Modelling economic returns to plant variety protection in the UK

This paper attempts an empirical assessment of the incentive effects of plant variety protection regimes in the generation of crop variety innovations. A duration model of plant variety protection certificates is used to infer the private appropriability of returns from agricultural crop variety innovations in the UK over the period 1965-2000. The results suggest that plant variety protection provides only modest appropriability of returns to innovators of agricultural crop varieties. The value distribution of plant variety protection certificates is highly skewed with a large proportion of innovations providing virtually no returns to innovators. Increasing competition from newer varieties appears to have accelerated the turnover of varieties reducing appropriability further. Plant variety protection emerges as a relatively weak instrument of protection.

Modelling the time-evolution of phytoplankton size spectra from satellite remote sensing

A dynamic size-structured model is developed for phytoplankton and nutrients in the oceanic mixed layer and applied to extract phytoplankton biomass at discrete size fractions from remotely sensed, ocean-colour data. General relationships between cell size and biophysical processes (such as sinking, grazing, and primary production) of phytoplankton were included in the model through a bottom–up approach. Time-dependent, mixed-layer depth was used as a forcing variable, and a sequential data-assimilation scheme was implemented to derive model trajectories. From a given time-series, the method produces estimates of size-structured biomass at every observation, so estimates seasonal succession of individual phytoplankton size, derived here from remote sensing for the first time. From these estimates, normalized phytoplankton biomass size spectra over a period of 9 years were calculated for one location in the North Atlantic. Further analysis demonstrated that strong relationships exist between the seasonal trends of the estimated size spectra and the mixed-layer depth, nutrient biomass, and total chlorophyll. The results contain useful information on the time-dependent biomass flux in the pelagic ecosystem.

The Madden-Julian Oscillation and the diurnal cycle over the Maritime Continent: scale interactions and modelling

The Maritime Continent archipelago, situated on the equator at 95-165E, has the strongest land-based precipitation on Earth. The latent heat release associated with the rainfall affects the atmospheric circulation throughout the tropics and into the extra-tropics. The greatest source of variability in precipitation is the diurnal cycle. The archipelago is within the convective region of the Madden-Julian Oscillation (MJO), which provides the greatest variability on intra-seasonal time scales: large-scale (∼10^7 km^2) active and suppressed convective envelopes propagate slowly (∼5 m s^-1) eastwards between the Indian and Pacific Oceans. High-resolution satellite data show that a strong diurnal cycle is triggered to the east of the advancing MJO envelope, leading the active MJO by one-eighth of an MJO cycle (∼6 days). Where the diurnal cycle is strong its modulation accounts for 81% of the variability in MJO precipitation. Over land this determines the structure of the diagnosed MJO. This is consistent with the equatorial wave dynamics in existing theories of MJO propagation. The MJO also affects the speed of gravity waves propagating offshore from the Maritime Continent islands. This is largely consistent with changes in static stability during the MJO cycle. The MJO and its interaction with the diurnal cycle are investigated in HiGEM, a high-resolution coupled model. Unlike many models, HiGEM represents the MJO well with eastward-propagating variability on intra-seasonal time scales at the correct zonal wavenumber, although the inter-tropical convergence zone's precipitation peaks strongly at the wrong time, interrupting the MJO's spatial structure. However, the modelled diurnal cycle is too weak and its phase is too early over land. The modulation of the diurnal amplitude by the MJO is also too weak and accounts for only 51% of the variability in MJO precipitation. Implications for forecasting and possible causes of the model errors are discussed, and further modelling studies are proposed.

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

Arctic Snow Microstructure Experiment for the development of snow emission modelling

The Arctic Snow Microstructure Experiment (ASMEx) took place in Sodankylä, Finland in the winters of 2013-2014 and 2014-2015. Radiometric, macro-, and microstructure measurements were made under different experimental conditions of homogenous snow slabs, extracted from the natural seasonal taiga snowpack. Traditional and modern measurement techniques were used for snow macro- and microstructure observations. Radiometric measurements of the microwave emission of snow on reflector and absorber bases were made at frequencies 18.7, 21.0, 36.5, 89.0 and 150.0 GHz, for both horizontal and vertical polarizations. Two measurement configurations were used for radiometric measurements: a reflecting surface and an absorbing base beneath the snow slabs. Simulations of brightness temperatures using two microwave emission models, Helsinki University of Technology (HUT) snow emission model and Microwave Emission Model of Layered Snowpacks (MEMLS), were compared to observed brightness temperatures. RMSE and bias were calculated; with the RMSE and bias values being smallest upon an absorbing base at vertical polarization. Simulations overestimated the brightness temperatures on absorbing base cases at horizontal polarization. With the other experimental conditions, the biases were small; with the exception of the HUT model 36.5 GHz simulation, which produced an underestimation for the reflector base cases. This experiment provides a solid framework for future research on the extinction of microwave radiation inside snow.