Elm Farm Research Centre Bulletin 82 February 2006

Regular newsletter with technical updates from the Organic Advisory Service Issue covers: organic sector payments, dietary health choices, avian influenza vaccination, tradable quotas, feeding cities, sewage sludge, organic aquaculture, organic poultry, biodiversity and productivity research, organic winter wheat varieties, linking farmers and scientists, Interreg Project, RAFAEL energy use greenhouse gas emissions food and farming

Hydraulic validation of two-dimensional simulations of braided river flow with spatially continuous aDcp data

Gravel‐bed braided rivers are characterized by shallow, branching flow across low relief, complex, and mobile bed topography. These conditions present a major challenge for the application of higher dimensional hydraulic models, the predictions of which are nevertheless vital to inform flood risk and ecosystem management. This paper demonstrates how high‐resolution topographic survey and hydraulic monitoring at a density commensurate with model discretization can be used to advance hydrodynamic simulations in braided rivers. Specifically, we detail applications of the shallow water model, Delft3d, to the Rees River, New Zealand, at two nested scales: a 300 m braid bar unit and a 2.5 km reach. In each case, terrestrial laser scanning was used to parameterize the topographic boundary condition at hitherto unprecedented resolution and accuracy. Dense observations of depth and velocity acquired from a mobile acoustic Doppler current profiler (aDcp), along with low‐altitude aerial photography, were then used to create a data‐rich framework for model calibration and testing at a range of discharges. Calibration focused on the estimation of spatially uniform roughness and horizontal eddy viscosity, νH, through comparison of predictions with distributed hydraulic data. Results revealed strong sensitivity to νH, which influenced cross‐channel velocity and localization of high shear zones. The high‐resolution bed topography partially accounts for form resistance, and the recovered roughness was found to scale by 1.2–1.4 D84 grain diameter. Model performance was good for a range of flows, with minimal bias and tight error distributions, suggesting that acceptable predictions can be achieved with spatially uniform roughness and νH.Field campaigns were primarily funded by NERC Grant NE/G005427/1 and NERC Geophysical Equipment Facility Loan 892 as well as NSERC and CFI (Canada) grants to Colin Rennie. Damia Vericat was supported by a Ramon y Cajal Fellowship (RYC‐2010‐06264) funded by the Spanish Ministry of Science and Innovation during the preparation of this manuscript. Numerical simulations were undertaken during a visit by Richard Williams to NIWA. This visit was funded by the British Hydrology Society and an Aberystwyth University Postgraduate Studentship. Murray Hicks and Richard Measures were funded by NIWA core funding under the Sustainable Water Allocation Programme

The regulation of equatorial Pacific new production and pCO 2 by silicate-limited diatoms

a b s t r a c t Modeling and data from the JGOFS EqPac program suggested that the eastern equatorial Pacific upwelling ecosystem includes a quasi-chemostat culture system dominated by diatoms and limited by Si(OH) 4 due to a low ratio of Si(OH) 4 to NO 3 in the upwelling source water, the Equatorial Undercurrent. Diatoms were hypothesized to be the major users of NO 3 in this system and the amount assimilated limited by the low amount of Si(OH) 4 available. As a consequence NO 3 is left in the surface waters along with unused CO 2 . Two cruises to the eastern equatorial Pacific (EB04 and EB05) were made to test the existing hypothesis of Si(OH) 4 limitation, and study the roles of source concentrations of Si(OH) 4 and Fe, and nutrient uptake kinetics for comparison with model predictions. Fractionated nitrogen uptake measurements showed that diatoms at times take up the major portion of the NO 3 . Picoplankton and some phytoplankton in the 4 5-mm size group carried out primarily regenerated production, i.e. NH 4 uptake in a grazing dominated system. Equatorial diatoms followed uptake kinetics for Si(OH) 4 and NO 3 uptake as observed in laboratory investigations of diatoms under Si(OH) 4 and Fe limitations. Si(OH) 4 uptake responded to additions of Si(OH) 4 on a time scale of hours in uptake kinetic experiments while NO 3 uptake was unaffected by added NO 3 . The uptake of Si(OH) 4 varied in a narrow range on a Michaelis-Menten hyperbola of Si(OH) 4 uptake vs. Si(OH) 4 concentration, with a maximal Si(OH) 4 uptake rate, V 0 maxSi set to a relatively low value by some factor(s) other than Fe on a longer time scale, i.e., days in shipboard enclosures. Simply enclosing water collected from the mid euphotic zone and incubating for some days on deck at 50% surface irradiance increased

Estimating iron and aluminum removal rates in the eastern equatorial Pacific Ocean using a box model approach.

a b s t r a c t Iron limitation plays an important role in maintaining the high-nitrate low-chlorophyll (HNLC) condition in the equatorial upwelling zone. The rate and depth of upwelling control Fe supply to the euphotic zone. This study constrains the transport fluxes and budget of two trace metals, Fe and Al, in the upper ocean. They are co-delivered to the eastern equatorial Pacific surface waters via the Equatorial Undercurrent and upwelling but show distinct biogeochemical cycling processes. We combine the results of the in situ measurements of dissolved Fe and Al (dFe and dAl) with the modeled velocity fields to calculate the physical fluxes. The model calculations are evaluated with the conservation of heat, volume transport, NO 3 and Si(OH) 4 budgets for the equatorial Pacific. The vertical flux due to upwelling provides averaged dFe and dAl supply rates of 1.45 mmol m , respectively. These estimates are equal to the net biological and chemical removal rates of dFe and dAl. The calculated dFe:C net removal ratio is in the range of 3-9 mmol:mol, which agrees with most other estimates. This suggests that the majority of net dFe removal is due to biological uptake in the upper water column. The results of this box model approach illustrate the usefulness of combining the modeled outputs and in situ measurements, which provide additional constraints on Fe transport and cycling in the equatorial Pacific and possibly other HNLC regions

Clinical Significance of Bronchodilator Responsiveness Evaluated by Forced Vital Capacity in COPD: SPIROMICS Cohort Analysis.

ObjectiveBronchodilator responsiveness (BDR) is prevalent in COPD, but its clinical implications remain unclear. We explored the significance of BDR, defined by post-bronchodilator change in FEV1 (BDRFEV1) as a measure reflecting the change in flow and in FVC (BDRFVC) reflecting the change in volume.MethodsWe analyzed 2974 participants from a multicenter observational study designed to identify varying COPD phenotypes (SPIROMICS). We evaluated the association of BDR with baseline clinical characteristics, rate of prospective exacerbations and mortality using negative binomial regression and Cox proportional hazards models.ResultsA majority of COPD participants exhibited BDR (52.7%). BDRFEV1 occurred more often in earlier stages of COPD, while BDRFVC occurred more frequently in more advanced disease. When defined by increases in either FEV1 or FVC, BDR was associated with a self-reported history of asthma, but not with blood eosinophil counts. BDRFVC was more prevalent in subjects with greater emphysema and small airway disease on CT. In a univariate analysis, BDRFVC was associated with increased exacerbations and mortality, although no significance was found in a model adjusted for post-bronchodilator FEV1.ConclusionWith advanced airflow obstruction in COPD, BDRFVC is more prevalent in comparison to BDRFEV1 and correlates with the extent of emphysema and degree of small airway disease. Since these associations appear to be related to the impairment of FEV1, BDRFVC itself does not define a distinct phenotype nor can it be more predictive of outcomes, but it can offer additional insights into the pathophysiologic mechanism in advanced COPD.Clinical trials registrationClinicalTrials.gov: NCT01969344T4

Comparing the effects of tofacitinib, methotrexate and the combination, on bone marrow oedema, synovitis and bone erosion in methotrexate-naive, early active rheumatoid arthritis: results of an exploratory randomised MRI study incorporating semiquantitative and quantitative techniques

Objectives To explore the effects of tofacitinib—an oral Janus kinase inhibitor for the treatment of rheumatoid arthritis (RA)—with or without methotrexate (MTX), on MRI endpoints in MTX-naive adult patients with early active RA and synovitis in an index wrist or hand. Methods In this exploratory, phase 2, randomised, double-blind, parallel-group study, patients received tofacitinib 10 mg twice daily + MTX, tofacitinib 10 mg twice daily + placebo (tofacitinib monotherapy), or MTX + placebo (MTX monotherapy), for 1 year. MRI endpoints (Outcome Measures in Rheumatology Clinical Trials RA MRI score (RAMRIS), quantitative RAMRIS (RAMRIQ) and dynamic contrast-enhanced (DCE) MRI) were assessed using a mixed-effect model for repeated measures. Treatment differences with p<0.05 (vs MTX monotherapy) were considered significant. Results In total, 109 patients were randomised and treated. Treatment differences in RAMRIS bone marrow oedema (BME) at month 6 were −1.55 (90% CI −2.52 to −0.58) for tofacitinib + MTX and −1.74 (−2.72 to −0.76) for tofacitinib monotherapy (both p0.05 vs MTX monotherapy). Treatment differences in RAMRIQ synovitis were statistically significant at month 3, consistent with DCE MRI findings. Less deterioration of RAMRIS and RAMRIQ erosive damage was seen at months 6 and 12 in both tofacitinib groups versus MTX monotherapy. Conclusions These results provide consistent evidence using three different MRI technologies that tofacitinib treatment leads to early reduction of inflammation and inhibits progression of structural damage

Stranding of a Pygmy Sperm Whale, Kogia breviceps, in the Northern Gulf of St. Lawrence, Canada

A Pygmy Sperm Whale, Kogia breviceps, stranded alive and later died in the Northern Gulf of St. Lawrence, Quebec, Canada on 28 August 2001. This is the northern-most stranding of this species in the western Atlantic. The whale was estimated to be approximately 3 m long and a longitudinal section from one tooth (31 mm long and 5.0 mm in diameter) revealed 3.5 growth layer groups

Development of a fine-scale salinity model for the Avon Heathcote Estuary Ihutai

Report prepared for Brian Mason Scientific & Technical Trust. Christchurch: University of Canterbury & NIWA, September 2016The focus of this study is on understanding salinity changes in the vicinity of the freshwater-saltwater interface in estuarine ecosystems. In these areas, species, habitats and ecosystems that are adapted to brackish conditions are expected to migrate in response to salinity changes under sea level rise. For the Avon Heathcote Estuary in Christchurch, an existing fine scale hydrodynamic model was available but not calibrated for salinity. A collaborative project was designed between the University of Canterbury and NIWA to calibrate the model and develop a scenario modelling approach for sea level rise at a level of resolution sufficient for understanding potential effects on important habitats. The purpose of this report is to provide a description of the model development process and an illustration of model outputs from an initial set of modelled scenarios for sea level rise