Local Data Assimilation in Specification of Open Boundary Conditions

A data assimilation approach to specify open boundary conditions is proposed. The boundary values are determined from the solution of the special optimization problem: minimization of the difference between the model and reference boundary values under the integral constraints on the open boundary. These constraints represent the energy, momentum, and mass fluxes through the open boundary. Reference values represent the a priori knowledge about the boundary values. They might be derived from observations, results of another model run, or from another approach to the specification of open boundary conditions. Optimized open boundary conditions are presented in detail for the barotropic case and when only one integral constraint is considered: energy Aux through the open boundary. It is shown that well-known radiation-type boundary conditions introduced by Reid and Bodine, and Flather, are special cases of the derived optimized conditions. The results of application of the proposed boundary conditions are demonstrated in the modeling of tidal and wind-driven circulation for a channel and for the northern part of the Adriatic Sea. The results of studies of the model predictions\u27 sensitivity to errors in the reference values used in the boundary conditions are presented. The applications of optimized open boundary conditions show a significant reduction in errors when compared to the commonly used, nonoptimized schemes

Local Data Assimilation in the Estimation of Barotropic and Baroclinic Open Boundary Conditions

The problem of data assimilation in the specification of open boundary conditions for limited area models is addressed in this paper. Optimization approaches are detailed, which are based on combining available data on an open boundary with the physics of the hydrodynamical model. In our case the physics is in terms of the flux of energy through the open boundary. These optimized boundary conditions, for both barotropic and baroclinic situations, interpreted physically as special Linearizations of the Bernoulli equation for each normal mode. Because of the complexity of decomposing variables into normal modes for open boundaries with varying bathymetry, we present two alter native approaches. The first is a simplification of the optimized baroclinic boundary condition based on normal modes. The second makes use of empirical orthogonal functions instead of normal modes. The results of testing and comparisons of these approaches are presented for coupling coarse- and fine-resolution models. In this case our approach is in assimilating values and variables from a large-scale model. (along the open boundaries of a limited area model). In the proposed coupling schemes the energy fluxes are estimated either from coarse or from fine-grid model results. With the progress of oceanographic observing systems we would like to explore ways of combining model outputs with the oceanographic measurements in order to estimate energy fluxes used in optimized open boundary conditions

Optimized Boundary Conditions and Data Assimilation with Application to the M-2 Tide in the Yellow Sea

An optimization approach is derived for assimilating tidal height information along the open boundaries of a numerical model. The approach is then extended so that similar data along transects inside a model domain can also be optimally assimilated. To test the application of such an optimized methodology, M-2 tidal simulations were conducted with a numerical ocean model of the Yellow Sea, an area with a strong tidal influence. The use of the optimized open boundary conditions and internal data assimilation leads to a significant improvement of the predictive skill of the model. Average errors can be reduced by up to 75% when compared to nonoptimized boundary conditions

Observed and Modeled Bio-Optical, Bioluminescent, and Physical Properties During a Coastal Upwelling Event in Monterey Bay, California

During spring and summer time, coastal upwelling influences circulation and ecosystem dynamics of the Monterey Bay, California, which is recognized as a National Marine Sanctuary. Observations of physical, bio‐optical properties (including bioluminescence) together with results from dynamical biochemical and bioluminescence models are used to interpret the development of the upwelling event during August 2003 in Monterey Bay, California. Observations and the biochemical model show the development of a phytoplankton bloom in the southern portion of Monterey Bay. Model results show an increase of nutrients in the southern portion of the bay, where nutrient‐rich water masses are brought in by the southward flow and cyclonic circulation inside the bay. This increase in nutrients together with the sluggish circulation in the southern portion of the bay provides favorable conditions for phytoplankton growth. Our observations and models suggest that with the development of upwelling the offshore water masses with the subsurface layer of bioluminescent zooplankton were replaced by water masses advected from the northern coast of the bay with a relatively high presence of mostly nonbioluminescent phytoplankton. Inshore observations from autonomous underwater vehicles (AUVs) show consistent coincidence of chlorophyll, backscatter, and bioluminescence maxima during upwellingdevelopment. Offshore AUV observations (taken at the entrance to the bay) show a deeper bioluminescence maximum below the surface layers of high chlorophyll and backscatter values during the earlier stages of upwelling development. Later, the observed deep offshore bioluminescence maximum disappeared and became a shallower and much weaker signal, coinciding with high chlorophyll and backscatter values offshore. Based on the biochemical and bioluminescence models, a methodology for estimating the nighttime water leaving radiance due to stimulated bioluminescence is demonstrated and evaluated

Can vertical migrations of dinoflagellates explain observed bioluminescence patterns during an upwelling event in Monterey Bay, California?

Extensive AUVs surveys showed that during the development of upwelling, bioluminescent dinoflagellates from the northern part of the Monterey Bay, California (called the upwelling shadow area), were able to avoid advection by southward flowing currents along the entrance to the Bay, while non-bioluminescent phytoplankton were advected by currents. It is known that vertical swimming of dinoflagellates to deeper layers helps them avoid losses due to advection. In the present paper, we investigate if modeling dinoflagellates’ vertical swimming can explain the observed dinoflagellates’ ability to avoid advection during the upwelling development. The dynamics of a dinoflagellate population is modeled with the tracer model with introduced vertical swimming velocity. Three swimming behaviors are considered: sinking, swimming to the target depth and diel vertical migration. Velocities in all swimming cases are considered in the ranges of documented velocities for the observed dinoflagellates species during the upwelling development in the Monterey Bay. Our modeling confirmed that observed bioluminescent dinoflagellates’ avoidance of advection during the upwelling development can be explained by their vertical swimming ability. In the case of swimming with 20 m/day (which is half of observed maximum swimming velocity), around 40% of dinoflagellates population from the northern part of the Bay were advected along the entrance to the Bay in comparison to the case without swimming. This is in agreement with the ratio of around 45% of observed mean bioluminescence intensity at the entrance to the Bay to the observed mean intensity in the northern part of the Bay. This mechanism also helps explain the general persistence of dinoflagellates in this part of the coastline

High-Resolution Sampling of a Broad Marine Life Size Spectrum Reveals Differing Size- and Composition-Based Associations With Physical Oceanographic Structure

Observing multiple size classes of organisms, along with oceanographic properties and water mass origins, can improve our understanding of the drivers of aggregations, yet acquiring these measurements remains a fundamental challenge in biological oceanography. By deploying multiple biological sampling systems, from conventional bottle and net sampling to in situ imaging and acoustics, we describe the spatial patterns of different size classes of marine organisms (several microns to ∼10 cm) in relation to local and regional (m to km) physical oceanographic conditions on the Delaware continental shelf. The imaging and acoustic systems deployed included (in ascending order of target organism size) an imaging flow cytometer (CytoSense), a digital holographic imaging system (HOLOCAM), an In Situ Ichthyoplankton Imaging System (ISIIS, 2 cameras with different pixel resolutions), and multi-frequency acoustics (SIMRAD, 18 and 38 kHz). Spatial patterns generated by the different systems showed size-dependent aggregations and differing connections to horizontal and vertical salinity and temperature gradients that would not have been detected with traditional station-based sampling (∼9-km resolution). A direct comparison of the two ISIIS cameras showed composition and spatial patchiness changes that depended on the organism size, morphology, and camera pixel resolution. Large zooplankton near the surface, primarily composed of appendicularians and gelatinous organisms, tended to be more abundant offshore near the shelf break. This region was also associated with high phytoplankton biomass and higher overall organism abundances in the ISIIS, acoustics, and targeted net sampling. In contrast, the inshore region was dominated by hard-bodied zooplankton and had relatively low acoustic backscatter. The nets showed a community dominated by copepods, but they also showed high relative abundances of soft-bodied organisms in the offshore region where these organisms were quantified by the ISIIS. The HOLOCAM detected dense patches of ciliates that were too small to be captured in the nets or ISIIS imagery. This near-simultaneous deployment of different systems enables the description of the spatial patterns of different organism size classes, their spatial relation to potential prey and predators, and their association with specific oceanographic conditions. These datasets can also be used to evaluate the efficacy of sampling techniques, ultimately aiding in the design of efficient, hypothesis-driven sampling programs that incorporate these complementary technologies

Mesenchymal Stem Cell Therapy for Spinal Cord Contusion: A Comparative Study on Small and Large Animal Models

Here, we provide a first comparative study of the therapeutic potential of allogeneic mesenchymal stem cells derived from bone marrow (BM-MSCs), adipose tissue (AD-MSCs), and dental pulp (DP-MSCs) embedded in fibrin matrix, in small (rat) and large (pig) spinal cord injury (SCI) models during subacute period of spinal contusion. Results of behavioral, electrophysiological, and histological assessment as well as immunohistochemistry and real-time polymerase chain reaction analysis suggest that application of AD-MSCs combined with a fibrin matrix within the subacute period in rats (2 weeks after injury), provides significantly higher post-traumatic regeneration compared to a similar application of BM-MSCs or DP-MSCs. Within the rat model, use of AD-MSCs resulted in a marked change in: (1) restoration of locomotor activity and conduction along spinal axons; (2) reduction of post-traumatic cavitation and enhancing tissue retention; and (3) modulation of microglial and astroglial activation. The effect of an autologous application of AD-MSCs during the subacute period after spinal contusion was also confirmed in pigs (6 weeks after injury). Effects included: (1) partial restoration of the somatosensory spinal pathways; (2) reduction of post-traumatic cavitation and enhancing tissue retention; and (3) modulation of astroglial activation in dorsal root entry zone. However, pigs only partially replicated the findings observed in rats. Together, these results indicate application of AD-MSCs embedded in fibrin matrix at the site of SCI during the subacute period can facilitate regeneration of nervous tissue in rats and pigs. These results, for the first time, provide robust support for the use of AD-MSC to treat subacute SCI

Advances in short bowel syndrome: an updated review

Short bowel syndrome (SBS) continues to be an important clinical problem due to its high mortality and morbidity as well as its devastating socioeconomic effects. The past 3 years have witnessed many advances in the investigation of this condition, with the aim of elucidating the cellular and molecular mechanisms of intestinal adaptation. Such information may provide opportunities to exploit various factors that act as growth agents for the remaining bowel mucosa and may suggest new therapeutic strategies to maintain gut integrity, eliminate dependence on total parenteral nutrition, and avoid the need for intestinal transplantation. This review summarizes current research on SBS over the last few years.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47168/1/383_2005_Article_1500.pd