Ensemble optimal interpolation for adjoint-free biogeochemical data assimilation.

Advanced marine ecosystem models can contain more than 100 biogeochemical variables, making data assimilation for these models a challenging prospect. Traditional variational data assimilation techniques like 4dVar rely on tangent linear and adjoint code, which can be difficult to create for complex ecosystem models with more than a few dozen variables. More recent hybrid ensemble-variational data assimilation techniques use ensembles of model forecasts to produce model statistics and can thus avoid the need for tangent linear or adjoint code. We present a new implementation of a four-dimensional ensemble optimal interpolation (4dEnOI) technique for use with coupled physical-ecosystem models. Our 4dEnOI implementation uses a small ensemble, and spatial and variable covariance localization to create reliable flow-dependent statistics. The technique is easy to implement, requires no tangent linear or adjoint code, and is computationally suitable for advanced ecosystem models. We test the 4dEnOI implementation in comparison to a 4dVar technique for a simple marine ecosystem model with 4 biogeochemical variables, coupled to a physical circulation model for the California Current System. In these tests, our 4dEnOI reference implementation performs similarly well to the 4dVar benchmark in lowering the model observation misfit. We show that the 4dEnOI results depend heavily on covariance localization generally, and benefit from variable localization in particular, when it is applied to reduce the coupling strength between the physical and biogeochemical model and the biogeochemical variables. The 4dEnOI results can be further improved by small modifications to the algorithm, such as multiple 4dEnOI iterations, albeit at additional computational cost.

Dual number-based variational data assimilation: Constructing exact tangent linear and adjoint code from nonlinear model evaluations.

Dual numbers allow for automatic, exact evaluation of the numerical derivative of high-dimensional functions at an arbitrary point with minimal coding effort. We use dual numbers to construct tangent linear and adjoint model code for a biogeochemical ocean model and apply it to a variational (4D-Var) data assimilation system when coupled to a realistic physical ocean circulation model with existing data assimilation capabilities. The resulting data assimilation system takes modestly longer to run than its hand-coded equivalent but is considerably easier to implement and updates automatically when modifications are made to the biogeochemical model, thus making its maintenance with code changes trivial.

Fit to predict? Eco-informatics for predicting the catchability of a pelagic fish in near real time.

The ocean is a dynamic environment inhabited by a diverse array of highly migratory species, many of which are under direct exploitation in targeted fisheries. The timescales of variability in the marine realm coupled with the extreme mobility of ocean-wandering species such as tuna and billfish complicates fisheries management. Developing eco-informatics solutions that allow for near real-time prediction of the distributions of highly mobile marine species is an important step towards the maturation of dynamic ocean management and ecological forecasting. Using 25 yr (1990-2014) of NOAA fisheries' observer data from the California drift gillnet fishery, we model relative probability of occurrence (presence-absence) and catchability (total catch per gillnet set) of broadbill swordfish Xiphias gladius in the California Current System. Using freely available environmental data sets and open source software, we explore the physical drivers of regional swordfish distribution. Comparing models built upon remotely sensed data sets with those built upon a data-assimilative configuration of the Regional Ocean Modelling System (ROMS), we explore trade-offs in model construction, and address how physical data can affect predictive performance and operational capacity. Swordfish catchability was found to be highest in deeper waters (>1,500 m) with surface temperatures in the 14-20°C range, isothermal layer depth (ILD) of 20-40 m, positive sea surface height (SSH) anomalies, and during the new moon (<20% lunar illumination). We observed a greater influence of mesoscale variability (SSH, wind speed, isothermal layer depth, eddy kinetic energy) in driving swordfish catchability (total catch) than was evident in predicting the relative probability of presence (presence-absence), confirming the utility of generating spatiotemporally dynamic predictions. Data-assimilative ROMS circumvent the limitations of satellite remote sensing in providing physical data fields for species distribution models (e.g., cloud cover, variable resolution, subsurface data), and facilitate broad-scale prediction of dynamic species distributions in near real time.

Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific.

At small spatial and temporal scales, genetic differentiation is largely controlled by constraints on gene flow, while genetic diversity across a species' distribution is shaped on longer temporal and spatial scales. We assess the hypothesis that oceanographic transport and other seascape features explain different scales of genetic structure of giant kelp, Macrocystis pyrifera. We followed a hierarchical approach to perform a microsatellite-based analysis of genetic differentiation in Macrocystis across its distribution in the northeast Pacific. We used seascape genetic approaches to identify large-scale biogeographic population clusters and investigate whether they could be explained by oceanographic transport and other environmental drivers. We then modelled population genetic differentiation within clusters as a function of oceanographic transport and other environmental factors. Five geographic clusters were identified: Alaska/Canada, central California, continental Santa Barbara, California Channel Islands and mainland southern California/Baja California peninsula. The strongest break occurred between central and southern California, with mainland Santa Barbara sites forming a transition zone between the two. Breaks between clusters corresponded approximately to previously identified biogeographic breaks, but were not solely explained by oceanographic transport. An isolation-by-environment (IBE) pattern was observed where the northern and southern Channel Islands clustered together, but not with closer mainland sites, despite the greater distance between them. The strongest environmental association with this IBE pattern was observed with light extinction coefficient, which extends suitable habitat to deeper areas. Within clusters, we found support for previous results showing that oceanographic connectivity plays an important role in the population genetic structure of Macrocystis in the Northern hemisphere.

Regional ocean data assimilation.

This article reviews the past 15 years of developments in regional ocean data assimilation. A variety of scientific, management, and safety-related objectives motivate marine scientists to characterize many ocean environments, including coastal regions. As in weather prediction, the accurate representation of physical, chemical, and/or biological properties in the ocean is challenging. Models and observations alone provide imperfect representations of the ocean state, but together they can offer improved estimates. Variational and sequential methods are among the most widely used in regional ocean systems, and there have been exciting recent advances in ensemble and four-dimensional variational approaches. These techniques are increasingly being tested and adapted for biogeochemical applications.

Modeled diversity effects on microbial ecosystem functions of primary production, nutrient uptake, and remineralization.

Ecosystem-wide primary productivity generally increases with primary producer diversity, emphasizing the importance of diversity for ecosystem function. However, most studies that demonstrate this positive relationship have focused on terrestrial and aquatic benthic systems, with little attention to the diverse marine pelagic primary producers that play an important role in regulating global climate. Here we show how phytoplankton biodiversity enhances overall marine ecosystem primary productivity and other ecosystem functions using a self-organizing ecosystem model. Diversity manipulation numerical experiments reveal positive, asymptotically saturating relationships between ecosystem-wide phytoplankton diversity and functions of productivity, nutrient uptake, remineralization, and diversity metrics used to identify mechanisms shaping these relationships. Increase in productivity with increasing diversity improves modeled ecosystem stability and model robustness and leads to productivity rates that exceed expected yields primarily through niche complementarity and facilitative interactions between coexisting phytoplankton types; the composition of traits in assemblages determines the magnitude of complementarity and selection effects. While findings based on these aggregate measures of diversity effects parallel those from the majority of experimental outcomes of terrestrial and benthic biodiversity-ecosystem function studies, we combine analyses of community diversity effects and investigations of the underlying interactions among phytoplankton types to demonstrate how an increase in recycled production of non-diatoms through an increase in new production of diatoms drives this diversity-cosystem function response. We demonstrate the important role that facilitation plays in the modeled marine plankton and how this facilitative interaction could amplify future climate-driven changes in ocean ecosystem productivity.

Abundance and distribution of major groups of diazotrophic cyanobacteria and their potential contribution to N2 fixation in the tropical Atlantic Ocean.

The abundances of six N2-fixing cyanobacterial phylotypes were profiled at 22 stations across the tropical Atlantic Ocean during June 2006, and used to model the contribution of the diazotrophs to N2 fixation. Diazotroph abundances were measured by targeting the nifH gene of Trichodesmium, unicellular groups A, B, C (UCYN-A, UCYN-B and UCYN-C), and diatom-cyanobiont symbioses Hemiaulus-Richelia, Rhizosolenia-Richelia and Chaetoceros-Calothrix. West to east gradients in temperature, salinity and nutrients [NO3⁻ + NO2⁻, PO4³â», Si(OH)4] showed the influence of the Amazon River plume and its effect on the distributions of the diazotrophs. Trichodesmium accounted for more than 93% of all nifH genes detected, dominated the warmer waters of the western Atlantic, and was the only diazotroph detected at the equatorial upwelling station. UCYN-A was the next most abundant (> 5% of all nifH genes) and dominated the cooler waters of the eastern Atlantic near the Cape Verde Islands. UCYN-C was found at a single depth (200 m) of high salinity and low temperature and nutrients, whereas UCYN-B cells were widespread but in very low abundance (6.1 × 10¹ ± 4.6 × 10² gene copies l⁻¹). The diatom-cyanobionts were observed primarily in the western Atlantic within or near the high Si(OH)4 input of the Amazon River plume. Overall, highest diazotroph abundances were observed at the surface and declined with depth, except for some subsurface peaks in Trichodesmium, UCYN-B and UCYN-A. Modelled contributions of Trichodesmium, UCYN-B and UCYN-A to total N2 fixation suggested that Trichodesmium had the largest input, except for the potential of UCYN-A at the Cape Verde Islands.

Management of anastomotic leaks after Roux-en-Y bypass using self-expanding polyester stents.

BACKGROUND: To analyze the outcomes of a series of endoscopically placed polyester self-expanding polyflex stents (SEPSs) for the management of anastomotic leaks after Roux-en-Y bypass. Anastomotic leaks after gastric bypass cause significant morbidity and mortality. Covered polyester SEPSs might have a role in the treatment of these leaks. METHODS: A retrospective chart review was performed from January 2006 to November 2006 that included all acute and chronic leaks treated with SEPSs. RESULTS: A total of 6 patients were treated with stents, with a mean procedure time of 22 minutes. Of these 6 patients, 5 had acute postoperative leaks and 1 had a chronic fistula. Five patients started oral intake 1-6 days after their procedure. All acute leaks had complete healing at a median of 44 days. The patient with a chronic gastrocutaneous fistula required revisional surgery for fistula closure. In addition, 5 patients had stent migration, and 3 required stent replacement. CONCLUSION: An endoscopically placed SEPS provides a less-invasive alternative to treat acute anastomotic leaks after Roux-en-Y bypass while simultaneously allowing oral intake. The results of this case series have demonstrated this treatment to be safe and effective.

Use of endoscopic stents to treat anastomotic complications after bariatric surgery.

BACKGROUND: Complications after bariatric surgery often require longterm parenteral nutrition to achieve healing. Recently, endoscopic treatments have become available that provide healing while allowing for oral nutrition. The purpose of this study was to present outcomes of the largest series to date treating staple line complications after bariatric surgery with endoscopic covered stents. STUDY DESIGN: A retrospective evaluation was performed of all patients treated for staple line complications after bariatric surgery at a single tertiary care bariatric center. Acute postoperative leaks, chronic gastrocutaneous fistulas, and anastomotic strictures refractory to endoscopic dilation after both gastric bypass and sleeve gastrectomy were included. RESULTS: From January 2006 to June 2007, 19 patients (11 with acute leaks, 2 with chronic fistulas, and 6 with strictures) were treated with a total of 34 endoscopic silicone covered stents (23 polyester, 11 metal). Mean followup was 3.6 months. Immediate symptomatic improvement occurred in 90% (91% of acute leaks, 100% of fistulas, and 84% of strictures). Oral feeding was started in 79% of patients immediately after stenting. Resolution of leak or stricture after stent treatment occurred in 16 of 19 patients (84%). Healing of leak, fistula, and stricture occurred at means of 33 days, 46 days, and 7 days, respectively. Three patients (1 with leak, 1 with fistula, and 1 with stricture) had unsuccessful stent treatment. Migration of the stent occurred in 58% of 34 stents placed. Most migration was minimal, but three stents were removed surgically after distal small bowel migration. There was no mortality. CONCLUSIONS: Treatment of anastomotic complications after bariatric surgery with endoscopic covered stents allows rapid healing while simultaneously allowing for oral nutrition. The primary morbidity is stent migration.

GROWTH AND CARBON CONTENT OF THREE DIFFERENT-SIZED DIAZOTROPHIC CYANOBACTERIA OBSERVED IN THE SUBTROPICAL NORTH PACIFIC(1).

To develop tools for modeling diazotrophic growth in the open ocean, we determined the maximum growth rate and carbon content for three diazotrophic cyanobacteria commonly observed at Station ALOHA (A Long-term Oligotrophic Habitat Assessment) in the subtropical North Pacific: filamentous nonheterocyst-forming Trichodesmium and unicellular Groups A and B. Growth-irradiance responses of Trichodesmium erythraeum Ehrenb. strain IMS101 and Crocosphaera watsonii J. Waterbury strain WH8501 were measured in the laboratory. No significant differences were detected between their fitted parameters (±CI) for maximum growth rate (0.51 ± 0.09 vs. 0.49 ± 0.17 d(-1) ), half-light saturation (73 ± 29 vs. 66 ± 37 µmol quanta · m(-2) · s(-1) ), and photoinhibition (0 and 0.00043 ± 0.00087 [µmol quanta · m(-2) · s(-1) ](-1) ). Maximum growth rates and carbon contents of Trichodesmium and Crocosphaera cultures conformed to published allometric relationships, demonstrating that these relationships apply to oceanic diazotrophic microorganisms. This agreement promoted the use of allometric models to approximate unknown parameters of maximum growth rate (0.77 d(-1) ) and carbon content (480 fg C · µm(-3) ) for the uncultivated, unicellular Group A cyanobacteria. The size of Group A was characterized from samples from the North Pacific Ocean using fluorescence-activated cell sorting and real-time quantitative PCR techniques. Knowledge of growth and carbon content properties of these organisms facilitates the incorporation of different types of cyanobacteria in modeling efforts aimed at assessing the relative importance of filamentous and unicellular diazotrophs to carbon and nitrogen cycling in the open ocean.

Modeled contributions of three types of diazotrophs to nitrogen fixation at Station ALOHA.

A diagnostic model based on biomass and growth was used to assess the relative contributions of filamentous nonheterocystous Trichodesmium and unicellular cyanobacteria, termed Groups A and B, to nitrogen fixation at the North Pacific Station ALOHA over a 2-year period. Average (and 95% confidence interval, CI) annual rates of modeled monthly values for Trichodesmium, Group B and Group A were 92 (52), 14 (4) and 12 (8) mmol N per m(2) per year, respectively. The fractional contribution to modeled instantaneous nitrogen fixation by each diazotroph fluctuated on interannual, seasonal and shorter time scales. Trichodesmium fixed substantially more nitrogen in year 1 (162) than year 2 (12). Group B fixed almost two times more nitrogen in year 1 (17) than year 2 (9). In contrast, Group A fixed two times more nitrogen in year 2 (16) than year 1 (8). When including uncertainties in our estimates using the bootstrap approach, the range of unicellular nitrogen fixation extended from 10% to 68% of the total annual rate of nitrogen fixation for all three diazotrophs. Furthermore, on a seasonal basis, the model demonstrated that unicellular diazotrophs fixed the majority (51%-97%) of nitrogen during winter and spring, whereas Trichodesmium dominated nitrogen fixation during summer and autumn (60%-96%). Sensitivity of the modeled rates to some parameters suggests that this unique attempt to quantify relative rates of nitrogen fixation by different diazotrophs may need to be reevaluated as additional information on cell size, variability in biomass and C:N, and growth characteristics of the different cyanobacterial diazotrophs become available.

Modelling the vertical distribution of Prochlorococcus and Synechococcus in the North Pacific Subtropical Ocean.

A simple model was developed to examine the vertical distribution of Prochlorococcus and Synechococcus ecotypes in the water column, based on their adaptation to light intensity. Model simulations were compared with a 14-year time series of Prochlorococcus and Synechococcus cell abundances at Station ALOHA in the North Pacific Subtropical Gyre. Data were analysed to examine spatial and temporal patterns in abundances and their ranges of variability in the euphotic zone, the surface mixed layer and the layer in the euphotic zone but below the base of the mixed layer. Model simulations show that the apparent occupation of the whole euphotic zone by a genus can be the result of a co-occurrence of different ecotypes that segregate vertically. The segregation of ecotypes can result simply from differences in light response. A sensitivity analysis of the model, performed on the parameter alpha (initial slope of the light-response curve) and the DIN concentration in the upper water column, demonstrates that the model successfully reproduces the observed range of vertical distributions. Results support the idea that intermittent mixing events may have important ecological and geochemical impacts on the phytoplankton community at Station ALOHA.

Surgical management of scimitar syndrome: an alternative approach.

OBJECTIVE: The scimitar syndrome is a congenital anomaly that consists in part of total or partial anomalous venous drainage of the right lung to the inferior vena cava. Surgical approaches to the scimitar syndrome have varied according to the anatomic and pathologic features presented in each case. The aim of this study was to present an alternative approach to the surgical correction of scimitar syndrome. METHODS: Nine patients with the scimitar syndrome were operated on between 1990 and 2000. They comprised 1 male and 8 female patients (mean age 11.5 +/- 17.6 years). All patients had symptoms, with recurrent pneumonia or respiratory tract infections and pulmonary/systemic flow ratios greater than 1.5:1.0. None of the patients had pulmonary hypertension or an atrial septal defect. All patients underwent repair of the anomalous scimitar vein by direct reimplantation into the left atrium without cardiopulmonary bypass. Two patients underwent concomitant resection of a right lower lobe sequestration. Follow-up was complete in all cases. RESULTS: There were no operative or late deaths, and no patients have required reoperation. At the time of follow-up (mean 55 +/- 46 months), echocardiography demonstrated a patent anastomosis in all patients without any evidence of restenosis. CONCLUSION: This clinical experience indicates that an alternative surgical approach to scimitar syndrome is direct anastomosis of the scimitar vein to the posterior aspect of the left atrium using a right thoracotomy without cardiopulmonary bypass. This procedure is safe and effective and obviates the need for long intra-atrial baffles and the use of the extracorporeal circuit.