The REFLEX project: Comparing different algorithms and implementations for the inversion of a terrestrial ecosystem model against eddy covariance data

We describe a model-data fusion (MDF) inter-comparison project (REFLEX), which compared various algorithms for estimating carbon (C) model parameters consistent with both measured carbon fluxes and states and a simple C model. Participants were provided with the model and with both synthetic net ecosystem exchange (NEE) of CO2 and leaf area index (LAI) data, generated from the model with added noise, and observed NEE and LAI data from two eddy covariance sites. Participants endeavoured to estimate model parameters and states consistent with the model for all cases over the two years for which data were provided, and generate predictions for one additional year without observations. Nine participants contributed results using Metropolis algorithms, Kalman filters and a genetic algorithm. For the synthetic data case, parameter estimates compared well with the true values. The results of the analyses indicated that parameters linked directly to gross primary production (GPP) and ecosystem respiration, such as those related to foliage allocation and turnover, or temperature sensitivity of heterotrophic respiration, were best constrained and characterised. Poorly estimated parameters were those related to the allocation to and turnover of fine root/wood pools. Estimates of confidence intervals varied among algorithms, but several algorithms successfully located the true values of annual fluxes from synthetic experiments within relatively narrow 90% confidence intervals, achieving >80% success rate and mean NEE confidence intervals <110 gC m−2 year−1 for the synthetic case. Annual C flux estimates generated by participants generally agreed with gap-filling approaches using half-hourly data. The estimation of ecosystem respiration and GPP through MDF agreed well with outputs from partitioning studies using half-hourly data. Confidence limits on annual NEE increased by an average of 88% in the prediction year compared to the previous year, when data were available. Confidence intervals on annual NEE increased by 30% when observed data were used instead of synthetic data, reflecting and quantifying the addition of model error. Finally, our analyses indicated that incorporating additional constraints, using data on C pools (wood, soil and fine roots) would help to reduce uncertainties for model parameters poorly served by eddy covariance data.

Precipitation distributions for explicit versus parameterized convection in a large-domain high-resolution tropical case study

Global climate and weather models tend to produce rainfall that is too light and too regular over the tropical ocean. This is likely because of convective parametrizations, but the problem is not well understood. Here, distributions of precipitation rates are analyzed for high-resolution UK Met Office Unified Model simulations of a 10 day case study over a large tropical domain (∼20°S–20°N and 42°E–180°E). Simulations with 12 km grid length and parametrized convection have too many occurrences of light rain and too few of heavier rain when interpolated onto a 1° grid and compared with Tropical Rainfall Measuring Mission (TRMM) data. In fact, this version of the model appears to have a preferred scale of rainfall around 0.4 mm h−1 (10 mm day−1), unlike observations of tropical rainfall. On the other hand, 4 km grid length simulations with explicit convection produce distributions much more similar to TRMM observations. The apparent preferred scale at lighter rain rates seems to be a feature of the convective parametrization rather than the coarse resolution, as demonstrated by results from 12 km simulations with explicit convection and 40 km simulations with parametrized convection. In fact, coarser resolution models with explicit convection tend to have even more heavy rain than observed. Implications for models using convective parametrizations, including interactions of heating and moistening profiles with larger scales, are discussed. One important implication is that the explicit convection 4 km model has temperature and moisture tendencies that favour transitions in the convective regime. Also, the 12 km parametrized convection model produces a more stable temperature profile at its extreme high-precipitation range, which may reduce the chance of very heavy rainfall. Further study is needed to determine whether unrealistic precipitation distributions are due to some fundamental limitation of convective parametrizations or whether parametrizations can be improved, in order to better simulate these distributions.

Simple and effective technical procedures for the packing and application of nanospray PicoFrit HPLC columns for proteomic analyses

A simple procedure was developed for packing PicoFrit HPLC columns with chromatographic stationary phase using a reservoir fabricated from standard laboratory HPLC fittings. Packed columns were mounted onto a stainless steel ultra-low volume precolumn filter assembly containing a 0.5-mu m pore size steel frit. This format provided a conduit for the application of the nanospray voltage and protected the column from obstruction by sample material. The system was characterised and operational performance assessed by analysis of a range of peptide standards (n = 9).

Boosting the globalization of plant proteomics through INPPO: current developments 3 and future prospects

The International Plant Proteomics Organization (INPPO) is a non-profit-organization consisting of people who are involved or interested in plant proteomics. INPPO is constantly growing in volume and activity, which is mostly due to the realization among plant proteomics researchers worldwide for the need of such a global platform. Their active participation resulted in the rapid growth within the first year of INPPO’s official launch in 2011 via its website (www.inppo.com) and publication of the ‘viewpoint paper’ in a special issue of PROTEOMICS (May 2011). Here, we will be highlighting the progress achieved in the year 2011 and the future targets for the year 2012 and onwards. INPPO has achieved a successful administrative structure, the Core Committee (CC; composed of President, Vice-President, and General Secretaries), Executive Council (EC), and General Body (GB) toward achieving the INPPO objectives by its proposed initiatives. Various committees and subcommittees are in the process of being functionalized via discussion amongst scientists around the globe. INPPO’s primary aim to popularize the plant proteomics research in biological sciences has also been recognized by PROTEOMICS where a new section has been introduced to plant proteomics starting January 2012, following the very first issue of this journal devoted to plant proteomics in May 2011. To disseminate organizational activities to the scientific community, INPPO has launched a biannual (in January & July) newsletter entitled “INPPO Express: News & Views” with the first issue published in January 2012. INPPO is also planning to have several activities in 2012, including programs within the Education Outreach committee in different countries, and the development of research ideas and proposals with priority on crop and horticultural plants, while keeping tight interactions with proteomics programs on model plants such as Arabidopsis thaliana, rice, or Medicago truncatula. Altogether, the INPPO progress and upcoming activities are because of immense support, dedication, and hard work of all members of the INPPO family, and also due to the wide encouragement and support from the communities (scientific and non-scientific).

Evaluation of ECMWF medium-range ensemble forecasts of precipitation for river basins

Providing probabilistic forecasts using Ensemble Prediction Systems has become increasingly popular in both the meteorological and hydrological communities. Compared to conventional deterministic forecasts, probabilistic forecasts may provide more reliable forecasts of a few hours to a number of days ahead, and hence are regarded as better tools for taking uncertainties into consideration and hedging against weather risks. It is essential to evaluate performance of raw ensemble forecasts and their potential values in forecasting extreme hydro-meteorological events. This study evaluates ECMWF’s medium-range ensemble forecasts of precipitation over the period 2008/01/01-2012/09/30 on a selected mid-latitude large scale river basin, the Huai river basin (ca. 270,000 km2) in central-east China. The evaluation unit is sub-basin in order to consider forecast performance in a hydrologically relevant way. The study finds that forecast performance varies with sub-basin properties, between flooding and non-flooding seasons, and with the forecast properties of aggregated time steps and lead times. Although the study does not evaluate any hydrological applications of the ensemble precipitation forecasts, its results have direct implications in hydrological forecasts should these ensemble precipitation forecasts be employed in hydrology.

Plane wave discontinuous Galerkin methods: exponential convergence of the hp-version

We consider the two-dimensional Helmholtz equation with constant coefficients on a domain with piecewise analytic boundary, modelling the scattering of acoustic waves at a sound-soft obstacle. Our discretisation relies on the Trefftz-discontinuous Galerkin approach with plane wave basis functions on meshes with very general element shapes, geometrically graded towards domain corners. We prove exponential convergence of the discrete solution in terms of number of unknowns.

A global proteomics approach identifies novel phosphorylated signaling proteins in GPVI-activated platelets: involvement of G6f, a novel platelet Grb2-binding membrane adapter.

Collagen-related peptide (CRP) stimulates powerful activation of platelets through the glycoprotein VI (GPVI)-FcR gamma-chain complex. We have combined proteomics and traditional biochemistry approaches to study the proteome of CRP-activated platelets, focusing in detail on tyrosine phosphorylation. In two separate approaches, phosphotyrosine immunoprecipitations followed by 1-D-PAGE, and 2-DE, were used for protein separation. Proteins were identified by MS. By following these approaches, 96 proteins were found to undergo PTM in response to CRP in human platelets, including 11 novel platelet proteins such as Dok-1, SPIN90, osteoclast stimulating factor 1, and beta-Pix. Interestingly, the type I transmembrane protein G6f was found to be specifically phosphorylated on Tyr-281 in response to platelet activation by CRP, providing a docking site for the adapter Grb2. G6f tyrosine phoshporylation was also found to take place in response to collagen, although not in response to the G protein-coupled receptor agonists, thrombin and ADP. Further, we also demonstrate for the first time that Grb2 and its homolog Gads are tyrosine-phosphorylated in CRP-stimulated platelets. This study provides new insights into the mechanism of platelet activation through the GPVI collagen receptor, helping to build the basis for the development of new drug targets for thrombotic disease.

Linking classroom learning and research to advance ideas about social-ecological resilience

There is an increasing demand in higher education institutions for training in complex environmental problems. Such training requires a careful mix of conventional methods and innovative solutions, a task not always easy to accomplish. In this paper we review literature on this theme, highlight relevant advances in the pedagogical literature, and report on some examples resulting from our recent efforts to teach complex environmental issues. The examples range from full credit courses in sustainable development and research methods to project-based and in-class activity units. A consensus from the literature is that lectures are not sufficient to fully engage students in these issues. A conclusion from the review of examples is that problem-based and project-based, e.g., through case studies, experiential learning opportunities, or real-world applications, learning offers much promise. This could greatly be facilitated by online hubs through which teachers, students, and other members of the practitioner and academic community share experiences in teaching and research, the way that we have done here.

Noether-type discrete conserved quantities arising from a finite element approximation of a variational problem

In this work, we prove a weak Noether-type Theorem for a class of variational problems that admit broken extremals. We use this result to prove discrete Noether-type conservation laws for a conforming finite element discretisation of a model elliptic problem. In addition, we study how well the finite element scheme satisfies the continuous conservation laws arising from the application of Noether’s first theorem (1918). We summarise extensive numerical tests, illustrating the conservation of the discrete Noether law using the p-Laplacian as an example and derive a geometric-based adaptive algorithm where an appropriate Noether quantity is the goal functional.

Anticipating future risk in social-ecological systems using fuzzy cognitive mapping: the case of wildfire in the Chiquitania, Bolivia

Understanding complex social-ecological systems, and anticipating how they may respond to rapid change, requires an approach that incorporates environmental, social, economic, and policy factors, usually in a context of fragmented data availability. We employed fuzzy cognitive mapping (FCM) to integrate these factors in the assessment of future wildfire risk in the Chiquitania region, Bolivia. In this region, dealing with wildfires is becoming increasingly challenging due to reinforcing feedbacks between multiple drivers. We conducted semi-structured interviews and constructed different FCMs in focus groups to understand the regional dynamics of wildfire from diverse perspectives. We used FCM modelling to evaluate possible adaptation scenarios in the context of future drier climatic conditions. Scenarios also considered possible failure to respond in time to the emergent risk. This approach proved of great potential to support decision-making for risk management. It helped identify key forcing variables and generate insights into potential risks and trade-offs of different strategies. All scenarios showed increased wildfire risk in the event of more droughts. The ‘Hands-off’ scenario resulted in amplified impacts driven by intensifying trends, affecting particularly the agricultural production. The ‘Fire management’ scenario, which adopted a bottom-up approach to improve controlled burning, showed less trade-offs between wildfire risk reduction and production compared to the ‘Fire suppression’ scenario. Findings highlighted the importance of considering strategies that involve all actors who use fire, and the need to nest these strategies for a more systemic approach to manage wildfire risk. The FCM model could be used as a decision-support tool and serve as a ‘boundary object’ to facilitate collaboration and integration of different forms of knowledge and perceptions of fire in the region. This approach has also the potential to support decisions in other dynamic frontier landscapes around the world that are facing increased risk of large wildfires.

Interacting effects of change in climate, human population, land use, and water use on biodiversity and ecosystem services

Human population growth and resource use, mediated by changes in climate, land use, and water use, increasingly impact biodiversity and ecosystem services provision. However, impacts of these drivers on biodiversity and ecosystem services are rarely analyzed simultaneously and remain largely unknown. An emerging question is how science can improve the understanding of change in biodiversity and ecosystem service delivery and of potential feedback mechanisms of adaptive governance. We analyzed past and future change in drivers in south-central Sweden. We used the analysis to identify main research challenges and outline important research tasks. Since the 19th century, our study area has experienced substantial and interlinked changes; a 1.6°C temperature increase, rapid population growth, urbanization, and massive changes in land use and water use. Considerable future changes are also projected until the mid-21st century. However, little is known about the impacts on biodiversity and ecosystem services so far, and this in turn hampers future projections of such effects. Therefore, we urge scientists to explore interdisciplinary approaches designed to investigate change in multiple drivers, underlying mechanisms, and interactions over time, including assessment and analysis of matching-scale data from several disciplines. Such a perspective is needed for science to contribute to adaptive governance by constantly improving the understanding of linked change complexities and their impacts.