBranch‐scale roughness can increase rates of mass transfer by a factor of 2 or more for the same bottom stress or form drag

We investigate the influence of wind stresses, stratification, and coastal mesoscale eddies on upwelling intensity, vertical nutrient fluxes, and phytoplankton biomass on the continental shelf off Ningaloo Reef in northwestern Australia during an austral spring‐summer period. A three‐dimensional (3‐D) hydrodynamic model, ROMS (Regional Ocean Modeling System), was coupled with a four‐component nitrogen‐based biogeochemical NPZD model (Nitrogen Phytoplankton Zooplankton Detritus) to resolve the shelf circulation as well as the coupled nutrient and phytoplankton dynamics within a broad shelf region surrounding Ningaloo Reef. The simulated currents, temperatures, and chlorophyll aconcentrations generally agreed well with both the remotely sensed satellite images and observational data collected during a field experiment from September to November 2010. Scenario tests for an individual wind‐driven upwelling event under a variety of hypothetical physical forcing conditions showed that shelf currents and biogeochemical variables were largely a function of wind stress and stratification. However, the functional relationships derived from this single wind event could not be extrapolated to other periods of the upwelling season, due to the additional influence of 3‐D mesoscale processes on the shelf. The presence, intensification, and propagation of a coastal anticyclonic eddy during the study period strongly influenced the spatial and temporal variations in nutrient profiles, which in turn caused fluctuations in vertical nutrient fluxes that were largely independent of wind stress. These results emphasize that it is necessary to fully capture the 3‐D details of the mesoscale and submesoscale coastal dynamics to properly predict upwelling‐induced coastal phytoplankton dynamics in eddy‐intensive shelf regions such as Ningaloo Reef. ROMS simulation captured the measured physical and pelagic processesWind stress and stratification affect coastal upwelling and biogeochemistryEddies influence vertical nutrient fluxes during wind‐driven upwelling

Wave breaking on the steep fore‐reef slopes of shallow fringing reefs can be effective at dissipating incident sea‐swell waves prior to reaching reef shorelines. However, wave setup and free infragravity waves generated during the sea‐swell breaking process are often the largest contributors to wave‐driven water levels (wave runup) at the shoreline. Laboratory flume experiments and a two‐dimensional vertical phase‐resolving nonhydrostatic wave‐flow model, which includes a canopy model to predict drag forces generated by roughness elements, were used to investigate wave‐driven water levels for along‐shore uniform fringing reefs. In contrast to many previous studies, both the laboratory experiment and the numerical model account for the effects of large bottom roughness. The numerical model reproduced the observations of the wave transformation and runup over both smooth and rough reef profiles. The numerical model was then extended to quantify the influence of reef geometry and compared to simulations of plane beaches lacking a reef. For a fixed offshore forcing condition, the fore‐reef slope controlled wave runup on reef‐fronted beaches, whereas the beach slope controlled wave runup on plane beaches. As a result, the coastal protection utility of reefs is dependent on these slopes. For our examples, with a fore‐reef slope of 1/5 and a 500 m prototype reef flat length, a beach slope of ∼1/30 marked the transition between the reef providing runup reduction for steeper beach slopes and enhancing wave runup for milder slopes. Roughness coverage, spacing, dimensions, and drag coefficient were investigated, with results indicating the greatest runup reductions were due to tall roughness elements on the reef flat. Wave breaking and bottom friction are effective at reducing incident sea‐swell waves before they can reach the shoreline of reef‐fronted coastlines. However, globally, mass mortality of coral reef‐building organisms is causing coral reefs to become structurally flatter, a process that may lower wave dissipation. Laboratory flume experiments and a multilayer phase‐resolving wave‐flow model that includes drag forces generated by roughness elements (representing coral reef forms) were used to investigate wave‐driven water levels in the lee of fringing reefs and assess the influence of reef geometry and roughness characteristics. The numerical model was able to reproduce laboratory observations of waves and water levels over both smooth and rough reef profiles. Wave runup, the vertical extent of wave uprush on a beach, was sensitive to the presence and characteristics of roughness. Roughness coverage, spacing, and dimensions were investigated with results indicating the greatest runup reductions were due to tall roughness elements on the reef flat. SWASH reproduced laboratory observations of waves and runup over both smooth and rough fringing reefsFore‐reef slope controls wave runup on reef‐fringed coasts as opposed to beach slope on plane open coast beachesWave runup was sensitive to bottom roughness with tall roughness elements on the reef flat generating the greatest runup reduction SWASH reproduced laboratory observations of waves and runup over both smooth and rough fringing reefs Fore‐reef slope controls wave runup on reef‐fringed coasts as opposed to beach slope on plane open coast beaches Wave runup was sensitive to bottom roughness with tall roughness elements on the reef flat generating the greatest runup reduction

IMPORTANCE: Most patients with asthma take fewer than half of prescribed doses of controller medication. Interventions to improve adherence have typically been costly, impractical, and at best only minimally successful. OBJECTIVE: To test a speech recognition (SR) intervention to improve adherence to pediatric asthma controller medication. DESIGN, SETTING, AND PARTICIPANTS: The Breathe Well study was a 24-month pragmatic randomized clinical trial. The study was conducted within Kaiser Permanente Colorado, a large, group-model health maintenance organization. A total of 1187 children aged 3 to 12 years with a persistent asthma diagnosis and prescription for an inhaled corticosteroid were randomized to the computerized SR intervention or usual care condition and followed up for 24 months between October 2009 and February 2013. INTERVENTIONS: Speech recognition telephone calls to parents in the intervention condition were triggered when an inhaled corticosteroid refill was due or overdue. Calls were automatically tailored with medical and demographic information from the electronic health record and from parent answers to questions in the call regarding recent refills or a desire to receive help refilling, learn more about asthma control, or speak with an asthma nurse or pharmacy staff member. MAIN OUTCOMES AND MEASURES: Adherence to pediatric asthma controller medication, measured as the medication possession ratio over 24 months. RESULTS: In the intention-to-treat analysis, inhaled corticosteroid adherence was 25.4% higher in the intervention group than in the usual care group (24-month mean [SE] adherence, 44.5% [1.2%] vs 35.5% [1.1%], respectively; P &lt; .001). Asthma-related urgent care events did not differ between the 2 groups. The intervention effect was consistent in subgroups stratified by age, sex, race/ethnicity, body mass index, and disease-related characteristics. CONCLUSIONS AND RELEVANCE: The intervention’s significant impact on adherence demonstrates strong potential for low-cost SR adherence programs integrated with an electronic health record. The absence of change in urgent care visits may be attributable to the already low number of asthma urgent care visits within Kaiser Permanente Colorado. Application of electronic health record–leveraged SR interventions may reduce health care utilization when applied in a population with less-controlled asthma. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT00958932

Although the oceans play a fundamental role in shaping the distribution and function of coral reefs worldwide, a modern understanding of the complex interactions between ocean and reef processes is still only emerging. These dynamics are especially challenging owing to both the broad range of spatial scales (less than a meter to hundreds of kilometers) and the complex physical and biological feedbacks involved. Here, we review recent advances in our understanding of these processes, ranging from the small-scale mechanics of flow around coral communities and their influence on nutrient exchange to larger, reef-scale patterns of wave- and tide-driven circulation and their effects on reef water quality and perceived rates of metabolism. We also examine regional-scale drivers of reefs such as coastal upwelling, internal waves, and extreme disturbances such as cyclones. Our goal is to show how a wide range of ocean-driven processes ultimately shape the growth and metabolism of coral reefs.

Laboratory experiments were performed in which an intrusive gravity current was observed using shadowgraph and particle tracking methods. The intrusion was generated in a two-layer fluid with a sharp interface by mixing the fluid behind a vertical lock gate and then suddenly withdrawing the gate from the tank. The purpose of the experiments was to determine the structure of the velocity field inside the intrusion and the stability characteristics of the interface. Soon after the removal of the lock gate, the front of the intrusive gravity current travelled at a constant speed close to the value predicted by theory for an energy-conserving gravity current. The observed structure of the flow inside the intrusion can be divided into three regions. At the front of the intrusion there is an energy-conserving head region in which the fluid velocity is nearly uniform with speed equal to the front speed. This is followed by a dissipative wake region in which large billows are present with their associated mixing and in which the fluid velocity is observed to be non-uniform and have a maximum speed approximately 50% greater than the front speed. Behind the wake region is a tail region in which there is very little mixing and the velocity field is nearly uniform with a speed slightly faster than the front speed.

Two‐dimensional mean wave‐driven flow and setup dynamics were investigated at a reef‐lagoon system at Ningaloo Reef, Western Australia, using the numerical wave‐flow model, SWASH. Phase‐resolved numerical simulations of the wave and flow fields, validated with highly detailed field observations (including >10 sensors through the energetic surf zone), were used to quantify the main mechanisms that govern the mean momentum balances and resulting mean current and setup patterns, with particular attention to the role of nonlinear wave shapes. Momentum balances from the phase‐resolved model indicated that onshore flows near the reef crest were primarily driven by the wave force (dominated by radiation stress gradients) due to intense breaking, whereas the flow over the reef flat and inside the lagoon and channels was primarily driven by a pressure gradient. Wave setup inside the lagoon was primarily controlled by the wave force and bottom stress. The bottom stress reduced the setup on the reef flat and inside the lagoon. Excluding the bottom stress contribution in the setup balance resulted in an over prediction of the wave‐setup inside the lagoon by up to 200–370%. The bottom stress was found to be caused by the combined presence of onshore directed wave‐driven currents and (nonlinear) waves. Exclusion of the bottom stress contribution from nonlinear wave shapes led to an over prediction of the setup inside the lagoon by approximately 20–40%. The inclusion of the nonlinear wave shape contribution to the bottom stress term was found to be particularly relevant in reef regions that experience a net onshore mass flux over the reef crest. Coral reefs that are located in close proximity to a coastline are typically characterized by a steep slope and reef crest that is connected to the coast or front a shallow lagoon. At the reef crest, waves break and drive onshore‐directed currents and elevate the mean (time‐averaged) water level in the lagoon. In this study, we combined measurements of waves, currents and water levels with simulations from an advanced computer model to understand the physical mechanisms that determine the current patterns and water level variations at a coral reef‐lagoon system in Western Australia. Friction generated by the water moving over the rough reef structures was found to reduce the mean water levels inside the lagoon. This friction was explained by the combined presence of both waves and mean currents. Furthermore, near the reef crest, the waves peak and pitch forward before they break, and this nonlinear wave shape was found to enhance the friction from the bottom. This contribution from nonlinear wave shapes however, is generally not accurately described in larger‐scale computer models and should be included in such computer models to provide more reliable simulations of the water motion in coral reefs. The numerical wave‐flow model, SWASH, reproduced highly detailed field measurements of waves and currents through the surf zone of a reef‐lagoon system (Ningaloo Reef, AU)Wave setup inside the lagoon was reduced by bottom stresses generated by the combined action of waves and currentsExclusion of the bottom stress contribution from nonlinear wave shapes resulted in a 20%–40% over prediction of the setup inside the lagoon The numerical wave‐flow model, SWASH, reproduced highly detailed field measurements of waves and currents through the surf zone of a reef‐lagoon system (Ningaloo Reef, AU) Wave setup inside the lagoon was reduced by bottom stresses generated by the combined action of waves and currents Exclusion of the bottom stress contribution from nonlinear wave shapes resulted in a 20%–40% over prediction of the setup inside the lagoon

Coral reefs generate substantial volumes of carbonate sediment, which is redistributed throughout the reef‐lagoon system. However, there is little understanding of the specific processes that transport this sediment produced on the outer portions of coral reefs throughout a reef‐lagoon system. Furthermore, the separate contributions of currents, sea‐swell waves, and infragravity waves to transport, which are all strongly influenced by the presence of a reef, is not fully understood. Here, we show that in reef‐lagoon systems most suspended sediment is transported close to the seabed and can, at times, be suspended higher in the water column during oscillatory flow transitions (i.e., near slack flow) at sea‐swell wave frequencies, and during the peak onshore oscillatory velocity phase at infragravity wave frequencies. While these wave frequencies contribute to the transport of suspended sediment offshore and onshore, respectively, the net flux is small. Mean currents are the primary transport mechanism and responsible for almost 2 orders of magnitude more suspended‐sediment flux than sea‐swell and infragravity waves. Whilst waves may not be the primary mechanism for the transport of sediment, our results suggest they are an important driver of sediment suspension from the seabed, as well as contributing to the partitioning of sediment grain sizes from the reef to the shoreline. As the ocean wave climate changes, sea level rises, and the composition of reef benthic communities change, the relative importance of mean currents, sea‐swell waves, and infragravity waves is likely to change, and this will affect how sediment is redistributed throughout reef‐lagoon systems. Most of the sandy sediment found on coral reef coastlines is produced by organisms living within the reef. This sediment is then transported by waves and currents across the reef and distributed throughout the lagoon. Little is known about these transport processes, including the relative importance of how currents or different types of waves drive transport. This study shows that most of the sediment in the water column (suspended sediment) is transported close to the seabed by mean currents. At times, this sediment can be suspended higher in the water column by short waves (5–25 s) when the flow transitions from being onshore directed to offshore directed, or when the velocities of longer period waves (25–250 s), called infragravity waves, are directed onshore. The timing of the suspension by these waves helps to sort the sediment into different sizes across the system, but the quantity of sediment transported is small. As the ocean wave climate changes, sea level rises, and reefs change, the relative importance of mean currents, sea‐swell waves, and infragravity waves is also likely to change, and this will affect how sediment is redistributed throughout reef‐lagoon systems. This study provides insight into what changes may be expected. Sediment transported in suspension is 3–4 times lower than sediment transported as bedloadSediment transported in suspension by mean currents is 2 orders of magnitude greater than sediment transported by wavesSea‐swell waves typically transport sediment offshore and infragravity waves and mean currents typically transport sediment onshore Sediment transported in suspension is 3–4 times lower than sediment transported as bedload Sediment transported in suspension by mean currents is 2 orders of magnitude greater than sediment transported by waves Sea‐swell waves typically transport sediment offshore and infragravity waves and mean currents typically transport sediment onshore

The editors thank the 2019 peer reviewers

The physical roughness (canopies) formed by organisms within aquatic ecosystems (e.g., seagrass, kelp, and mangroves) modifies the local wave‐driven hydrodynamics within coastal and estuarine regions. In wave‐dominated environments, an understanding of the mean wave‐driven flows generated within and above canopies is important, as it governs material transport (e.g., of nutrients, sediment, and biota). However, until recently the effect of submerged canopies on wave‐current interactions and the resulting mean (wave‐averaged) flow dynamics has received relatively little attention. In this study, a combination of wave flume experiments and numerical modeling is used to investigate the wave‐induced mean flow profiles in the presence of a submerged canopy. The measured velocities and vegetation forces were used to derive bulk drag and inertia coefficients, and to validate a nonhydrostatic 2DV wave‐flow model. The numerical model results were used to conduct an in‐depth analysis of the mean horizontal momentum terms responsible for driving the mean (horizontal) flow within and above the submerged canopies. We show that the mean canopy hydrodynamics are driven by vertical gradients in wave and turbulent Reynolds stresses, balanced by the mean canopy drag forces. The wave Reynolds stress gradient is the dominant force driving the in‐canopy mean flow and is directly related to the vorticity that is generated when the wave orbital motions become rotational near the canopy interface. This study provides new insight in the mechanisms responsible for wave‐driven mean flows within submerged canopies and guidance for how these hydrodynamics can be predicted in coastal wave‐circulation models. Aquatic plants that grow in estuaries and coastal oceans (such as seagrass, kelp, and mangroves) have a considerable influence on water flow (currents) and on waves propagating toward the shore. However, mean flows generated by the waves interacting with aquatic vegetation (with time scales much longer than the individual wave periods) have not been comprehensively studied. This study provides a description of how submerged vegetation alters the mean wave‐driven flow structure. A combination of detailed experiments conducted in a wave flume and numerical simulations are used to show that the mean flow just above the vegetation is relatively strong (up to 20% to 50% of the maximum wave velocity above the canopy), while it is considerably weaker inside the vegetation. We identified three forces that govern the mean current profile: the wave Reynolds stress gradient, the turbulent Reynolds stress gradient, and the vegetation drag force. These forces are usually not accurately described in larger‐scale computer simulations of coastal processes. However, reliable simulation of processes in the coastal ocean such as sediment transport and nutrient exchange requires an accurate prediction of mean flows, and thus these forces need to be properly incorporated in computer models when applied to regions with aquatic vegetation. Physical and numerical modeling is used to investigate the wave‐induced mean flow profiles in the presence of submerged vegetationThe multilayered phase‐resolving wave‐ flow model was able to accurately reproduce the depth variation of the wave‐driven mean flow profilesWave‐driven mean flows inside vegetation canopies are driven by vertical gradients in the wave and turbulent Reynolds stresses

The article presents the poem "The Box," by Ryan Lowe. First Line: Glass breaks over my face; Last Line: So I turn my TV off.